From a125e227d103ba6944889cf44426c99b962de12b Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 4 Oct 2017 17:23:27 +0200
Subject: [PATCH] upload of zip project is possible
---
.gitignore | 1 +
.../converter/ComplexZipConverter.java | 678 ++--
.../converter/ComplexZipConverterParams.java | 217 +-
.../lcsb/mapviewer/converter/AllTests.java | 7 +-
.../ComplexZipConverterParamsTest.java | 22 +
frontend-js/.gitignore | 2 +
frontend-js/src/main/js/ServerConnector.js | 132 +-
.../src/main/js/gui/admin/AddProjectDialog.js | 14 +-
.../src/test/js/ServerConnector-test.js | 217 +-
.../js/gui/admin/AddProjectDialog-test.js | 3 +-
.../POST_token=MOCK_TOKEN_ID& | 7 +
.../POST_token=MOCK_TOKEN_ID& | 7 +
...ame=test.txt&length=5&token=MOCK_TOKEN_ID& | 7 +
...me=test.xml&length=13&token=MOCK_TOKEN_ID& | 7 +
.../model/cache/UploadedFileEntry.java | 70 +-
persist/src/db/11.1.0/fix_db_20171004.sql | 12 +
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 517 +--
.../mapviewer/api/files/FileController.java | 59 +
.../mapviewer/api/files/FileRestImpl.java | 107 +
.../api/projects/ProjectRestImpl.java | 42 +-
.../resources/applicationContext-rest.xml | 2 +
.../java/lcsb/mapviewer/api/AllRestTests.java | 8 +-
.../lcsb/mapviewer/api/RestTestFunctions.java | 492 +--
.../mapviewer/api/files/AllFileTests.java | 11 +
.../mapviewer/api/files/FileRestImplTest.java | 80 +
.../mapviewer/services/SecurityException.java | 20 +-
.../services/impl/LayoutService.java | 4 +
.../services/impl/ProjectService.java | 2926 +++++++++--------
28 files changed, 3081 insertions(+), 2590 deletions(-)
create mode 100644 converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterParamsTest.java
create mode 100644 frontend-js/testFiles/apiCalls/files/6790.uploadContent/POST_token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/files/6791.uploadContent/POST_token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/files/POST_filename=test.txt&length=5&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/files/POST_filename=test.xml&length=13&token=MOCK_TOKEN_ID&
create mode 100644 persist/src/db/11.1.0/fix_db_20171004.sql
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
create mode 100644 rest-api/src/test/java/lcsb/mapviewer/api/files/AllFileTests.java
create mode 100644 rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
diff --git a/.gitignore b/.gitignore
index a402933690..bbcea90463 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,4 @@ service/minerva-big/
npm-debug.log
.idea/workspace.xml
+.idea/libraries/
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index dc91e510ca..e2640f0b3e 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -52,355 +52,365 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class ComplexZipConverter {
- /**
- * Size of the buffer used for accessing single chunk of data from input
- * stream.
- */
- private static final int BUFFER_SIZE = 1024;
+ /**
+ * Size of the buffer used for accessing single chunk of data from input stream.
+ */
+ private static final int BUFFER_SIZE = 1024;
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
- /**
- * Class used to create single submap from a file.
- */
- private Class<? extends IConverter> converterClazz;
+ /**
+ * Class used to create single submap from a file.
+ */
+ private Class<? extends IConverter> converterClazz;
- /**
- * Default constructor. Checks if the class given in the parameter is proper
- * {@link IConverter} implementation.
- *
- * @param clazz
- * {@link IConverter} class used for creation of the single submap
- */
- public ComplexZipConverter(Class<? extends IConverter> clazz) {
- if (Modifier.isAbstract(clazz.getModifiers())) {
- throw new InvalidClassException("Param class cannot be abstract");
- }
+ /**
+ * Default constructor. Checks if the class given in the parameter is proper
+ * {@link IConverter} implementation.
+ *
+ * @param clazz
+ * {@link IConverter} class used for creation of the single submap
+ */
+ public ComplexZipConverter(Class<? extends IConverter> clazz) {
+ if (Modifier.isAbstract(clazz.getModifiers())) {
+ throw new InvalidClassException("Param class cannot be abstract");
+ }
- if (Modifier.isInterface(clazz.getModifiers())) {
- throw new InvalidClassException("Param class cannot be an interface");
- }
+ if (Modifier.isInterface(clazz.getModifiers())) {
+ throw new InvalidClassException("Param class cannot be an interface");
+ }
- converterClazz = clazz;
- }
+ converterClazz = clazz;
+ }
- /**
- * Creates complex {@link Model} that contains submaps.
- *
- * @param params
- * {@link ComplexZipConverterParams object} with information about
- * data from which result is going to be created
- * @return complex {@link Model} created from input data
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with accessing input data
- */
- public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
- try {
- ZipFile zipFile = params.getZipFile();
- Enumeration<? extends ZipEntry> entries;
- String mapping = validateSubmodelInformation(params, zipFile);
+ /**
+ * Creates complex {@link Model} that contains submaps.
+ *
+ * @param params
+ * {@link ComplexZipConverterParams object} with information about data
+ * from which result is going to be created
+ * @return complex {@link Model} created from input data
+ * @throws InvalidInputDataExecption
+ * thrown when there is a problem with accessing input data
+ */
+ public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
+ try {
+ ZipFile zipFile = params.getZipFile();
+ Enumeration<? extends ZipEntry> entries;
+ String mapping = validateSubmodelInformation(params, zipFile);
- IConverter converter = createConverterInstance();
- Map<String, Model> filenameModelMap = new HashMap<String, Model>();
- Map<String, Model> nameModelMap = new HashMap<String, Model>();
+ IConverter converter = createConverterInstance();
+ Map<String, Model> filenameModelMap = new HashMap<String, Model>();
+ Map<String, Model> nameModelMap = new HashMap<String, Model>();
- entries = zipFile.entries();
- Model result = null;
- List<Layout> layouts = new ArrayList<Layout>();
- List<DataMiningSet> dataMiningSets = new ArrayList<>();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- ZipEntryFile zef = params.getEntry(entry.getName());
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- InputStream is = zipFile.getInputStream(entry);
- ConverterParams cParams = new ConverterParams();
- cParams.inputStream(is);
- Model model = converter.createModel(cParams);
- model.setName(modelEntryFile.getName());
- filenameModelMap.put(entry.getName(), model);
- nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()), model);
- if (modelEntryFile.isRoot()) {
- result = model;
- }
- } else if (zef instanceof LayoutZipEntryFile) {
- layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
- } else if (zef instanceof ImageZipEntryFile) {
- continue;
- // imageEntries.add((ImageZipEntryFile) zef);
- } else if (zef instanceof DataMiningZipEntryFile) {
- dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
- } else {
- throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
- }
- }
- }
+ entries = zipFile.entries();
+ Model result = null;
+ List<Layout> layouts = new ArrayList<Layout>();
+ List<DataMiningSet> dataMiningSets = new ArrayList<>();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ ZipEntryFile zef = params.getEntry(entry.getName());
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ InputStream is = zipFile.getInputStream(entry);
+ ConverterParams cParams = new ConverterParams();
+ cParams.inputStream(is);
+ Model model = converter.createModel(cParams);
+ model.setName(modelEntryFile.getName());
+ filenameModelMap.put(entry.getName(), model);
+ nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()), model);
+ if (modelEntryFile.isRoot()) {
+ result = model;
+ }
+ } else if (zef instanceof LayoutZipEntryFile) {
+ layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
+ } else if (zef instanceof ImageZipEntryFile) {
+ continue;
+ // imageEntries.add((ImageZipEntryFile) zef);
+ } else if (zef instanceof DataMiningZipEntryFile) {
+ dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
+ } else {
+ throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
+ }
+ }
+ }
- result.addDataMiningSets(dataMiningSets);
+ result.addDataMiningSets(dataMiningSets);
- for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
- String filename = entry.getKey();
- Model model = entry.getValue();
- ZipEntryFile zef = params.getEntry(filename);
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
- ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
- submodel.setName(modelEntryFile.getName());
- result.addSubmodelConnection(submodel);
- }
- }
- }
- for (Layout layout : layouts) {
- Layout topLayout = new Layout(layout);
- result.addLayout(topLayout);
- int modelId = 0;
- topLayout.setDirectory(topLayout.getDirectory() + modelId);
- modelId++;
- for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
- Layout childLayout = new Layout(layout);
- // we need to set separate directory names for different submodels
- childLayout.setDirectory(childLayout.getDirectory() + modelId);
- modelId++;
- childLayout.setParentLayout(topLayout);
- connection.getSubmodel().addLayout(childLayout);
- }
- }
- Model mappingModel = filenameModelMap.get(mapping);
- if (mappingModel != null) {
- for (Reaction reaction : mappingModel.getReactions()) {
- processReaction(mapping, nameModelMap, result, reaction);
- }
- }
- return result;
- } catch (IOException e) {
- throw new InvalidArgumentException(e);
- }
- }
+ for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
+ String filename = entry.getKey();
+ Model model = entry.getValue();
+ ZipEntryFile zef = params.getEntry(filename);
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
+ ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
+ submodel.setName(modelEntryFile.getName());
+ result.addSubmodelConnection(submodel);
+ }
+ }
+ }
+ for (Layout layout : layouts) {
+ Layout topLayout = new Layout(layout);
+ result.addLayout(topLayout);
+ int modelId = 0;
+ topLayout.setDirectory(topLayout.getDirectory() + modelId);
+ modelId++;
+ for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+ Layout childLayout = new Layout(layout);
+ // we need to set separate directory names for different submodels
+ childLayout.setDirectory(childLayout.getDirectory() + modelId);
+ modelId++;
+ childLayout.setParentLayout(topLayout);
+ connection.getSubmodel().addLayout(childLayout);
+ }
+ }
+ Model mappingModel = filenameModelMap.get(mapping);
+ if (mappingModel != null) {
+ for (Reaction reaction : mappingModel.getReactions()) {
+ processReaction(mapping, nameModelMap, result, reaction);
+ }
+ }
+ return result;
+ } catch (IOException e) {
+ throw new InvalidArgumentException(e);
+ }
+ }
- /**
- * Process a single reaction in mapping file (transfomring reaction into
- * connection between submodels).
- *
- * @param mapping
- * name of the mapping file
- * @param nameModelMap
- * mapping between file names and models
- * @param topModel
- * top model
- * @param reaction
- * reaction to transform into connection
- */
- public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
- if (reaction.getReactants().size() > 1) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
- } else if (reaction.getProducts().size() > 1) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
- } else if (reaction.getModifiers().size() > 0) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
- } else {
- Element fromAlias = reaction.getReactants().get(0).getElement();
- Element toAlias = reaction.getProducts().get(0).getElement();
- if (!(fromAlias instanceof Species)) {
- logger
- .warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
- } else if (!(toAlias instanceof Species)) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
- } else {
- Complex complexFrom = ((Species) fromAlias).getComplex();
- Complex complexTo = ((Species) toAlias).getComplex();
- if (complexFrom == null) {
- logger.warn(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
- } else if (complexTo == null && (!(toAlias instanceof Complex))) {
- logger.warn(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
- } else {
- if (complexTo == null) {
- complexTo = (Complex) toAlias;
- }
- String fromName = complexFrom.getName();
- String toName = complexTo.getName();
- Model fromModel = nameModelMap.get(fromName);
- Model toModel = nameModelMap.get(toName);
- if (fromModel == null) {
- throw new InvalidArgumentException("Mapping file references to " + fromName + " submodel. But such model doesn't exist");
- } else if (toModel == null) {
- throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
- }
- Element source = fromModel.getElementByElementId(fromAlias.getName());
- if (source == null) {
- throw new InvalidArgumentException("Mapping file references to element with alias: " + fromAlias.getName() + ". But such element doesn't exist");
- }
- Element dest = null;
- if (!(toAlias instanceof Complex)) {
- dest = fromModel.getElementByElementId(toAlias.getName());
- }
- SubmodelType type = SubmodelType.UNKNOWN;
- if (fromAlias instanceof Protein) {
- type = SubmodelType.DOWNSTREAM_TARGETS;
- } else if (fromAlias instanceof Phenotype) {
- type = SubmodelType.PATHWAY;
- }
- ElementSubmodelConnection connection = new ElementSubmodelConnection(toModel, type);
- connection.setFromElement(source);
- connection.setToElement(dest);
- connection.setName(toModel.getName());
- source.setSubmodel(connection);
- }
- }
- }
- }
+ /**
+ * Process a single reaction in mapping file (transfomring reaction into
+ * connection between submodels).
+ *
+ * @param mapping
+ * name of the mapping file
+ * @param nameModelMap
+ * mapping between file names and models
+ * @param topModel
+ * top model
+ * @param reaction
+ * reaction to transform into connection
+ */
+ public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
+ if (reaction.getReactants().size() > 1) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains too many reactants. Skipped");
+ } else if (reaction.getProducts().size() > 1) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains too many products. Skipped");
+ } else if (reaction.getModifiers().size() > 0) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains modifiers. Skipped");
+ } else {
+ Element fromAlias = reaction.getReactants().get(0).getElement();
+ Element toAlias = reaction.getProducts().get(0).getElement();
+ if (!(fromAlias instanceof Species)) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't start in species. Skipped");
+ } else if (!(toAlias instanceof Species)) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't end in species. Skipped");
+ } else {
+ Complex complexFrom = ((Species) fromAlias).getComplex();
+ Complex complexTo = ((Species) toAlias).getComplex();
+ if (complexFrom == null) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't start inside complex. Skipped");
+ } else if (complexTo == null && (!(toAlias instanceof Complex))) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't end inside complex. Skipped");
+ } else {
+ if (complexTo == null) {
+ complexTo = (Complex) toAlias;
+ }
+ String fromName = complexFrom.getName();
+ String toName = complexTo.getName();
+ Model fromModel = nameModelMap.get(fromName);
+ Model toModel = nameModelMap.get(toName);
+ if (fromModel == null) {
+ throw new InvalidArgumentException(
+ "Mapping file references to " + fromName + " submodel. But such model doesn't exist");
+ } else if (toModel == null) {
+ throw new InvalidArgumentException(
+ "Mapping file references to " + toName + " submodel. But such model doesn't exist");
+ }
+ Element source = fromModel.getElementByElementId(fromAlias.getName());
+ if (source == null) {
+ throw new InvalidArgumentException("Mapping file references to element with alias: " + fromAlias.getName()
+ + ". But such element doesn't exist");
+ }
+ Element dest = null;
+ if (!(toAlias instanceof Complex)) {
+ dest = fromModel.getElementByElementId(toAlias.getName());
+ }
+ SubmodelType type = SubmodelType.UNKNOWN;
+ if (fromAlias instanceof Protein) {
+ type = SubmodelType.DOWNSTREAM_TARGETS;
+ } else if (fromAlias instanceof Phenotype) {
+ type = SubmodelType.PATHWAY;
+ }
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(toModel, type);
+ connection.setFromElement(source);
+ connection.setToElement(dest);
+ connection.setName(toModel.getName());
+ source.setSubmodel(connection);
+ }
+ }
+ }
+ }
- /**
- * This method validates if information about model and submodels in the
- * params are sufficient. If not then apropriate exception will be thrown.
- *
- * @param params
- * parameters to validate
- * @param zipFile
- * original {@link ZipFile}
- * @return name of the file containg mapping between submodels
- */
- protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- Set<String> processed = new HashSet<String>();
+ /**
+ * This method validates if information about model and submodels in the params
+ * are sufficient. If not then appropriate exception will be thrown.
+ *
+ * @param params
+ * parameters to validate
+ * @param zipFile
+ * original {@link ZipFile}
+ * @return name of the file containing mapping between submodels
+ */
+ protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ Set<String> processed = new HashSet<>();
- String root = null;
- String mapping = null;
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- String name = entry.getName();
- ZipEntryFile zef = params.getEntry(name);
- if (zef == null) {
- throw new InvalidArgumentException("No information found in params about file: " + name);
- }
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- if (modelEntryFile.isRoot()) {
- if (root != null) {
- throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
- }
- root = name;
- }
- if (modelEntryFile.isMappingFile()) {
- if (mapping != null) {
- throw new InvalidArgumentException("Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
- }
- mapping = name;
- }
- }
- processed.add(name);
- }
- }
- if (root == null) {
- throw new InvalidArgumentException("No root map found.");
- }
- for (String entryName : params.getFilenames()) {
- if (!processed.contains(entryName)) {
- throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
- }
- }
- return mapping;
- }
+ String root = null;
+ String mapping = null;
+ logger.debug(params.getFilenames());
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ String name = entry.getName();
+ ZipEntryFile zef = params.getEntry(name);
+ if (zef == null) {
+ throw new InvalidArgumentException("No information found in params about file: " + name);
+ }
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ if (modelEntryFile.isRoot()) {
+ if (root != null) {
+ throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
+ }
+ root = name;
+ }
+ if (modelEntryFile.isMappingFile()) {
+ if (mapping != null) {
+ throw new InvalidArgumentException(
+ "Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
+ }
+ mapping = name;
+ }
+ }
+ processed.add(name.toLowerCase());
+ }
+ }
+ if (root == null) {
+ throw new InvalidArgumentException("No root map found.");
+ }
+ for (String entryName : params.getFilenames()) {
+ if (!processed.contains(entryName)) {
+ throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
+ }
+ }
+ return mapping;
+ }
- /**
- * Transforms {@link DataMiningZipEntryFile} into {@link DataMiningSet}.
- *
- * @param zipFile
- * original {@link ZipFile}
- * @param entry
- * entry in a zip file
- * @param dmEntry
- * {@link DataMiningZipEntryFile} to transform
- * @return {@link DataMiningSet} for a given {@link DataMiningZipEntryFile}
- * @throws IOException
- * thrown when there is a problem with accessing {@link ZipFile}
- */
- protected DataMiningSet dataMiningZipEntryToDataMiningSet(ZipFile zipFile, ZipEntry entry, DataMiningZipEntryFile dmEntry) throws IOException {
- DataMiningSet dmSet = new DataMiningSet();
- dmSet.setName(dmEntry.getName());
- dmSet.setInputData(IOUtils.toByteArray(zipFile.getInputStream(entry)));
- dmSet.setDescription(dmEntry.getDescription());
- dmSet.setSource(dmEntry.getSource());
- dmSet.setType(dmEntry.getType());
- return dmSet;
- }
+ /**
+ * Transforms {@link DataMiningZipEntryFile} into {@link DataMiningSet}.
+ *
+ * @param zipFile
+ * original {@link ZipFile}
+ * @param entry
+ * entry in a zip file
+ * @param dmEntry
+ * {@link DataMiningZipEntryFile} to transform
+ * @return {@link DataMiningSet} for a given {@link DataMiningZipEntryFile}
+ * @throws IOException
+ * thrown when there is a problem with accessing {@link ZipFile}
+ */
+ protected DataMiningSet dataMiningZipEntryToDataMiningSet(ZipFile zipFile, ZipEntry entry,
+ DataMiningZipEntryFile dmEntry) throws IOException {
+ DataMiningSet dmSet = new DataMiningSet();
+ dmSet.setName(dmEntry.getName());
+ dmSet.setInputData(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+ dmSet.setDescription(dmEntry.getDescription());
+ dmSet.setSource(dmEntry.getSource());
+ dmSet.setType(dmEntry.getType());
+ return dmSet;
+ }
- /**
- * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
- *
- * @param zipFile
- * original {@link ZipFile}
- * @param entry
- * entry in a zip file
- * @param params
- * parameters used to make general conversion (we use directory where
- * layout should be stored)
- * @param layoutEntry
- * {@link LayoutZipEntryFile} to transform
- * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
- * @throws IOException
- * thrown when there is a problem with accessing {@link ZipFile}
- */
- protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry, LayoutZipEntryFile layoutEntry)
- throws IOException {
- Layout layout = new Layout();
- layout.setDescription(layoutEntry.getDescription());
- layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
- fileEntry.setOriginalFileName(entry.getName());
- layout.setInputData(fileEntry);
- layout.setPublicLayout(true);
- layout.setTitle(layoutEntry.getName());
- return layout;
- }
+ /**
+ * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
+ *
+ * @param zipFile
+ * original {@link ZipFile}
+ * @param entry
+ * entry in a zip file
+ * @param params
+ * parameters used to make general conversion (we use directory where
+ * layout should be stored)
+ * @param layoutEntry
+ * {@link LayoutZipEntryFile} to transform
+ * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
+ * @throws IOException
+ * thrown when there is a problem with accessing {@link ZipFile}
+ */
+ protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry,
+ LayoutZipEntryFile layoutEntry) throws IOException {
+ Layout layout = new Layout();
+ layout.setDescription(layoutEntry.getDescription());
+ layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+ fileEntry.setOriginalFileName(entry.getName());
+ fileEntry.setLength(fileEntry.getFileContent().length);
+ layout.setInputData(fileEntry);
+ layout.setPublicLayout(true);
+ layout.setTitle(layoutEntry.getName());
+ return layout;
+ }
- /**
- * Copy file from zip entry into temporary file.
- *
- * @param zipFile
- * input zip file
- * @param entry
- * entry in the zip file
- * @return {@link File} with a copy of data from zip entry
- * @throws IOException
- * thrown when there is a problem with input or output file
- */
- protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
- InputStream is = zipFile.getInputStream(entry);
- File result = File.createTempFile("temp-file-name", ".png");
- FileOutputStream fos = new FileOutputStream(result);
- byte[] bytes = new byte[BUFFER_SIZE];
- int length;
- while ((length = is.read(bytes)) >= 0) {
- fos.write(bytes, 0, length);
- }
- fos.close();
- return result;
- }
+ /**
+ * Copy file from zip entry into temporary file.
+ *
+ * @param zipFile
+ * input zip file
+ * @param entry
+ * entry in the zip file
+ * @return {@link File} with a copy of data from zip entry
+ * @throws IOException
+ * thrown when there is a problem with input or output file
+ */
+ protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
+ InputStream is = zipFile.getInputStream(entry);
+ File result = File.createTempFile("temp-file-name", ".png");
+ FileOutputStream fos = new FileOutputStream(result);
+ byte[] bytes = new byte[BUFFER_SIZE];
+ int length;
+ while ((length = is.read(bytes)) >= 0) {
+ fos.write(bytes, 0, length);
+ }
+ fos.close();
+ return result;
+ }
- /**
- * Creates inctance of {@link IConverter} used as a template parameter for
- * this class instatiation.
- *
- * @return inctance of {@link IConverter}
- */
- protected IConverter createConverterInstance() {
- IConverter converter;
- try {
- converter = converterClazz.newInstance();
- } catch (InstantiationException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- } catch (IllegalAccessException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- }
- return converter;
- }
+ /**
+ * Creates inctance of {@link IConverter} used as a template parameter for this
+ * class instatiation.
+ *
+ * @return inctance of {@link IConverter}
+ */
+ protected IConverter createConverterInstance() {
+ IConverter converter;
+ try {
+ converter = converterClazz.newInstance();
+ } catch (InstantiationException e) {
+ throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ }
+ return converter;
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
index 2001d886ed..8d8daf907d 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
@@ -19,113 +19,112 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
*/
public class ComplexZipConverterParams {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ComplexZipConverterParams.class);
-
- /**
- * Zip file where all maps are stored.
- */
- private ZipFile zipFile;
-
- /**
- * Mapping between filename and information provided by the user about the
- * file.
- */
- private Map<String, ZipEntryFile> entries = new HashMap<>();
-
- /**
- * Directory where additional visualization files should be stored.
- */
- private String visualizationDir = null;
-
- /**
- * Sets {@link #zipFile}.
- *
- * @param zipFile
- * {@link #zipFile}
- * @return object with all parameters
- */
- public ComplexZipConverterParams zipFile(ZipFile zipFile) {
- this.zipFile = zipFile;
- return this;
- }
-
- /**
- * Sets {@link #zipFile}.
- *
- * @param filename
- * name of the {@link #zipFile}
- * @return object with all parameters
- * @throws IOException
- * throw when there is a problem with a file
- */
- public ComplexZipConverterParams zipFile(String filename) throws IOException {
- this.zipFile = new ZipFile(filename);
- return this;
- }
-
- /**
- * Sets information about single entry in the zip file.
- *
- * @param entry
- * set of information about single zip entry
- * @return object with all parameters
- */
- public ComplexZipConverterParams entry(ZipEntryFile entry) {
- this.entries.put(entry.getFilename(), entry);
- return this;
- }
-
- /**
- * @return the zipFile
- * @see #zipFile
- */
- public ZipFile getZipFile() {
- return zipFile;
- }
-
- /**
- * Returns set of filenames put in this param object.
- *
- * @return set of filenames put in this param object
- */
- public Set<String> getFilenames() {
- return entries.keySet();
- }
-
- /**
- * Sets {@link #visualizationDir} value.
- *
- * @param string
- * new value
- * @return instance of this class
- */
- public ComplexZipConverterParams visualizationDir(String string) {
- this.visualizationDir = string;
- return this;
- }
-
- /**
- * Returns {@link #visualizationDir}.
- *
- * @return {@link #visualizationDir}
- */
- public String getVisualizationDir() {
- return visualizationDir;
- }
-
- /**
- * Return {@link ZipEntryFile entry} with information about single file in the
- * zip archive identified by file name.
- *
- * @param name
- * name of the file in zip archive
- * @return {@link ZipEntryFile entry} with information about file
- */
- public ZipEntryFile getEntry(String name) {
- return entries.get(name);
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ComplexZipConverterParams.class);
+
+ /**
+ * Zip file where all maps are stored.
+ */
+ private ZipFile zipFile;
+
+ /**
+ * Mapping between filename and information provided by the user about the file.
+ */
+ private Map<String, ZipEntryFile> entries = new HashMap<>();
+
+ /**
+ * Directory where additional visualization files should be stored.
+ */
+ private String visualizationDir = null;
+
+ /**
+ * Sets {@link #zipFile}.
+ *
+ * @param zipFile
+ * {@link #zipFile}
+ * @return object with all parameters
+ */
+ public ComplexZipConverterParams zipFile(ZipFile zipFile) {
+ this.zipFile = zipFile;
+ return this;
+ }
+
+ /**
+ * Sets {@link #zipFile}.
+ *
+ * @param filename
+ * name of the {@link #zipFile}
+ * @return object with all parameters
+ * @throws IOException
+ * throw when there is a problem with a file
+ */
+ public ComplexZipConverterParams zipFile(String filename) throws IOException {
+ this.zipFile = new ZipFile(filename);
+ return this;
+ }
+
+ /**
+ * Sets information about single entry in the zip file.
+ *
+ * @param entry
+ * set of information about single zip entry
+ * @return object with all parameters
+ */
+ public ComplexZipConverterParams entry(ZipEntryFile entry) {
+ this.entries.put(entry.getFilename().toLowerCase(), entry);
+ return this;
+ }
+
+ /**
+ * @return the zipFile
+ * @see #zipFile
+ */
+ public ZipFile getZipFile() {
+ return zipFile;
+ }
+
+ /**
+ * Returns set of filenames put in this param object.
+ *
+ * @return set of filenames put in this param object
+ */
+ public Set<String> getFilenames() {
+ return entries.keySet();
+ }
+
+ /**
+ * Sets {@link #visualizationDir} value.
+ *
+ * @param string
+ * new value
+ * @return instance of this class
+ */
+ public ComplexZipConverterParams visualizationDir(String string) {
+ this.visualizationDir = string;
+ return this;
+ }
+
+ /**
+ * Returns {@link #visualizationDir}.
+ *
+ * @return {@link #visualizationDir}
+ */
+ public String getVisualizationDir() {
+ return visualizationDir;
+ }
+
+ /**
+ * Return {@link ZipEntryFile entry} with information about single file in the
+ * zip archive identified by file name (file name is case insensitive).
+ *
+ * @param name
+ * name of the file in zip archive
+ * @return {@link ZipEntryFile entry} with information about file
+ */
+ public ZipEntryFile getEntry(String name) {
+ return entries.get(name.toLowerCase());
+ }
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
index f69bc17894..39feccf210 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
@@ -5,9 +5,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ComplexZipConverterTest.class, //
- OverviewParserTest.class, //
- ProjectFactoryTest.class,//
+@SuiteClasses({ ComplexZipConverterParamsTest.class, //
+ ComplexZipConverterTest.class, //
+ OverviewParserTest.class, //
+ ProjectFactoryTest.class,//
})
public class AllTests {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterParamsTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterParamsTest.java
new file mode 100644
index 0000000000..c3ba1883c4
--- /dev/null
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterParamsTest.java
@@ -0,0 +1,22 @@
+package lcsb.mapviewer.converter;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+
+public class ComplexZipConverterParamsTest {
+
+ @Test
+ public void testCaseInsensivity() {
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ ZipEntryFile entry = new LayoutZipEntryFile("TEST.xml", "test", null);
+ params.entry(entry);
+ assertNotNull(params.getEntry("TEST.xml"));
+ assertNotNull(params.getEntry("test.xml"));
+ assertNotNull(params.getEntry("TEST.XML"));
+ }
+
+}
diff --git a/frontend-js/.gitignore b/frontend-js/.gitignore
index 6e21c03544..163769681a 100644
--- a/frontend-js/.gitignore
+++ b/frontend-js/.gitignore
@@ -1,5 +1,7 @@
.idea/workspace.xml
+.idea/jsLibraryMappings.xml
/dist/
/coverage/
/node_modules/
/npm-debug.log
+
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 8f1db201c7..1024eb4590 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -73,7 +73,7 @@ ServerConnector.registerListenerType("onDataLoadStart");
ServerConnector.registerListenerType("onDataLoadStop");
ServerConnector.init();
-ServerConnector.getMinOverlayColorInt = function() {
+ServerConnector.getMinOverlayColorInt = function () {
var self = this;
return self.getLoggedUser().then(function (user) {
var userColor = user.getMinColor();
@@ -96,7 +96,7 @@ ServerConnector.returnUserOrSystemColor = function (userColor, systemPromisedCol
ServerConnector.getSimpleOverlayColorInt = function () {
var self = this;
- return self.getLoggedUser().then(function(user) {
+ return self.getLoggedUser().then(function (user) {
var userColor = user.getSimpleColor();
return self.returnUserOrSystemColor(userColor, self.getConfigurationParam(ConfigurationType.SIMPLE_COLOR_VAL));
});
@@ -152,10 +152,10 @@ ServerConnector._sendRequest = function (params) {
return new Promise(function (resolve, reject) {
request(params, function (error, response, body) {
if (error) {
- reject(new NetworkError(error.message, {
- content: body,
- url: url
- }));
+ reject(new NetworkError(error.message, {
+ content: body,
+ url: url
+ }));
} else if (response.statusCode !== 200) {
reject(new NetworkError(params.url + " rejected with status code: " + response.statusCode, {
content: body,
@@ -229,8 +229,8 @@ ServerConnector.getApiBaseUrl = function () {
ServerConnector.getServerBaseUrl = function () {
if (this._serverBaseUrl === undefined) {
var url = "" + window.location.href;
- if (url.indexOf("?")>=0) {
- url = url.substr(0,url.indexOf("?"));
+ if (url.indexOf("?") >= 0) {
+ url = url.substr(0, url.indexOf("?"));
}
if (!url.endsWith("/")) {
url = url.substr(0, url.lastIndexOf("/") + 1);
@@ -566,6 +566,30 @@ ServerConnector.getProjectSourceUrl = function (queryParams, filterParams) {
});
};
+
+ServerConnector.getFilesUrl = function () {
+ return this.getApiUrl({
+ type: "files/"
+ });
+};
+
+ServerConnector.getCreateFileUrl = function () {
+ return this.getApiUrl({
+ url: this.getFilesUrl()
+ });
+};
+ServerConnector.getFileUrl = function (queryParams) {
+ return this.getApiUrl({
+ url: this.getFilesUrl() + "/" + queryParams.id
+ });
+};
+ServerConnector.getUploadFileUrl = function (queryParams) {
+ return this.getApiUrl({
+ url: this.getFileUrl(queryParams) + ":uploadContent"
+ });
+};
+
+
ServerConnector.getUsersUrl = function (queryParams, filterParams) {
return this.getApiUrl({
type: "users/",
@@ -619,7 +643,7 @@ ServerConnector.getModels = function (projectId) {
var queryParams = {};
var filterParams = {};
var self = this;
- return self.getProjectId(projectId).then(function(result) {
+ return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getModelsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -650,7 +674,7 @@ ServerConnector.getProject = function (projectId) {
}
project = self._projectsById[projectId];
return self.getModels(projectId);
- }).then(function(models) {
+ }).then(function (models) {
project.setModel(models[0]);
return self.getLoggedUser();
}).then(function (user) {
@@ -802,13 +826,13 @@ ServerConnector.getProjectStatistics = function (projectId) {
var filterParams = {};
var self = this;
var content;
- return self.getProjectId(projectId).then(function(result) {
+ return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getProjectStatisticsUrl(queryParams, filterParams));
}).then(function (result) {
content = JSON.parse(result);
return self.getConfiguration();
- }).then(function(configuration) {
+ }).then(function (configuration) {
return new ProjectStatistics(content, configuration);
});
};
@@ -933,17 +957,17 @@ ServerConnector.getOverlays = function (params) {
});
};
-ServerConnector.getOverlayElements = function(overlayId, projectId) {
+ServerConnector.getOverlayElements = function (overlayId, projectId) {
var self = this;
if (overlayId === undefined) {
throw new Error("Layout id must be defined");
}
var queryParams = {
- overlayId : overlayId,
- modelId : "*",
+ overlayId: overlayId,
+ modelId: "*",
};
var filterParams = {};
- return self.getProjectId(projectId).then(function(result) {
+ return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getOverlayElementsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1041,7 +1065,7 @@ ServerConnector.getReactions = function (params) {
columns: params.columns,
participantId: params.participantId,
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
if (filterParams.id.length > 100 || filterParams.participantId.length > 100) {
return self.sendPostRequest(self.getReactionsUrl(queryParams), filterParams);
@@ -1059,10 +1083,10 @@ ServerConnector.getReactions = function (params) {
});
};
-ServerConnector.getAliases = function(params) {
+ServerConnector.getAliases = function (params) {
var self = this;
var queryParams = {
- modelId : params.modelId,
+ modelId: params.modelId,
};
if (params.ids === undefined) {
params.ids = [];
@@ -1081,14 +1105,14 @@ ServerConnector.getAliases = function(params) {
includedCompartmentIds: params.includedCompartmentIds,
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
if (filterParams.id.length > 100) {
return self.sendPostRequest(self.getAliasesUrl(queryParams), filterParams);
} else {
return self.sendGetRequest(self.getAliasesUrl(queryParams, filterParams));
}
- }).then(function(content) {
+ }).then(function (content) {
var array = JSON.parse(content);
var result = [];
for (var i = 0; i < array.length; i++) {
@@ -1098,22 +1122,22 @@ ServerConnector.getAliases = function(params) {
});
};
-ServerConnector.getLightComments = function(params) {
- params.columns = [ "id", "elementId", "modelId", "type", "icon", "removed", "pinned" ];
+ServerConnector.getLightComments = function (params) {
+ params.columns = ["id", "elementId", "modelId", "type", "icon", "removed", "pinned"];
return this.getComments(params);
};
-ServerConnector.getComments = function(params) {
+ServerConnector.getComments = function (params) {
var self = this;
var queryParams = {
- elementId : params.elementId,
- elementType : params.elementType,
- coordinates : params.coordinates,
+ elementId: params.elementId,
+ elementType: params.elementType,
+ coordinates: params.coordinates,
};
var filterParams = {
- columns : params.columns
+ columns: params.columns
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getCommentsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1229,13 +1253,13 @@ ServerConnector.getDrugsByQuery = function (params) {
});
};
-ServerConnector.getMiRnasByQuery = function(params) {
+ServerConnector.getMiRnasByQuery = function (params) {
var self = this;
var queryParams = {};
var filterParams = {
- query : params.query
+ query: params.query
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchMiRnasUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1412,7 +1436,7 @@ ServerConnector.addComment = function (params) {
elementId: params.elementId,
elementType: params.elementType,
coordinates: self.pointToString(params.coordinates),
- modelId: params.modelId,
+ modelId: params.modelId
};
var filterParams = params;
delete filterParams.elementId;
@@ -1443,7 +1467,7 @@ ServerConnector.addOverlay = function (params) {
name: overlay.getName(),
description: overlay.getDescription(),
content: overlay.getContent(),
- filename: overlay.getFilename(),
+ filename: overlay.getFilename()
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
@@ -1456,14 +1480,14 @@ ServerConnector.addOverlay = function (params) {
ServerConnector.updateOverlay = function (overlay) {
var self = this;
var queryParams = {
- overlayId: overlay.getId(),
+ overlayId: overlay.getId()
};
var filterParams = {
overlay: {
name: overlay.getName(),
description: overlay.getDescription(),
creator: overlay.getCreator(),
- publicOverlay: overlay.getPublicOverlay(),
+ publicOverlay: overlay.getPublicOverlay()
}
};
return self.sendPatchRequest(self.updateOverlayUrl(queryParams), filterParams);
@@ -1524,9 +1548,9 @@ ServerConnector.getPublications = function (params) {
length: params.length,
sortColumn: params.sortColumn,
sortOrder: params.sortOrder,
- search: params.search,
+ search: params.search
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getPublicationsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1534,7 +1558,7 @@ ServerConnector.getPublications = function (params) {
});
};
-ServerConnector.getReferenceGenome = function(params) {
+ServerConnector.getReferenceGenome = function (params) {
var self = this;
var filterParams = {};
return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
@@ -1542,4 +1566,34 @@ ServerConnector.getReferenceGenome = function(params) {
});
};
+ServerConnector.uploadFile = function (params) {
+ var CHUNK_SIZE = 65535;
+ var self = this;
+ var data = new Uint8Array(params.content);
+ var filterParams = {
+ filename: params.filename,
+ length: data.length
+ };
+
+ return self.sendPostRequest(self.getCreateFileUrl(), filterParams).then(function (response) {
+ var uploadedLength = 0;
+ var createPromise = function (resultFileJson) {
+ var resultFile = JSON.parse(resultFileJson);
+ if (uploadedLength >= data.length) {
+ return Promise.resolve(resultFile);
+ } else {
+ var chunk = data.slice(uploadedLength, uploadedLength + CHUNK_SIZE);
+ logger.debug("SEND " + chunk.length + " bytes");
+ var url = self.getUploadFileUrl({id: resultFile.id});
+ return self.sendRequest({method: "POST", url: url, body: chunk}).then(function (resultFileJson) {
+ uploadedLength += chunk.length;
+ logger.debug("RESPONSE ", resultFileJson);
+ return createPromise(resultFileJson);
+ })
+ }
+ };
+ return createPromise(response);
+ });
+};
+
module.exports = ServerConnector;
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 966d914461..c6766dbec4 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -675,7 +675,7 @@ AddProjectDialog.prototype.processFile = function (file) {
if (file) {
return new Promise(function (resolve, reject) {
var reader = new FileReader();
- reader.readAsText(file);
+ reader.readAsArrayBuffer(file);
reader.onload = function (evt) {
try {
self.setFileContent(evt.target.result);
@@ -694,7 +694,6 @@ AddProjectDialog.prototype.processFile = function (file) {
};
AddProjectDialog.prototype.setFileContent = function (fileContent) {
- logger.debug(fileContent);
this._fileContent = fileContent;
};
AddProjectDialog.prototype.getFileContent = function () {
@@ -771,6 +770,7 @@ AddProjectDialog.prototype.setSemanticZooming = function (value) {
AddProjectDialog.prototype.setFileParserForFilename = function (filename) {
var self = this;
+ self._filename = filename;
var select = $("[name='project-format']", self.getElement)[0];
var options = select.options;
var optionId = 0;
@@ -803,18 +803,20 @@ AddProjectDialog.prototype.getConverter = function () {
AddProjectDialog.prototype.onSaveClicked = function () {
var self = this;
+ var parserClass;
return self.checkValidity().then(function () {
return self.getConverter();
}).then(function (converter) {
- var parserClass;
if (converter !== null) {
parserClass = converter.handler;
}
+ return ServerConnector.uploadFile({filename: self._filename, content: self.getFileContent()});
+ }).then(function (file) {
var options = {
"projectId": self.getProjectId(),
"name": self.getName(),
"parser": parserClass,
- "file-content": self.getFileContent(),
+ "file-id": file.id,
"auto-resize": self.isAutoMargin(),
"cache": self.isCache(),
"notify-email": self.getNotifyEmail(),
@@ -978,4 +980,8 @@ AddProjectDialog.prototype.getEntryByFilename = function (filename) {
return null;
};
+AddProjectDialog.prototype.getFilename = function () {
+ return this._filename;
+};
+
module.exports = AddProjectDialog;
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index ab6fc4ec0a..0e756aae63 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -20,80 +20,80 @@ var logger = require('./logger');
var chai = require('chai');
var assert = chai.assert;
-describe('ServerConnector', function() {
- describe('getProject', function() {
- it('default', function() {
- return ServerConnector.getProject().then(function(result) {
+describe('ServerConnector', function () {
+ describe('getProject', function () {
+ it('default', function () {
+ return ServerConnector.getProject().then(function (result) {
assert.ok(result instanceof Project);
assert.equal(result.getProjectId(), "sample");
assert.equal(logger.getWarnings().length, 0);
});
});
- it('invalid project id', function() {
- return ServerConnector.getProject("invalid_project_id").then(function(result) {
+ it('invalid project id', function () {
+ return ServerConnector.getProject("invalid_project_id").then(function (result) {
assert.equal(result, null);
});
});
- it('caching', function() {
+ it('caching', function () {
var project;
- return ServerConnector.getProject().then(function(result) {
+ return ServerConnector.getProject().then(function (result) {
project = result;
return ServerConnector.getProject();
- }).then(function(result) {
+ }).then(function (result) {
assert.ok(result === project);
});
});
});
- describe('updateProject', function() {
- it('default', function() {
+ describe('updateProject', function () {
+ it('default', function () {
var project;
var newVersion = "2.01";
- return ServerConnector.getProject().then(function(result) {
+ return ServerConnector.getProject().then(function (result) {
project = result;
project.setVersion(newVersion);
return ServerConnector.updateProject(project);
- }).then(function(result) {
+ }).then(function (result) {
assert.ok(project === result);
assert.equal(newVersion, result.getVersion());
});
});
});
- describe('removeProject', function() {
- it('default', function() {
+ describe('removeProject', function () {
+ it('default', function () {
var project;
- return ServerConnector.getProject().then(function(result) {
+ return ServerConnector.getProject().then(function (result) {
project = result;
return ServerConnector.removeProject(project.getProjectId());
- }).then(function(result) {
+ }).then(function (result) {
assert.ok(project === result);
});
});
});
- it('getModels', function() {
- return ServerConnector.getModels("sample").then(function(models) {
+ it('getModels', function () {
+ return ServerConnector.getModels("sample").then(function (models) {
assert.equal(1, models.length);
assert.ok(models[0] instanceof MapModel);
});
});
- it('getPublications', function() {
- return ServerConnector.getPublications().then(function(result) {
+ it('getPublications', function () {
+ return ServerConnector.getPublications().then(function (result) {
assert.equal(result.totalSize, 1);
});
});
- it('getProjectId from GET params', function() {
+ it('getProjectId from GET params', function () {
helper.setUrl("http://test/?id=test");
- return ServerConnector.getProjectId().then(function(result) {
+ return ServerConnector.getProjectId().then(function (result) {
assert.equal(result, "test");
});
});
- it('getReactions with empty list of ids', function() {
- return ServerConnector.getReactions([]).then(function(result) {
+ it('getReactions with empty list of ids', function () {
+ return ServerConnector.getReactions([]).then(function (result) {
assert.equal(result.length, 2);
var reaction = result[0];
assert.ok(reaction instanceof Reaction);
@@ -102,8 +102,8 @@ describe('ServerConnector', function() {
});
});
- it('getReactions without ids', function() {
- return ServerConnector.getReactions([]).then(function(result) {
+ it('getReactions without ids', function () {
+ return ServerConnector.getReactions([]).then(function (result) {
assert.equal(result.length, 2);
var reaction = result[0];
assert.ok(reaction instanceof Reaction);
@@ -112,8 +112,8 @@ describe('ServerConnector', function() {
});
});
- it('getElements with empty list of ids', function() {
- return ServerConnector.getAliases({}).then(function(result) {
+ it('getElements with empty list of ids', function () {
+ return ServerConnector.getAliases({}).then(function (result) {
assert.equal(result.length, 30);
var alias = result[0];
assert.ok(alias instanceof Alias);
@@ -121,8 +121,8 @@ describe('ServerConnector', function() {
});
});
- it('getOverlayElements', function() {
- return ServerConnector.getOverlayElements(18077).then(function(result) {
+ it('getOverlayElements', function () {
+ return ServerConnector.getOverlayElements(18077).then(function (result) {
assert.equal(result.length, 1);
var layoutAlias = result[0];
assert.ok(layoutAlias instanceof LayoutAlias);
@@ -132,80 +132,80 @@ describe('ServerConnector', function() {
});
});
- it('idsToString', function() {
- var ids = [ 3, 2, 9, 1, 6, 8, 3, 2, 9, 1, 7, 3 ];
+ it('idsToString', function () {
+ var ids = [3, 2, 9, 1, 6, 8, 3, 2, 9, 1, 7, 3];
var str = ServerConnector.idsToString(ids);
assert.equal(str, "1,2,3,6,7,8,9");
});
- it('getOverlaySourceDownloadUrl', function() {
+ it('getOverlaySourceDownloadUrl', function () {
var id = 17296;
return ServerConnector.getOverlaySourceDownloadUrl({
- overlayId : id
- }).then(function(url) {
+ overlayId: id
+ }).then(function (url) {
assert.ok(url);
assert.ok(url.indexOf(id) >= 0);
return ServerConnector.sendGetRequest(url);
});
});
- it('getImageDownloadUrl', function() {
+ it('getImageDownloadUrl', function () {
var modelId = 15781;
return ServerConnector.getImageDownloadUrl({
- modelId : modelId,
- handlerClass : "lcsb.mapviewer.converter.graphics.PngImageGenerator",
- }).then(function(url) {
+ modelId: modelId,
+ handlerClass: "lcsb.mapviewer.converter.graphics.PngImageGenerator",
+ }).then(function (url) {
assert.ok(url);
assert.ok(url.indexOf(modelId) >= 0);
return ServerConnector.sendGetRequest(url);
});
});
- it('getModelDownloadUrl', function() {
+ it('getModelDownloadUrl', function () {
var modelId = 15781;
return ServerConnector.getModelDownloadUrl({
- modelId : modelId,
- handlerClass : "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
- }).then(function(url) {
+ modelId: modelId,
+ handlerClass: "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
+ }).then(function (url) {
assert.ok(url);
assert.ok(url.indexOf(modelId) >= 0);
return ServerConnector.sendGetRequest(url);
});
});
- it('getProjectSourceDownloadUrl', function() {
- return ServerConnector.getProjectSourceDownloadUrl().then(function(url) {
+ it('getProjectSourceDownloadUrl', function () {
+ return ServerConnector.getProjectSourceDownloadUrl().then(function (url) {
assert.ok(url);
return ServerConnector.sendGetRequest(url);
});
});
- it('addOverlay', function() {
+ it('addOverlay', function () {
return ServerConnector.addOverlay({
- overlay : new LayoutData({
- name : "test nam",
- description : "test desc",
- content : "name color\nCAPN1 #00FF00\nPARK7 #AC0000",
- filename : "test.txt"
+ overlay: new LayoutData({
+ name: "test nam",
+ description: "test desc",
+ content: "name color\nCAPN1 #00FF00\nPARK7 #AC0000",
+ filename: "test.txt"
}),
- }).then(function(overlay) {
+ }).then(function (overlay) {
assert.ok(overlay);
});
});
- it('removeOverlay', function() {
+ it('removeOverlay', function () {
return ServerConnector.removeOverlay({
- overlayId : 17296,
+ overlayId: 17296,
});
});
- it('removeComment', function() {
+ it('removeComment', function () {
return ServerConnector.removeComment({
- commentId : 4290,
+ commentId: 4290,
});
});
- it('updateOverlay', function() {
+ it('updateOverlay', function () {
var overlay = new LayoutData({});
overlay.setId(17296);
overlay.setName("test nam2");
@@ -214,142 +214,153 @@ describe('ServerConnector', function() {
return ServerConnector.updateOverlay(overlay);
});
- it('logout', function() {
- return ServerConnector.logout().then(function() {
+ it('logout', function () {
+ return ServerConnector.logout().then(function () {
assert.equal(ServerConnector.getSessionData().getToken(), undefined);
});
});
- it('getToken', function() {
+ it('getToken', function () {
ServerConnector.getSessionData(null).setToken(undefined);
- return ServerConnector.getToken().then(function(token) {
+ return ServerConnector.getToken().then(function (token) {
assert.ok(token !== undefined);
});
});
- it('getModelDownloadUrl', function() {
+ it('getModelDownloadUrl', function () {
return ServerConnector.getModelDownloadUrl({
- backgroundOverlayId : "cv14081",
- }).then(function(url) {
+ backgroundOverlayId: "cv14081",
+ }).then(function (url) {
assert.ok(url);
});
});
- it('getOverlayById', function() {
- return ServerConnector.getOverlayById(18083, "complex_model_with_submaps").then(function(overlay) {
+ it('getOverlayById', function () {
+ return ServerConnector.getOverlayById(18083, "complex_model_with_submaps").then(function (overlay) {
assert.ok(overlay);
});
});
- it('getConfiguration', function() {
- return ServerConnector.getConfiguration().then(function(configuration) {
+ it('getConfiguration', function () {
+ return ServerConnector.getConfiguration().then(function (configuration) {
assert.ok(configuration instanceof Configuration);
assert.ok(configuration.getElementTypes().length > 0);
assert.ok(configuration.getReactionTypes().length > 0);
});
});
- describe('getProjects', function() {
- it('test caching', function() {
+ describe('getProjects', function () {
+ it('test caching', function () {
var projects;
- return ServerConnector.getProjects().then(function(result) {
+ return ServerConnector.getProjects().then(function (result) {
projects = result;
return ServerConnector.getProjects();
- }).then(function(result) {
+ }).then(function (result) {
assert.ok(result === projects);
});
});
- it('test force reload', function() {
+ it('test force reload', function () {
var projects;
var originalName;
- return ServerConnector.getProjects().then(function(result) {
+ return ServerConnector.getProjects().then(function (result) {
projects = result;
originalName = projects[0].getName();
projects[0].setName("test name");
return ServerConnector.getProjects(true);
- }).then(function(result) {
+ }).then(function (result) {
assert.ok(result === projects);
assert.equal(originalName, projects[0].getName());
});
});
});
- describe('login', function() {
- it('try invalid credentials', function() {
+ describe('login', function () {
+ it('try invalid credentials', function () {
var method = ServerConnector.sendPostRequest;
- ServerConnector.sendPostRequest = function() {
+ ServerConnector.sendPostRequest = function () {
return Promise.reject(new NetworkError("xxx", {
- statusCode : HttpStatus.FORBIDDEN
+ statusCode: HttpStatus.FORBIDDEN
}));
};
- return ServerConnector.login("unknown", "unknown password").then(function() {
+ return ServerConnector.login("unknown", "unknown password").then(function () {
ServerConnector.sendPostRequest = method;
assert.ok(false);
- }, function(error) {
+ }, function (error) {
ServerConnector.sendPostRequest = method;
assert.ok(error.message.indexOf("credentials") >= 0);
});
});
});
- describe('getServerBaseUrl', function() {
- it('url with GET arg that looks similar to original url', function() {
- helper.setUrl("http://localhost:8080/minerva/login.xhtml?from=http://localhost:8080/minerva/?id=sample");
- var url = ServerConnector.getServerBaseUrl();
- assert.ok(url.indexOf("?")===-1);
- });
+ describe('getServerBaseUrl', function () {
+ it('url with GET arg that looks similar to original url', function () {
+ helper.setUrl("http://localhost:8080/minerva/login.xhtml?from=http://localhost:8080/minerva/?id=sample");
+ var url = ServerConnector.getServerBaseUrl();
+ assert.ok(url.indexOf("?") === -1);
});
+ });
-
- describe('returnUserOrSystemColor ', function() {
- it('user has empty color', function() {
+ describe('returnUserOrSystemColor ', function () {
+ it('user has empty color', function () {
var systemColor = {};
- return ServerConnector.returnUserOrSystemColor("", Promise.resolve(systemColor)).then(function(result) {
+ return ServerConnector.returnUserOrSystemColor("", Promise.resolve(systemColor)).then(function (result) {
assert.ok(result = systemColor);
});
});
- it('user has defined color', function() {
+ it('user has defined color', function () {
var userColor = {};
var systemColor = {};
- return ServerConnector.returnUserOrSystemColor(userColor, Promise.resolve(systemColor)).then(function(result) {
+ return ServerConnector.returnUserOrSystemColor(userColor, Promise.resolve(systemColor)).then(function (result) {
assert.ok(result = userColor);
});
});
});
- describe('readFile', function() {
- it('check session expired', function() {
+ describe('readFile', function () {
+ it('check session expired', function () {
ServerConnector.getSessionData().setToken(undefined);
assert.ok(ServerConnector.getSessionData().getLogin());
- return ServerConnector.sendGetRequest("package.json", "Downloading projects").then(function() {
+ return ServerConnector.sendGetRequest("package.json", "Downloading projects").then(function () {
assert.notOk(ServerConnector.getSessionData().getLogin());
});
});
});
- describe('getUsers', function() {
- it('default', function() {
- return ServerConnector.getUsers().then(function(users) {
+ describe('getUsers', function () {
+ it('default', function () {
+ return ServerConnector.getUsers().then(function (users) {
assert.ok(users.length > 0);
});
});
- it('refresh', function() {
+ it('refresh', function () {
var user;
var users;
var modifiedName = "xxx name";
- return ServerConnector.getUsers().then(function(result) {
+ return ServerConnector.getUsers().then(function (result) {
users = result;
user = users[0];
user.setName(modifiedName);
return ServerConnector.getUsers(true);
- }).then(function(result) {
+ }).then(function (result) {
assert.ok(users === result);
assert.ok(user.getName() !== modifiedName);
});
});
});
+ describe('uploadFile', function () {
+ it('small file', function () {
+ return ServerConnector.uploadFile({
+ filename: "test.txt",
+ content: new Uint8Array([1, 65, 90, 4, 8])
+ }).then(function (file) {
+ logger.debug(file);
+ assert.ok(file.id);
+ });
+ });
+ });
+
});
diff --git a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
index 219804ccf8..3e1807a016 100644
--- a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
@@ -139,7 +139,7 @@ describe('AddProjectDialog', function () {
}).then(function () {
assert.ok(options["name"] !== undefined);
assert.ok(options["projectId"] !== undefined);
- assert.ok(options["file-content"] !== undefined);
+ assert.ok(options["file-id"] !== undefined);
assert.ok(options["parser"] !== undefined);
assert.ok(options["auto-resize"] !== undefined);
assert.ok(options["cache"] !== undefined);
@@ -148,6 +148,7 @@ describe('AddProjectDialog', function () {
assert.ok(options["organism"] !== undefined);
assert.ok(options["sbgn"] !== undefined);
assert.ok(options["semantic-zoom"] !== undefined);
+ }).finally(function () {
return dialog.destroy();
});
});
diff --git a/frontend-js/testFiles/apiCalls/files/6790.uploadContent/POST_token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/files/6790.uploadContent/POST_token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..b5a2599fb1
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/files/6790.uploadContent/POST_token=MOCK_TOKEN_ID&
@@ -0,0 +1,7 @@
+{
+ "owner": "admin",
+ "filename": "test.txt",
+ "uploadedDataLength": 5,
+ "length": 5,
+ "id": 6790
+}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/files/6791.uploadContent/POST_token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/files/6791.uploadContent/POST_token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..78115f94a8
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/files/6791.uploadContent/POST_token=MOCK_TOKEN_ID&
@@ -0,0 +1,7 @@
+{
+ "owner": "admin",
+ "filename": "test.xml",
+ "uploadedDataLength": 13,
+ "length": 13,
+ "id": 6791
+}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/files/POST_filename=test.txt&length=5&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/files/POST_filename=test.txt&length=5&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..bd4d1f74f1
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/files/POST_filename=test.txt&length=5&token=MOCK_TOKEN_ID&
@@ -0,0 +1,7 @@
+{
+ "owner": "admin",
+ "filename": "test.txt",
+ "uploadedDataLength": 0,
+ "length": 5,
+ "id": 6790
+}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/files/POST_filename=test.xml&length=13&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/files/POST_filename=test.xml&length=13&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..232463c23b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/files/POST_filename=test.xml&length=13&token=MOCK_TOKEN_ID&
@@ -0,0 +1,7 @@
+{
+ "owner": "admin",
+ "filename": "test.xml",
+ "uploadedDataLength": 0,
+ "length": 13,
+ "id": 6791
+}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
index 0ef8844970..acecea373d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
@@ -4,6 +4,10 @@ import java.io.Serializable;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.model.user.User;
/**
* Database object representing file uploaded into system.
@@ -15,26 +19,50 @@ import javax.persistence.Entity;
@DiscriminatorValue("UPLOADED_FILE_ENTRY")
public class UploadedFileEntry extends FileEntry implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UploadedFileEntry() {
-
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param original
- * original object from which data will bbe copied
- */
- public UploadedFileEntry(UploadedFileEntry original) {
- super(original);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Length of the file.
+ */
+ private long length;
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ private User owner;
+
+ /**
+ * Default constructor.
+ */
+ public UploadedFileEntry() {
+
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param original
+ * original object from which data will bbe copied
+ */
+ public UploadedFileEntry(UploadedFileEntry original) {
+ super(original);
+ }
+
+ public long getLength() {
+ return length;
+ }
+
+ public void setLength(long length) {
+ this.length = length;
+ }
+
+ public User getOwner() {
+ return owner;
+ }
+
+ public void setOwner(User owner) {
+ this.owner = owner;
+ }
}
diff --git a/persist/src/db/11.1.0/fix_db_20171004.sql b/persist/src/db/11.1.0/fix_db_20171004.sql
new file mode 100644
index 0000000000..bf80845a97
--- /dev/null
+++ b/persist/src/db/11.1.0/fix_db_20171004.sql
@@ -0,0 +1,12 @@
+--uploaded files that are uploaded in chunks should have info about how big should be the file
+alter table file_entry add column length bigint;
+update file_entry set length = octet_length(filecontent);
+
+--add foreign key
+alter table file_entry add column owner_iddb integer;
+ALTER TABLE file_entry ADD CONSTRAINT file_entry_owner_constraint FOREIGN KEY (owner_iddb)
+ REFERENCES public.user_table (iddb) MATCH SIMPLE
+ ON UPDATE NO ACTION ON DELETE NO ACTION;
+
+--add owners for layout files
+update file_entry SET owner_iddb = (select (max(creator_iddb)) from layout where file_entry_iddb = file_entry.iddb);
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 9918dfa4cf..7729b2296f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -38,263 +38,264 @@ import lcsb.mapviewer.services.view.AnnotationView;
@Transactional(value = "txManager")
public abstract class BaseRestImpl {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(BaseRestImpl.class);
-
- @Autowired
- private IModelService modelService;
-
- @Autowired
- private IProjectService projectService;
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private MiriamConnector miriamConnector;
-
- @Autowired
- private PubmedParser pubmedParser;
-
- @Autowired
- private ElementMatcher elementMatcher;
-
- protected Map<String, Object> okStatus() {
- Map<String, Object> result = new HashMap<>();
- return result;
- }
-
- protected Map<String, Object> createMinifiedSearchResult(Object object) {
- Map<String, Object> result = new HashMap<>();
- if (object instanceof Element) {
- result.put("type", ElementIdentifierType.ALIAS);
- Element element = (Element) object;
- result.put("id", element.getId());
- result.put("modelId", element.getModel().getId());
- } else if (object instanceof Reaction) {
- result.put("type", ElementIdentifierType.REACTION);
- Reaction element = (Reaction) object;
- result.put("id", element.getId());
- result.put("modelId", element.getModel().getId());
-
- } else {
- throw new InvalidStateException("Unknown type of result: " + object.getClass());
- }
- return result;
- };
-
- protected Map<String, Object> createAnnotation(MiriamData annotation) {
- if (annotation != null && annotation.getDataType() != null) {
- Map<String, Object> result = new HashMap<>();
- if (annotation.getDataType().getUris().size() > 0) {
- try {
- result.put("link", miriamConnector.getUrlString(annotation));
- } catch (Exception e) {
- logger.error("Problem with miriam: " + annotation, e);
- }
- }
- if (MiriamType.PUBMED.equals(annotation.getDataType())) {
- try {
- Article article = pubmedParser.getPubmedArticleById(Integer.valueOf(annotation.getResource()));
- result.put("article", article);
- } catch (PubmedSearchException e) {
- logger.error("Problem with accessing info about pubmed", e);
- }
- }
- result.put("type", annotation.getDataType().name());
- result.put("resource", annotation.getResource());
- result.put("id", annotation.getId());
- return result;
- } else {
- throw new InvalidArgumentException("invalid miriam data: " + annotation);
- }
- };
-
- protected Map<String, Object> createAnnotation(AnnotationView annotation) {
- Map<String, Object> result = new HashMap<>();
- if (annotation != null && annotation.getType() != null) {
- MiriamType type = MiriamType.getTypeByCommonName(annotation.getType());
- result.put("link", annotation.getLink());
- if (MiriamType.PUBMED.equals(type)) {
- try {
- Article article = pubmedParser.getPubmedArticleById(Integer.valueOf(annotation.getResource()));
- result.put("article", article);
- } catch (PubmedSearchException e) {
- logger.error("Problem with accessing info about pubmed", e);
- }
- }
- result.put("type", type);
- result.put("resource", annotation.getResource());
- result.put("id", annotation.getIdObject());
- }
- return result;
- }
-
- protected Map<String, Object> createAnnotation(Article article) {
- Map<String, Object> result = new HashMap<>();
- if (article != null) {
- MiriamType type = MiriamType.PUBMED;
- result.put("link", miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, article.getId())));
- result.put("article", article);
- result.put("type", type);
- result.put("resource", article.getId());
- }
- return result;
- }
-
- protected List<Map<String, Object>> createAnnotations(Collection<?> references) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (Object miriamData : references) {
- if (miriamData instanceof MiriamData) {
- result.add(createAnnotation((MiriamData) miriamData));
- } else if (miriamData instanceof AnnotationView) {
- result.add(createAnnotation((AnnotationView) miriamData));
- } else if (miriamData instanceof Article) {
- result.add(createAnnotation((Article) miriamData));
- } else {
- throw new InvalidArgumentException();
- }
- }
- return result;
- }
-
- protected List<Model> getModels(String projectId, String modelId, String token) throws SecurityException {
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
- List<Model> models = new ArrayList<>();
-
- if (!modelId.equals("*")) {
- for (String str : modelId.split(",")) {
- models.add(model.getSubmodelById(Integer.valueOf(str)));
- }
- } else {
- models.addAll(model.getSubmodels());
- models.add(model);
- }
- return models;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- protected List<Map<String, Object>> prepareTargets(Collection<Target> targets, List<Model> models) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (Target target : targets) {
- result.add(prepareTarget(target, models));
- }
- result.sort(new Comparator<Map<String, Object>>() {
-
- @Override
- public int compare(Map<String, Object> o1, Map<String, Object> o2) {
- List<?> targetedObjects1 = (List<?>) o1.get("targetElements");
- List<?> targetedObjects2 = (List<?>) o2.get("targetElements");
- Integer size1 = 0;
- Integer size2 = 0;
- if (targetedObjects1 != null) {
- size1 = targetedObjects1.size();
- }
- if (targetedObjects2 != null) {
- size2 = targetedObjects2.size();
- }
- return -size1.compareTo(size2);
- }
- });
- return result;
- }
-
- protected Map<String, Object> prepareTarget(Target target, List<Model> models) {
- Map<String, Object> result = new HashMap<>();
- result.put("name", target.getName());
- result.put("references", createAnnotations(target.getReferences()));
- result.put("targetParticipants", createAnnotations(target.getGenes()));
-
- List<Map<String, Object>> targetedObjects = new ArrayList<>();
- for (Model model : models) {
- for (BioEntity object : model.getBioEntities()) {
- if (elementMatcher.elementMatch(target, object)) {
- Map<String, Object> elementMapping = new HashMap<>();
-
- elementMapping.put("id", object.getId());
- elementMapping.put("type", getType(object));
- elementMapping.put("modelId", model.getId());
- targetedObjects.add(elementMapping);
- }
- }
- }
-
- result.put("targetElements", targetedObjects);
-
- return result;
- }
-
- private String getType(BioEntity object) {
- if (object instanceof Reaction) {
- return ElementIdentifierType.REACTION.getJsName();
- } else if (object instanceof Element) {
- return ElementIdentifierType.ALIAS.getJsName();
- } else {
- throw new InvalidArgumentException("Unknown type of element " + object.getClass());
- }
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- protected IConverter getModelParser(String handlerClass) throws QueryException {
- IConverter parser;
- if (SbgnmlXmlConverter.class.getCanonicalName().equals(handlerClass)) {
- parser = new SbgnmlXmlConverter();
- } else if (CellDesignerXmlParser.class.getCanonicalName().equals(handlerClass)) {
- parser = new CellDesignerXmlParser();
- } else {
- throw new QueryException("Unknown handlerClass: " + handlerClass);
- }
- return parser;
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(BaseRestImpl.class);
+
+ @Autowired
+ private IModelService modelService;
+
+ @Autowired
+ private IProjectService projectService;
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ @Autowired
+ private ElementMatcher elementMatcher;
+
+ protected Map<String, Object> okStatus() {
+ Map<String, Object> result = new HashMap<>();
+ return result;
+ }
+
+ protected Map<String, Object> createMinifiedSearchResult(Object object) {
+ Map<String, Object> result = new HashMap<>();
+ if (object instanceof Element) {
+ result.put("type", ElementIdentifierType.ALIAS);
+ Element element = (Element) object;
+ result.put("id", element.getId());
+ result.put("modelId", element.getModel().getId());
+ } else if (object instanceof Reaction) {
+ result.put("type", ElementIdentifierType.REACTION);
+ Reaction element = (Reaction) object;
+ result.put("id", element.getId());
+ result.put("modelId", element.getModel().getId());
+
+ } else {
+ throw new InvalidStateException("Unknown type of result: " + object.getClass());
+ }
+ return result;
+ };
+
+ protected Map<String, Object> createAnnotation(MiriamData annotation) {
+ if (annotation != null && annotation.getDataType() != null) {
+ Map<String, Object> result = new HashMap<>();
+ if (annotation.getDataType().getUris().size() > 0) {
+ try {
+ result.put("link", miriamConnector.getUrlString(annotation));
+ } catch (Exception e) {
+ logger.error("Problem with miriam: " + annotation, e);
+ }
+ }
+ if (MiriamType.PUBMED.equals(annotation.getDataType())) {
+ try {
+ Article article = pubmedParser.getPubmedArticleById(Integer.valueOf(annotation.getResource()));
+ result.put("article", article);
+ } catch (PubmedSearchException e) {
+ logger.error("Problem with accessing info about pubmed", e);
+ }
+ }
+ result.put("type", annotation.getDataType().name());
+ result.put("resource", annotation.getResource());
+ result.put("id", annotation.getId());
+ return result;
+ } else {
+ throw new InvalidArgumentException("invalid miriam data: " + annotation);
+ }
+ };
+
+ protected Map<String, Object> createAnnotation(AnnotationView annotation) {
+ Map<String, Object> result = new HashMap<>();
+ if (annotation != null && annotation.getType() != null) {
+ MiriamType type = MiriamType.getTypeByCommonName(annotation.getType());
+ result.put("link", annotation.getLink());
+ if (MiriamType.PUBMED.equals(type)) {
+ try {
+ Article article = pubmedParser.getPubmedArticleById(Integer.valueOf(annotation.getResource()));
+ result.put("article", article);
+ } catch (PubmedSearchException e) {
+ logger.error("Problem with accessing info about pubmed", e);
+ }
+ }
+ result.put("type", type);
+ result.put("resource", annotation.getResource());
+ result.put("id", annotation.getIdObject());
+ }
+ return result;
+ }
+
+ protected Map<String, Object> createAnnotation(Article article) {
+ Map<String, Object> result = new HashMap<>();
+ if (article != null) {
+ MiriamType type = MiriamType.PUBMED;
+ result.put("link", miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, article.getId())));
+ result.put("article", article);
+ result.put("type", type);
+ result.put("resource", article.getId());
+ }
+ return result;
+ }
+
+ protected List<Map<String, Object>> createAnnotations(Collection<?> references) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Object miriamData : references) {
+ if (miriamData instanceof MiriamData) {
+ result.add(createAnnotation((MiriamData) miriamData));
+ } else if (miriamData instanceof AnnotationView) {
+ result.add(createAnnotation((AnnotationView) miriamData));
+ } else if (miriamData instanceof Article) {
+ result.add(createAnnotation((Article) miriamData));
+ } else {
+ throw new InvalidArgumentException();
+ }
+ }
+ return result;
+ }
+
+ protected List<Model> getModels(String projectId, String modelId, String token) throws SecurityException {
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+ List<Model> models = new ArrayList<>();
+
+ if (!modelId.equals("*")) {
+ for (String str : modelId.split(",")) {
+ models.add(model.getSubmodelById(Integer.valueOf(str)));
+ }
+ } else {
+ models.addAll(model.getSubmodels());
+ models.add(model);
+ }
+ return models;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ protected List<Map<String, Object>> prepareTargets(Collection<Target> targets, List<Model> models) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Target target : targets) {
+ result.add(prepareTarget(target, models));
+ }
+ result.sort(new Comparator<Map<String, Object>>() {
+
+ @Override
+ public int compare(Map<String, Object> o1, Map<String, Object> o2) {
+ List<?> targetedObjects1 = (List<?>) o1.get("targetElements");
+ List<?> targetedObjects2 = (List<?>) o2.get("targetElements");
+ Integer size1 = 0;
+ Integer size2 = 0;
+ if (targetedObjects1 != null) {
+ size1 = targetedObjects1.size();
+ }
+ if (targetedObjects2 != null) {
+ size2 = targetedObjects2.size();
+ }
+ return -size1.compareTo(size2);
+ }
+ });
+ return result;
+ }
+
+ protected Map<String, Object> prepareTarget(Target target, List<Model> models) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("name", target.getName());
+ result.put("references", createAnnotations(target.getReferences()));
+ result.put("targetParticipants", createAnnotations(target.getGenes()));
+
+ List<Map<String, Object>> targetedObjects = new ArrayList<>();
+ for (Model model : models) {
+ for (BioEntity object : model.getBioEntities()) {
+ if (elementMatcher.elementMatch(target, object)) {
+ Map<String, Object> elementMapping = new HashMap<>();
+
+ elementMapping.put("id", object.getId());
+ elementMapping.put("type", getType(object));
+ elementMapping.put("modelId", model.getId());
+ targetedObjects.add(elementMapping);
+ }
+ }
+ }
+
+ result.put("targetElements", targetedObjects);
+
+ return result;
+ }
+
+ private String getType(BioEntity object) {
+ if (object instanceof Reaction) {
+ return ElementIdentifierType.REACTION.getJsName();
+ } else if (object instanceof Element) {
+ return ElementIdentifierType.ALIAS.getJsName();
+ } else {
+ throw new InvalidArgumentException("Unknown type of element " + object.getClass());
+ }
+ }
+
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService
+ * the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ protected IConverter getModelParser(String handlerClass) throws QueryException {
+ IConverter parser;
+ if (SbgnmlXmlConverter.class.getCanonicalName().equals(handlerClass)) {
+ parser = new SbgnmlXmlConverter();
+ } else if (CellDesignerXmlParser.class.getCanonicalName().equals(handlerClass)) {
+ parser = new CellDesignerXmlParser();
+ } else {
+ throw new QueryException("Unknown handlerClass: " + handlerClass);
+ }
+ return parser;
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
new file mode 100644
index 0000000000..ed2a03cd09
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
@@ -0,0 +1,59 @@
+package lcsb.mapviewer.api.files;
+
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class FileController extends BaseController {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(FileController.class);
+
+ @Autowired
+ private FileRestImpl fileRest;
+
+ @RequestMapping(value = "/files/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> createFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "filename") String filename, //
+ @RequestParam(value = "length") String length //
+ ) throws SecurityException {
+ return fileRest.createFile(token, filename, length);
+ }
+
+ @RequestMapping(value = "/files/{id}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "id") String id //
+ ) throws SecurityException, ObjectNotFoundException {
+ return fileRest.getFile(token, id);
+ }
+
+ @RequestMapping(value = "/files/{id}:uploadContent", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> uploadContent(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "id") String id, //
+ @RequestBody byte[] data) throws SecurityException, ObjectNotFoundException {
+ return fileRest.uploadContent(token, id, data);
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
new file mode 100644
index 0000000000..bb2ecfeae8
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
@@ -0,0 +1,107 @@
+package lcsb.mapviewer.api.files;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.hibernate.QueryException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+
+@Transactional(value = "txManager")
+public class FileRestImpl extends BaseRestImpl {
+
+ @Autowired
+ private ILayoutService overlayService;
+
+ @Autowired
+ private UploadedFileEntryDao uploadedFileEntryDao;
+
+ public Map<String, Object> createFile(String token, String filename, String length) throws SecurityException {
+ User user = getUserService().getUserByToken(token);
+ if (!getUserService().userHasPrivilege(user, PrivilegeType.ADD_MAP)
+ && overlayService.getAvailableCustomLayoutsNumber(user) == 0) {
+ throw new SecurityException("Access denied");
+ }
+ UploadedFileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName(filename);
+ entry.setFileContent(new byte[] {});
+ entry.setLength(Long.valueOf(length));
+ entry.setOwner(user);
+ uploadedFileEntryDao.add(entry);
+ try {
+ return getFile(token, entry.getId() + "");
+ } catch (ObjectNotFoundException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ public Map<String, Object> getFile(String token, String id) throws SecurityException, ObjectNotFoundException {
+ User user = getUserService().getUserByToken(token);
+ int fileId = Integer.valueOf(id);
+ UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
+ if (fileEntry == null) {
+ throw new ObjectNotFoundException("Object not found");
+ }
+ if (fileEntry.getOwner() == null) {
+ throw new SecurityException("Access denied");
+ }
+ if (!fileEntry.getOwner().getLogin().equals(user.getLogin())) {
+ throw new SecurityException("Access denied");
+ }
+ return serializeEntry(fileEntry);
+ }
+
+ private Map<String, Object> serializeEntry(UploadedFileEntry fileEntry) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("id", fileEntry.getId());
+ result.put("filename", fileEntry.getOriginalFileName());
+ result.put("length", fileEntry.getLength());
+ result.put("owner", fileEntry.getOwner().getLogin());
+ result.put("uploadedDataLength", fileEntry.getFileContent().length);
+ return result;
+ }
+
+ public Map<String, Object> uploadContent(String token, String id, byte[] data) throws SecurityException, ObjectNotFoundException {
+ User user = getUserService().getUserByToken(token);
+ int fileId = Integer.valueOf(id);
+ UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
+ if (fileEntry == null) {
+ throw new ObjectNotFoundException("Object not found");
+ }
+ if (fileEntry.getOwner() == null) {
+ throw new SecurityException("Access denied");
+ }
+ if (!fileEntry.getOwner().getLogin().equals(user.getLogin())) {
+ throw new SecurityException("Access denied");
+ }
+ long missingByteLength = fileEntry.getLength() - fileEntry.getFileContent().length;
+ if (data.length > missingByteLength) {
+ throw new QueryException(
+ "Too many bytes sent. There are " + missingByteLength + " missing bytes, but " + data.length + " sent.");
+ }
+ byte[] newConent = ArrayUtils.addAll(fileEntry.getFileContent(), data);
+ fileEntry.setFileContent(newConent);
+ uploadedFileEntryDao.update(fileEntry);
+ return serializeEntry(fileEntry);
+ }
+
+ public UploadedFileEntryDao getUploadedFileEntryDao() {
+ return uploadedFileEntryDao;
+ }
+
+ public void setUploadedFileEntryDao(UploadedFileEntryDao uploadedFileEntryDao) {
+ this.uploadedFileEntryDao = uploadedFileEntryDao;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 6a50de4c1f..802493819f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -7,7 +7,6 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
@@ -38,16 +37,15 @@ import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
import lcsb.mapviewer.commands.SubModelCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
@@ -66,6 +64,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IProjectService;
@@ -105,6 +104,9 @@ public class ProjectRestImpl extends BaseRestImpl {
@Autowired
private OverviewImageViewFactory factory;
+ @Autowired
+ private UploadedFileEntryDao uploadedFileEntryDao;
+
public ProjectMetaData getProject(String projectId, String token) throws SecurityException, ObjectNotFoundException {
AuthenticationToken authenticationToken = getUserService().getToken(token);
Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
@@ -294,9 +296,10 @@ public class ProjectRestImpl extends BaseRestImpl {
imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
- FileEntry entry = new UploadedFileEntry();
+ UploadedFileEntry entry = new UploadedFileEntry();
entry.setOriginalFileName("map." + extension);
entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
+ entry.setLength(entry.getFileContent().length);
file.delete();
return entry;
@@ -342,9 +345,10 @@ public class ProjectRestImpl extends BaseRestImpl {
String fileExtension = parser.getFileExtension();
- FileEntry entry = new UploadedFileEntry();
+ UploadedFileEntry entry = new UploadedFileEntry();
entry.setOriginalFileName("model." + fileExtension);
entry.setFileContent(IOUtils.toByteArray(is));
+ entry.setLength(entry.getFileContent().length);
return entry;
}
@@ -490,9 +494,16 @@ public class ProjectRestImpl extends BaseRestImpl {
}
CreateProjectParams params = new CreateProjectParams();
String directory = path + "/../map_images/" + md5(projectId) + "/";
- String fileContent = getFirstValue(data.get("file-content"));
- if (fileContent == null) {
- throw new QueryException("file-content is obligatory");
+ String fileId = getFirstValue(data.get("file-id"));
+ if (fileId == null) {
+ throw new QueryException("file-id is obligatory");
+ }
+ UploadedFileEntry file = uploadedFileEntryDao.getById(Integer.valueOf(fileId));
+ if (file == null) {
+ throw new QueryException("Invalid file id: " + fileId);
+ }
+ if (file.getOwner() == null || !file.getOwner().getLogin().equals(user.getLogin())) {
+ throw new SecurityException("Access denied to source file");
}
String parserClass = getFirstValue(data.get("parser"));
if (parserClass == null) {
@@ -517,7 +528,7 @@ public class ProjectRestImpl extends BaseRestImpl {
params.notifyEmail(getFirstValue(data.get("notify-email")));
params.projectDir(directory);
params.projectDisease(getFirstValue(data.get("disease")));
- params.projectFile(new ByteArrayInputStream(fileContent.getBytes()));
+ params.projectFile(new ByteArrayInputStream(file.getFileContent()));
params.projectId(projectId);
params.projectName(getFirstValue(data.get("name")));
params.projectOrganism(getFirstValue(data.get("organism")));
@@ -545,6 +556,7 @@ public class ProjectRestImpl extends BaseRestImpl {
ZipEntryFile entry = null;
String entryType = (String) data.get("zip-entries[" + fileIndex + "][_type]").get(0);
String filename = (String) data.get("zip-entries[" + fileIndex + "][_filename]").get(0);
+ logger.debug(filename);
if ("MAP".equalsIgnoreCase(entryType)) {
String submodelTypeKey = "zip-entries[" + fileIndex + "][_data][type][id]";
String rootKey = "zip-entries[" + fileIndex + "][_data][root]";
@@ -607,7 +619,7 @@ public class ProjectRestImpl extends BaseRestImpl {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < mdbytes.length; i++) {
// CHECKSTYLE:OFF
- // this magic formula transforms int into hex value
+ // this magic formula transforms integer into hex value
sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
// CHECKSTYLE:ON
}
@@ -627,4 +639,12 @@ public class ProjectRestImpl extends BaseRestImpl {
return getProject(projectId, token);
}
+ public UploadedFileEntryDao getUploadedFileEntryDao() {
+ return uploadedFileEntryDao;
+ }
+
+ public void setUploadedFileEntryDao(UploadedFileEntryDao uploadedFileEntryDao) {
+ this.uploadedFileEntryDao = uploadedFileEntryDao;
+ }
+
}
diff --git a/rest-api/src/main/resources/applicationContext-rest.xml b/rest-api/src/main/resources/applicationContext-rest.xml
index 2642267ee9..60c2553716 100644
--- a/rest-api/src/main/resources/applicationContext-rest.xml
+++ b/rest-api/src/main/resources/applicationContext-rest.xml
@@ -13,6 +13,8 @@
<bean id="ConfigurationRestImpl" class="lcsb.mapviewer.api.configuration.ConfigurationRestImpl"/>
+ <bean id="FileRestImpl" class="lcsb.mapviewer.api.files.FileRestImpl"/>
+
<bean id="CommentRestImpl" class="lcsb.mapviewer.api.projects.comments.CommentRestImpl"/>
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.projects.ProjectRestImpl"/>
<bean id="ModelRestImpl" class="lcsb.mapviewer.api.projects.models.ModelRestImpl"/>
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
index ced165d503..f1f28f0d09 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
@@ -5,15 +5,17 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.api.configuration.AllConfigurationTests;
+import lcsb.mapviewer.api.files.AllFileTests;
import lcsb.mapviewer.api.genomics.AllGenomicsTests;
import lcsb.mapviewer.api.projects.AllProjectTests;
import lcsb.mapviewer.api.users.AllUserTests;
@RunWith(Suite.class)
@SuiteClasses({ AllConfigurationTests.class, //
- AllGenomicsTests.class, //
- AllProjectTests.class, //
- AllUserTests.class,//
+ AllFileTests.class, //
+ AllGenomicsTests.class, //
+ AllProjectTests.class, //
+ AllUserTests.class,//
})
public class AllRestTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index a1a84dbd5f..d6fec72043 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -63,253 +63,253 @@ import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
@Rollback(true)
-@ContextConfiguration(
- locations = { "/applicationContext-persist.xml", "/applicationContext-annotation.xml", "/applicationContext-service.xml", "/applicationContext-rest.xml" })
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", "/applicationContext-annotation.xml",
+ "/applicationContext-service.xml", "/applicationContext-rest.xml" })
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class RestTestFunctions {
- private Logger logger = Logger.getLogger(RestTestFunctions.class);
-
- public double EPSILON = 1e-6;
-
- @Autowired
- protected PasswordEncoder passwordEncoder;
-
- @Autowired
- protected IUserService userService;
-
- @Autowired
- protected DbUtils dbUtils;
-
- protected AuthenticationToken token;
-
- protected AuthenticationToken adminToken;
-
- @Before
- public void generalSetUp() {
- dbUtils.setAutoFlush(false);
-
- token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
-
- // assume that we have admin account with all the privileges
- adminToken = userService.login("admin", "admin");
-
- }
-
- @After
- public void generatTearDown() throws IOException {
- File f = new File("map_images");
- if (f.exists()) {
- logger.info("Removing output test directory: " + f.getAbsolutePath());
- FileUtils.deleteDirectory(f);
- }
-
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- Model result = null;
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- result = getModelForFile(fileName);
- } else {
- result = RestTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- result = getModelForFile(fileName);
- RestTestFunctions.models.put(fileName, result);
- }
- }
- return result;
- }
-
- private Model getModelForFile(String fileName) throws InvalidInputDataExecption, IOException {
- if (fileName.endsWith("zip")) {
- ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
- ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(fileName);
- ZipEntryFile entry1 = new ModelZipEntryFile("main.xml", "main", true, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry2 = new ModelZipEntryFile("submaps/s1.xml", "s1", false, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry3 = new ModelZipEntryFile("submaps/s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry4 = new ModelZipEntryFile("submaps/s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry5 = new ModelZipEntryFile("submaps/mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- complexParams.entry(entry1);
- complexParams.entry(entry2);
- complexParams.entry(entry3);
- complexParams.entry(entry4);
- complexParams.entry(entry5);
-
- Model model =parser.createModel(complexParams);
- model.setTileSize(256);
- for (ModelSubmodelConnection connection: model.getSubmodelConnections()) {
- connection.getSubmodel().setTileSize(256);
- }
- model.setProject(new Project());
- return model;
-
- } else {
- Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- model.setTileSize(256);
- model.setProject(new Project());
- return model;
- }
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
+ private Logger logger = Logger.getLogger(RestTestFunctions.class);
+
+ public double EPSILON = 1e-6;
+
+ @Autowired
+ protected PasswordEncoder passwordEncoder;
+
+ @Autowired
+ protected IUserService userService;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ protected AuthenticationToken token;
+
+ protected AuthenticationToken adminToken;
+
+ @Before
+ public void generalSetUp() {
+ dbUtils.setAutoFlush(false);
+
+ token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
+
+ // assume that we have admin account with all the privileges
+ adminToken = userService.login("admin", "admin");
+
+ }
+
+ @After
+ public void generatTearDown() throws IOException {
+ File f = new File("map_images");
+ if (f.exists()) {
+ logger.info("Removing output test directory: " + f.getAbsolutePath());
+ FileUtils.deleteDirectory(f);
+ }
+
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ Model result = null;
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ result = getModelForFile(fileName);
+ } else {
+ result = RestTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ result = getModelForFile(fileName);
+ RestTestFunctions.models.put(fileName, result);
+ }
+ }
+ return result;
+ }
+
+ private Model getModelForFile(String fileName) throws InvalidInputDataExecption, IOException {
+ if (fileName.endsWith("zip")) {
+ ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
+ ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(fileName);
+ ZipEntryFile entry1 = new ModelZipEntryFile("main.xml", "main", true, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry2 = new ModelZipEntryFile("submaps/s1.xml", "s1", false, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry3 = new ModelZipEntryFile("submaps/s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry4 = new ModelZipEntryFile("submaps/s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry5 = new ModelZipEntryFile("submaps/mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
+ complexParams.entry(entry1);
+ complexParams.entry(entry2);
+ complexParams.entry(entry3);
+ complexParams.entry(entry4);
+ complexParams.entry(entry5);
+
+ Model model = parser.createModel(complexParams);
+ model.setTileSize(256);
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ connection.getSubmodel().setTileSize(256);
+ }
+ model.setProject(new Project());
+ return model;
+
+ } else {
+ Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ model.setTileSize(256);
+ model.setProject(new Project());
+ return model;
+ }
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/files/AllFileTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/files/AllFileTests.java
new file mode 100644
index 0000000000..25e1d4be31
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/files/AllFileTests.java
@@ -0,0 +1,11 @@
+package lcsb.mapviewer.api.files;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ FileRestImplTest.class })
+public class AllFileTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
new file mode 100644
index 0000000000..69ef990fdf
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
@@ -0,0 +1,80 @@
+package lcsb.mapviewer.api.files;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.Map;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+
+public class FileRestImplTest extends RestTestFunctions {
+
+ @Autowired
+ UploadedFileEntryDao uploadedFileEntryDao;
+
+ @Autowired
+ FileRestImpl fileRestImpl;
+
+ @Test(expected = lcsb.mapviewer.services.SecurityException.class)
+ public void testCreateFileWithoutPrivilege() throws Exception {
+ fileRestImpl.createFile(token.getId(), "test.txt", "100");
+ }
+
+ @Test
+ public void testCreateFile() throws Exception {
+ Map<String, Object> result = fileRestImpl.createFile(adminToken.getId(), "test.txt", "100");
+ assertNotNull(result);
+ int id = (Integer) result.get("id");
+ UploadedFileEntry file = uploadedFileEntryDao.getById(id);
+ assertNotNull(file);
+ assertEquals(100, file.getLength());
+ assertEquals(0, file.getFileContent().length);
+ uploadedFileEntryDao.delete(file);
+ }
+
+ @Test
+ public void testUploadContent() throws Exception {
+ byte[] dataChunk = new byte[] { 105, 103 };
+ byte[] dataChunk2 = new byte[] { 32, 73 };
+ byte[] dataChunkMerged = ArrayUtils.addAll(dataChunk, dataChunk2);
+ Map<String, Object> result = fileRestImpl.createFile(adminToken.getId(), "test.txt", "100");
+ int id = (Integer) result.get("id");
+ fileRestImpl.uploadContent(adminToken.getId(), id + "", dataChunk);
+
+ UploadedFileEntry file = uploadedFileEntryDao.getById(id);
+ assertEquals(100, file.getLength());
+ assertEquals(2, file.getFileContent().length);
+ assertArrayEquals(dataChunk, file.getFileContent());
+
+ fileRestImpl.uploadContent(adminToken.getId(), id + "", dataChunk2);
+
+ assertEquals(100, file.getLength());
+ assertEquals(4, file.getFileContent().length);
+ assertArrayEquals(dataChunkMerged, file.getFileContent());
+
+ uploadedFileEntryDao.delete(file);
+ }
+
+ @Test
+ public void testUploadInvalidContent() throws Exception {
+ byte[] dataChunk = new byte[100];
+ Map<String, Object> result = fileRestImpl.createFile(adminToken.getId(), "test.txt", "100");
+ int id = (Integer) result.get("id");
+
+ try {
+ fileRestImpl.uploadContent(adminToken.getId(), id + "", dataChunk);
+ } finally {
+ uploadedFileEntryDao.getById(id);
+ UploadedFileEntry file = uploadedFileEntryDao.getById(id);
+ uploadedFileEntryDao.delete(file);
+ }
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/SecurityException.java b/service/src/main/java/lcsb/mapviewer/services/SecurityException.java
index dae25a9822..de076a2bbc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/SecurityException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/SecurityException.java
@@ -2,13 +2,17 @@ package lcsb.mapviewer.services;
public class SecurityException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public SecurityException(String message) {
- super(message);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public SecurityException(String message) {
+ super(message);
+ }
+
+ public SecurityException() {
+ super();
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 646931a612..91f445f061 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -351,6 +351,8 @@ public class LayoutService implements ILayoutService {
UploadedFileEntry fileEntry = new UploadedFileEntry();
fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
fileEntry.setOriginalFileName(params.getLayoutFileName());
+ fileEntry.setLength(fileEntry.getFileContent().length);
+ fileEntry.setOwner(params.getUser());
topLayout.setInputData(fileEntry);
topLayout.setDescription(params.getDescription());
params.getModel().addLayout(topLayout);
@@ -511,6 +513,8 @@ public class LayoutService implements ILayoutService {
UploadedFileEntry fileEntry = new UploadedFileEntry();
fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
fileEntry.setOriginalFileName(params.getLayoutFileName());
+ fileEntry.setLength(fileEntry.getFileContent().length);
+ fileEntry.setOwner(params.getUser());
topLayout.setInputData(fileEntry);
topLayout.setDescription(params.getDescription());
params.getModel().addLayout(topLayout);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index db91fe0556..f50002b773 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -119,1455 +119,1481 @@ import lcsb.mapviewer.services.view.ProjectViewFactory;
@Transactional(value = "txManager")
public class ProjectService implements IProjectService {
- /**
- * Size of the artifitial buffer that will be released when
- * {@link OutOfMemoryError} is thrown to gain some free memory and report
- * problem.
- */
- private static final int OUT_OF_MEMORY_BACKUP_BUFFER_SIZE = 10000;
-
- /**
- * How much time (out of 1.00) is used for creation of the data from file.
- */
- private static final double CREATION_OF_DATA = 0.50;
-
- /**
- * How much time (out of 1.00) is used for upploading of the data from file.
- */
- private static final double UPLOAD_OF_DATA = 0.50;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ProjectService.class);
-
- /**
- * Data access object for projects.
- */
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Data access object for models.
- */
- @Autowired
- private ModelDao modelDao;
-
- /**
- * Data access object for users.
- */
- @Autowired
- private UserDao userDao;
-
- /**
- * Service that allows to access and manage models.
- */
- @Autowired
- private IModelService modelService;
-
- /**
- * Service that allows to access and manage comments.
- */
- @Autowired
- private ICommentService commentService;
-
- /**
- * Service used to access logs.
- *
- * @see ILogService
- */
- @Autowired
- private ILogService logService;
-
- /**
- * Service that manages and gives access to configuration parameters.
- */
- @Autowired
- private IConfigurationService configurationService;
-
- /**
- * Services that manages and gives access to user information.
- */
- @Autowired
- private IUserService userService;
-
- /**
- * Services that accessa data about chemicals.
- */
- @Autowired
- private IChemicalService chemicalService;
-
- /**
- * Services that accessa data about drugs.
- */
- @Autowired
- private IDrugService drugService;
-
- /**
- * Services that accessa data about mirna.
- */
- @Autowired
- private IMiRNAService mirnaService;
-
- /**
- * Service that manages data mining information.
- */
- @Autowired
- private IDataMiningService dataMiningService;
-
- /**
- * Data access object for comments.
- */
- @Autowired
- private CommentDao commentDao;
-
- /**
- * Service that provides password encoding.
- */
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- /**
- * Module that allows to annotate maps.
- */
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Factory object for {@link ProjectView} elements.
- */
- @Autowired
- private ProjectViewFactory projectViewFactory;
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private MeSHParser meshParser;
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- /**
- * Class that helps to generate images for google maps API.
- */
- private MapGenerator generator = new MapGenerator();
-
- @Override
- public Project getProjectByProjectId(String name, AuthenticationToken token) throws UserAccessException {
- Project result = projectDao.getProjectByProjectId(name);
- if (result == null) {
- return result;
- }
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, result)) {
- return result;
- } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return result;
- }
- throw new UserAccessException("User cannot access project");
- }
-
- @Override
- public boolean projectExists(String projectName) {
- if (projectName == null || projectName.equals("")) {
- return false;
- }
- return projectDao.isProjectExistsByName(projectName);
- }
-
- @Override
- public List<Project> getAllProjects(AuthenticationToken token) {
- List<Project> projects = projectDao.getAll();
- if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return projects;
- }
- List<Project> result = new ArrayList<>();
- for (Project project : projects) {
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
- result.add(project);
- }
- }
- return result;
- }
-
- @Override
- public List<ProjectView> getAllProjectViews(AuthenticationToken token) {
- List<ProjectView> result = new ArrayList<>();
- List<Project> projects = getAllProjects(token);
- for (Project project : projects) {
- result.add(projectViewFactory.create(project));
- }
- return result;
- }
-
- @Override
- public void updateProject(ProjectView selectedProject) {
- Project project = projectDao.getById(selectedProject.getIdObject());
- project.setProjectId(selectedProject.getProjectId());
- project.setName(selectedProject.getProjectName());
- project.setVersion(selectedProject.getVersion());
- project.setNotifyEmail(selectedProject.getNotifyEmail());
- MiriamData disease = null;
- MiriamData organism = null;
- if (selectedProject.getNewDiseaseName() != null && !selectedProject.getNewDiseaseName().isEmpty()) {
- disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
- }
- if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
- }
- try {
- if (meshParser.isValidMeshId(disease)) {
- project.setDisease(disease);
- } else {
- project.setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing mesh", e);
- project.setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- try {
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- project.setOrganism(organism);
- } else {
- project.setOrganism(null);
- selectedProject.setNewOrganismName(null);
- }
- } catch (TaxonomySearchException e) {
- logger.error("Problem with accessing taxonomy db", e);
- project.setOrganism(null);
- selectedProject.setNewOrganismName(null);
- }
- for (ModelData model : project.getModels()) {
- if (model.getId().equals(selectedProject.getModelId())) {
- modelService.updateModel(model, selectedProject);
- }
- }
- projectDao.update(project);
- }
-
- @Override
- public void removeProject(ProjectView selectedProject, String homeDir, boolean async, AuthenticationToken token) throws UserAccessException {
- Project project = projectDao.getById(selectedProject.getIdObject());
- removeProject(project, homeDir, async, token);
- }
-
- /**
- * Removes all types of privileges from every user to the project given in the
- * parameter.
- *
- * @param project
- * from which project we remove privileges
- */
- private void removePrivilegesForProject(Project project) {
- for (PrivilegeType type : PrivilegeType.values()) {
- if (type.getPrivilegeObjectType() == Project.class) {
- userService.dropPrivilegesForObjectType(type, project.getId());
- }
- }
- }
-
- @Override
- public ProjectView getProjectViewByProjectId(String name, AuthenticationToken token) throws UserAccessException {
- Project project = getProjectByProjectId(name, token);
- return projectViewFactory.create(project);
- }
-
- @Override
- public void removeProject(final Project p, final String dir, final boolean async, AuthenticationToken token) throws UserAccessException {
- if (!userService.userHasPrivilege(userService.getUserByToken(token), PrivilegeType.PROJECT_MANAGEMENT)) {
- throw new UserAccessException("User cannot remove project");
- }
-
- final String homeDir;
- if (dir != null) {
- if (p.getDirectory() != null) {
- homeDir = dir + "/../map_images/" + p.getDirectory() + "/";
- } else {
- homeDir = dir + "/../map_images/";
- }
- } else {
- if (p.getDirectory() != null) {
- homeDir = p.getDirectory() + "/";
- } else {
- homeDir = null;
- }
- }
- removePrivilegesForProject(p);
- updateProjectStatus(p, ProjectStatus.REMOVING, 0, new CreateProjectParams());
- Thread computations = new Thread(new Runnable() {
-
- @Override
- public void run() {
- if (async) {
- // because we are running this in separate thread we need to open a
- // new
- // session for db connection
- dbUtils.createSessionForCurrentThread();
- }
-
- Project project = projectDao.getById(p.getId());
-
- try {
- String email = null;
- MapGenerator mapGenerator = new MapGenerator();
- for (ModelData originalModel : project.getModels()) {
- List<ModelData> models = new ArrayList<ModelData>();
- models.add(originalModel);
- for (ModelSubmodelConnection connection : originalModel.getSubmodels()) {
- models.add(connection.getSubmodel());
- }
- modelService.removeModelFromCache(originalModel);
- for (ModelData model : models) {
- logger.debug("Remove model: " + model.getId());
- commentService.removeCommentsForModel(model);
-
- for (Layout layout : model.getLayouts()) {
- try {
- mapGenerator.removeLayout(layout, homeDir);
- } catch (IOException e) {
- logger.error("Problem with removing directory: " + layout.getDirectory(), e);
- }
- }
- }
- email = project.getNotifyEmail();
- }
- projectDao.delete(project);
- if (async) {
- projectDao.commit();
- }
-
- LogParams params = new LogParams().type(LogType.MAP_REMOVED).object(project);
- logService.log(params);
-
- if (email != null) {
- try {
- sendSuccesfullRemoveEmail(project.getProjectId(), email);
- } catch (MessagingException e) {
- logger.error("Problem with sending remove email.", e);
- }
- }
- modelService.removeModelFromCacheByProjectId(p.getProjectId());
-
- } catch (HibernateException e) {
- logger.error("Problem with database", e);
- handleHibernateExceptionRemovingReporting(project, e, token);
- } finally {
- if (async) {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- }
- }
- if (homeDir != null) {
- File homeDirFile = new File(homeDir);
- if (homeDirFile.exists()) {
- logger.debug("Removing project directory: " + homeDirFile.getAbsolutePath());
- try {
- FileUtils.deleteDirectory(homeDirFile);
- } catch (IOException e) {
- logger.error("Problem with removing diriectory", e);
- }
- }
- }
-
- }
- });
-
- if (async) {
- computations.start();
- } else {
- computations.run();
- }
-
- }
-
- /**
- * When we encountered hibernate exception we need to handle error reporting
- * differently (hibernate session is broken). This method handles such case
- * when hibernate excedption occured when removing project.
- *
- * @param originalProject
- * project that was beining removed
- * @param exception
- * hibernate exception that caused problems
- */
- protected void handleHibernateExceptionRemovingReporting(Project originalProject, HibernateException exception, AuthenticationToken token) {
- // we need to open separate thread because current one thrown db exception
- // and transaction is corrupetd and will be rolledback
- Thread reportInSeparateThread = new Thread(new Runnable() {
-
- @Override
- public void run() {
- dbUtils.createSessionForCurrentThread();
- try {
- // we need to get the project from db, because session where
- // originalProject was retrieved is broken
- Project project = getProjectByProjectId(originalProject.getProjectId(), token);
- String errorMessage = "Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
- + "\nMore information can be found in log file.";
- project.setErrors(errorMessage + "\n" + project.getErrors());
- project.setStatus(ProjectStatus.FAIL);
- projectDao.update(project);
- } catch (UserAccessException e) {
- logger.error(e, e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- });
- reportInSeparateThread.start();
- }
-
- @Override
- public void addProject(Project project) {
- projectDao.add(project);
-
- }
-
- @Override
- public ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException {
- Project project = projectDao.getById(id);
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
- return projectViewFactory.create(project);
- } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return projectViewFactory.create(project);
- } else {
- throw new UserAccessException("User cannot access project");
- }
- }
-
- /**
- * This methods add privileges for the users listed in params to the project.
- *
- * @param project
- * to which project we add privileges
- * @param params
- * which users should be included to have privileges to the project
- */
- private void addUsers(Project project, CreateProjectParams params) {
- if (project == null) {
- logger.warn("Users won't be added. Project not defined");
- return;
- }
- List<String[]> users = params.getUsers();
- String[][] newUsers = new String[users.size() + 1][2];
- for (int i = 0; i < users.size(); i++) {
- for (int j = 0; j < 2; j++) {
- newUsers[i][j] = users.get(i)[j];
- }
- }
- newUsers[users.size()][0] = "anonymous";
- newUsers[users.size()][1] = "";
- for (int i = 0; i < newUsers.length; i++) {
- boolean admin = (users.size() != i);
- String login = newUsers[i][0];
- String passwd = newUsers[i][1];
- User user = userService.getUserByLogin(login);
- if (userService.getUserByLogin(login) == null) {
- logger.debug("User " + login + " does not exist. Creating");
- user = new User();
- user.setCryptedPassword(passwordEncoder.encode(passwd));
- user.setLogin(login);
- userService.addUser(user);
- }
- if (project != null) {
- logger.debug("Privileges for " + login + " for project " + project.getProjectId());
- ObjectPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user);
- userService.setUserPrivilege(user, privilege);
- if (admin) {
- privilege = new ObjectPrivilege(project, 1, PrivilegeType.LAYOUT_MANAGEMENT, user);
- userService.setUserPrivilege(user, privilege);
- privilege = new ObjectPrivilege(project, 1, PrivilegeType.EDIT_COMMENTS_PROJECT, user);
- userService.setUserPrivilege(user, privilege);
- }
-
- }
- }
- }
-
- /**
- * This method creates set of images for the model layouts.
- *
- * @param originalModel
- * model for which we create layout images
- * @param params
- * configuration parameters including set of layouts to generate
- * @throws IOException
- * thrown when there are problems with generating files
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- * @throws CommandExecutionException
- * thrown when one of the files describing layouts is invalid
- */
- protected void createImages(final Model originalModel, final CreateProjectParams params) throws IOException, DrawingException, CommandExecutionException {
- if (!params.isImages()) {
- return;
- }
- updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES, 0, params);
-
- List<Model> models = new ArrayList<Model>();
- models.add(originalModel);
- int size = originalModel.getLayouts().size();
- for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
- models.add(connection.getSubmodel().getModel());
- size += connection.getSubmodel().getModel().getLayouts().size();
- }
- int counter = 0;
- for (final Model model : models) {
- for (int i = 0; i < model.getLayouts().size(); i++) {
- Layout layout = model.getLayouts().get(i);
- if (layout.getInputData() == null) {
- final double imgCounter = counter;
- final double finalSize = size;
- IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(
- originalModel.getProject(), ProjectStatus.GENERATING_IMAGES, IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize,
- params);
- }
- };
-
- generateImagesForBuiltInOverlay(params, model, layout, updater);
- }
- counter++;
- }
- }
- }
-
- private void generateImagesForBuiltInOverlay(final CreateProjectParams params, final Model model, Layout layout, IProgressUpdater updater)
- throws CommandExecutionException, IOException, DrawingException {
- String directory = layout.getDirectory();
- Model output = model;
- if (layout.isHierarchicalView()) {
- output = new CopyCommand(model).execute();
- new SetFixedHierarchyLevelCommand(output, layout.getHierarchyViewLevel()).execute();
- }
- if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
- output = new CopyCommand(model).execute();
- new ClearColorModelCommand(output).execute();
- }
-
- MapGeneratorParams imgParams = generator.new MapGeneratorParams()
- .directory(directory).sbgn(params.isSbgnFormat()).nested(layout.isHierarchicalView()).updater(updater);
- imgParams.model(output);
- generator.generateMapImages(imgParams);
- }
-
- /**
- * Creates project. Loads model from the input and run PostLoadModification.
- *
- * @param params
- * params used to create model
- * @param dbProject
- * project where the model should be placed
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with input file
- */
- protected void createModel(final CreateProjectParams params, Project dbProject) throws InvalidInputDataExecption {
- ModelData modelData = modelDao.getLastModelForProjectIdentifier(params.getProjectId(), false);
- if (modelData != null) {
- throw new InvalidArgumentException("Model with the given name already exists");
- }
-
- final Project project = dbProject;
- updateProjectStatus(project, ProjectStatus.PARSING_DATA, 0.0, params);
-
- if (params.isComplex()) {
- try {
- Class<? extends IConverter> clazz = CellDesignerXmlParser.class;
- if (params.getParser() != null) {
- clazz = params.getParser().getClass();
- }
- ComplexZipConverter parser = new ComplexZipConverter(clazz);
- ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
- complexParams.visualizationDir(params.getProjectDir());
- for (ZipEntryFile entry : params.getZipEntries()) {
- complexParams.entry(entry);
- }
- ProjectFactory projectFactory = new ProjectFactory(parser);
- projectFactory.create(complexParams, dbProject);
- } catch (IOException e) {
- throw new InvalidInputDataExecption(e);
- }
- } else {
- IConverter parser;
- if (params.getParser() != null) {
- parser = params.getParser();
- } else if (params.getProjectFile().endsWith("sbgn")) {
- parser = new SbgnmlXmlConverter();
- } else {
- parser = new CellDesignerXmlParser();
- }
- try {
- Model model = parser
- .createModel(new ConverterParams().filename(params.getProjectFile()).sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
- model.setName(params.getProjectName());
- project.addModel(model);
- } catch (FileNotFoundException ex) {
- throw new InvalidInputDataExecption(ex);
- }
- }
- Model topModel = project.getModels().iterator().next().getModel();
- topModel.setZoomLevels(generator.computeZoomLevels(topModel));
- topModel.setTileSize(MapGenerator.TILE_SIZE);
- dbProject.setNotifyEmail(params.getNotifyEmail());
-
- updateProjectStatus(project, ProjectStatus.UPLOADING_TO_DB, 0.0, params);
- dbUtils.setAutoFlush(false);
- projectDao.update(project);
- dbUtils.setAutoFlush(true);
- projectDao.flush();
-
- List<BuildInLayout> buildInLayouts = new ArrayList<>();
- BuildInLayout nested = null;
- if (params.isSemanticZoom()) {
- nested = BuildInLayout.SEMANTIC;
- } else {
- nested = BuildInLayout.NESTED;
- }
- if (params.isNetworkLayoutAsDefault()) {
- buildInLayouts.add(BuildInLayout.NORMAL);
- buildInLayouts.add(nested);
- } else {
- buildInLayouts.add(nested);
- buildInLayouts.add(BuildInLayout.NORMAL);
- }
- buildInLayouts.add(BuildInLayout.CLEAN);
-
- // reverse the order of build in layouts, so we can insert them at the
- // beginning of list of layouts (the order will be the same)
- Collections.reverse(buildInLayouts);
-
- for (BuildInLayout buildInLayout : buildInLayouts) {
- Layout topLayout = new Layout(
- buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + topModel.getId() + "/", true);
- topLayout.setStatus(LayoutStatus.NA);
- topLayout.setProgress(0.0);
- topLayout.setHierarchicalView(buildInLayout.isNested());
- topModel.addLayout(0, topLayout);
- int submodelId = 1;
- List<Layout> semanticLevelOverlays = new ArrayList<>();
- if (buildInLayout.equals(BuildInLayout.SEMANTIC)) {
- for (int i = 0; i <= topModel.getZoomLevels(); i++) {
- String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-" + topModel.getId() + "/";
- Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
- semanticOverlay.setStatus(LayoutStatus.NA);
- semanticOverlay.setProgress(0.0);
- semanticOverlay.setHierarchicalView(buildInLayout.isNested());
- semanticOverlay.setHierarchyViewLevel(i);
- semanticLevelOverlays.add(semanticOverlay);
- topModel.addLayout(1, semanticOverlay);
- }
- }
- for (ModelSubmodelConnection connection : topModel.getSubmodelConnections()) {
- Layout layout = new Layout(buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + submodelId + "/", true);
- layout.setStatus(LayoutStatus.NA);
- layout.setProgress(0.0);
- layout.setHierarchicalView(buildInLayout.isNested());
- layout.setParentLayout(topLayout);
- connection.getSubmodel().addLayout(0, layout);
-
- connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
- connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
- if (buildInLayout.equals(BuildInLayout.SEMANTIC)) {
- for (int i = 0; i <= topModel.getZoomLevels(); i++) {
- String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-" + submodelId + "/";
- Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
- semanticOverlay.setStatus(LayoutStatus.NA);
- semanticOverlay.setProgress(0.0);
- semanticOverlay.setHierarchicalView(buildInLayout.isNested());
- semanticOverlay.setParentLayout(semanticLevelOverlays.get(i));
- semanticOverlay.setHierarchyViewLevel(i);
- connection.getSubmodel().addLayout(1, semanticOverlay);
- }
- }
- submodelId++;
- }
- }
-
- if (params.isUpdateAnnotations()) {
- Map<Class<?>, List<ElementAnnotator>> annotators = null;
- if (params.getAnnotatorsMap() != null) {
- annotators = new HashMap<Class<?>, List<ElementAnnotator>>();
- for (Class<?> clazz : params.getAnnotatorsMap().keySet()) {
- annotators.put(clazz, modelAnnotator.getAnnotatorsFromCommonNames(params.getAnnotatorsMap().get(clazz)));
- }
- }
- logger.debug("Updating annotations");
- modelAnnotator.performAnnotations(topModel, new IProgressUpdater() {
-
- @Override
- public void setProgress(final double progress) {
- updateProjectStatus(project, ProjectStatus.ANNOTATING, progress, params);
- }
- }, annotators);
- logger.debug("Annotations updated");
- }
- updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, 0.0, params);
- processDataMining(topModel, topModel.getDataMiningSets(), new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, progress, params);
- }
-
- });
- updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, IProgressUpdater.MAX_PROGRESS, params);
- logger.debug("Model created");
-
- }
-
- /**
- * Process data mining files and assign suggested connections to the model.
- *
- * @param model
- * model where the suggested connections will be added
- * @param dataMiningSets
- * set of files to process
- * @param progressUpdater
- * callback function informing higher layer about progress
- * @throws InvalidDataMiningInputFile
- * thrown when one of the files is invalid
- */
- private void processDataMining(Model model, List<DataMiningSet> dataMiningSets, final IProgressUpdater progressUpdater) throws InvalidDataMiningInputFile {
- Set<Element> nodes = new HashSet<>();
- nodes.addAll(model.getElements());
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- nodes.addAll(connection.getSubmodel().getElements());
- }
- Set<Reaction> reactions = new HashSet<Reaction>();
- reactions.addAll(model.getReactions());
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- reactions.addAll(connection.getSubmodel().getReactions());
- }
-
- int fileCounter = 0;
- final int filesCount = dataMiningSets.size();
- for (DataMiningSet dmSet : dataMiningSets) {
-
- final double offset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount;
- IProgressUpdater secondPartUpdater = new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- progressUpdater.setProgress((progress * CREATION_OF_DATA) / ((double) filesCount) + offset);
- }
- };
- Set<DataMining> result = dataMiningService.parseData(dmSet, nodes, reactions, secondPartUpdater);
- double size = result.size();
- double count = 0;
-
- double updateOffset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount + CREATION_OF_DATA / ((double) filesCount);
- for (DataMining missingConnection : result) {
- missingConnection.setType(dmSet.getType());
- missingConnection.getElement().addDataMining(missingConnection);
- count++;
- progressUpdater.setProgress(updateOffset + IProgressUpdater.MAX_PROGRESS * count / size * UPLOAD_OF_DATA);
- }
- }
- }
-
- /**
- * Updates status of the generating project.
- *
- * @param project
- * project that is generated
- * @param status
- * what is the current status
- * @param progress
- * what is the progress
- * @param params
- * parameters used for project creation
- */
- private void updateProjectStatus(Project project, ProjectStatus status, double progress, CreateProjectParams params) {
- if (project != null) {
- if (!status.equals(project.getStatus()) || (Math.abs(progress - project.getProgress()) > IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION)) {
- project.setStatus(status);
- project.setProgress(progress);
- projectDao.update(project);
- if (params.isAsync()) {
- projectDao.commit();
- }
- }
- } else {
- logger.debug("status: " + status + ", " + progress);
- }
- }
-
- @Override
- public void createProject(final CreateProjectParams params) throws SecurityException {
- if (!userService.userHasPrivilege(params.getAuthenticationToken(), PrivilegeType.ADD_MAP)) {
- throw new SecurityException("Adding projects not allowed.");
- }
-
- // this count down is used to wait for asynchronous thread to initialize
- // data in the db (probably it would be better to move the initialization to
- // main thread)
- final CountDownLatch waitForInitialData = new CountDownLatch(1);
-
- Thread computations = new Thread(new Runnable() {
-
- @Override
- public void run() {
- if (params.isAsync()) {
- // because we are running this in separate thread we need to open a
- // new session for db connection
- dbUtils.createSessionForCurrentThread();
- }
-
- Project project = new Project();
- project.setProjectId(params.getProjectId());
- project.setName(params.getProjectName());
- if (params.getProjectDir() == null) {
- logger.warn("Project directory not set");
- project.setDirectory(null);
- } else {
- project.setDirectory(new File(params.getProjectDir()).getName());
- }
- project.setSbgnFormat(params.isSbgnFormat());
-
- MiriamData disease = null;
- if (params.getDisease() != null && !params.getDisease().isEmpty()) {
- disease = new MiriamData(MiriamType.MESH_2012, params.getDisease());
- }
- MiriamData organism = null;
- if (params.getOrganism() != null && !params.getOrganism().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, params.getOrganism());
- }
- project.setVersion(params.getVersion());
- projectDao.add(project);
- if (params.isAsync()) {
- projectDao.commit();
- }
- waitForInitialData.countDown();
- double[] outOfMemoryBuffer;
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- logger.debug("Running: " + params.getProjectId() + "; " + params.getProjectFile());
- outOfMemoryBuffer = new double[OUT_OF_MEMORY_BACKUP_BUFFER_SIZE];
- for (int i = 0; i < OUT_OF_MEMORY_BACKUP_BUFFER_SIZE; i++) {
- outOfMemoryBuffer[i] = Math.random() * OUT_OF_MEMORY_BACKUP_BUFFER_SIZE;
- }
-
- File inputFile = new File(params.getProjectFile());
- if (inputFile.exists()) {
- UploadedFileEntry file = new UploadedFileEntry();
- file.setFileContent(IOUtils.toByteArray(new FileInputStream(inputFile)));
- file.setOriginalFileName(FilenameUtils.getName(params.getProjectFile()));
- project.setInputData(file);
- }
-
- createModel(params, project);
- Model originalModel = project.getModels().iterator().next().getModel();
- if (!params.isSemanticZoom()) {
- new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel), generator.computeZoomFactor(originalModel)).execute();
- }
-
- addUsers(project, params);
- createImages(originalModel, params);
-
- for (Layout layout : originalModel.getLayouts()) {
- String[] tmp = layout.getDirectory().split("[\\\\/]");
- layout.setDirectory(tmp[tmp.length - 1]);
- }
- for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
- for (Layout layout : connection.getSubmodel().getLayouts()) {
- String[] tmp = layout.getDirectory().split("[\\\\/]");
- layout.setDirectory(tmp[tmp.length - 1]);
- }
- }
-
- try {
- if (meshParser.isValidMeshId(disease)) {
- project.setDisease(disease);
- } else {
- logger.warn("No valid disease is provided for project:" + project.getName());
- }
- } catch (AnnotatorException e1) {
- logger.warn("Problem with accessing mesh db. More info in logs.");
- }
-
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- project.setOrganism(organism);
- } else {
- logger.warn("No valid organism is provided for project:" + project.getName());
- }
-
- modelDao.update(originalModel);
-
- if (params.isCacheModel()) {
- cacheData(originalModel, params);
- }
-
- if (params.isAnalyzeAnnotations()) {
- analyzeAnnotations(originalModel, params);
- }
- Logger.getRootLogger().removeAppender(appender);
- project.addLoggingInfo(appender);
- updateProjectStatus(project, ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS, params);
- if (project.getNotifyEmail() != null && !project.getNotifyEmail().equals("")) {
- try {
- sendSuccesfullEmail(originalModel);
- } catch (MessagingException e) {
- logger.error(e, e);
- }
- }
-
- LogParams params = new LogParams().description("Created successfully").type(LogType.MAP_CREATED).object(originalModel);
- logService.log(params);
-
- } catch (HibernateException e) {
- outOfMemoryBuffer = null;
- logger.error("Problem with database", e);
- handleHibernateExceptionReporting(params, e);
- } catch (Exception e) {
- outOfMemoryBuffer = null;
- handleCreateProjectException(params, e);
- } catch (OutOfMemoryError oome) {
- // release some memory
- outOfMemoryBuffer = null;
- logger.error("Out of memory", oome);
- if (project != null) {
- project.setErrors("Out of memory: " + oome.getMessage());
- }
- updateProjectStatus(project, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
- } finally {
- if (params.isAsync()) {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- }
- Logger.getRootLogger().removeAppender(appender);
- }
- }
- });
- if (params.isAsync()) {
- computations.start();
- } else {
- computations.run();
- }
-
- try {
- waitForInitialData.await();
- } catch (InterruptedException e1) {
- logger.error(e1, e1);
- }
-
- }
-
- /**
- * Cache pubmed data for the model.
- *
- * @param originalModel
- * model for which we want to cache data.
- * @param params
- * parameters used for model generation
- */
- private void cacheData(final Model originalModel, final CreateProjectParams params) {
- modelService.cacheAllPubmedIds(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING, progress, params);
- }
- });
- modelService.cacheAllMiriamLinks(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MIRIAM, progress, params);
- }
- });
-
- chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
- }
- });
-
- drugService.cacheDataForModel(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_DRUG, progress, params);
- }
- });
-
- mirnaService.cacheDataForModel(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MI_RNA, progress, params);
- }
- });
-
- }
-
- /**
- * @return the modelDao
- * @see #modelDao
- */
- public ModelDao getModelDao() {
- return modelDao;
- }
-
- /**
- * @param modelDao
- * the modelDao to set
- * @see #modelDao
- */
- public void setModelDao(ModelDao modelDao) {
- this.modelDao = modelDao;
- }
-
- /**
- * @return the commentService
- * @see #commentService
- */
- public ICommentService getCommentService() {
- return commentService;
- }
-
- /**
- * @param commentService
- * the commentService to set
- * @see #commentService
- */
- public void setCommentService(ICommentService commentService) {
- this.commentService = commentService;
- }
-
- /**
- * @return the passwordEncoder
- * @see #passwordEncoder
- */
- public PasswordEncoder getPasswordEncoder() {
- return passwordEncoder;
- }
-
- /**
- * @param passwordEncoder
- * the passwordEncoder to set
- * @see #passwordEncoder
- */
- public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
- this.passwordEncoder = passwordEncoder;
- }
-
- /**
- * @return the commentDao
- * @see #commentDao
- */
- public CommentDao getCommentDao() {
- return commentDao;
- }
-
- /**
- * @param commentDao
- * the commentDao to set
- * @see #commentDao
- */
- public void setCommentDao(CommentDao commentDao) {
- this.commentDao = commentDao;
- }
-
- /**
- * @return the modelAnnotator
- * @see #modelAnnotator
- */
- public ModelAnnotator getModelAnnotator() {
- return modelAnnotator;
- }
-
- /**
- * @param modelAnnotator
- * the modelAnnotator to set
- * @see #modelAnnotator
- */
- public void setModelAnnotator(ModelAnnotator modelAnnotator) {
- this.modelAnnotator = modelAnnotator;
- }
-
- /**
- * @return the dbUtils
- * @see #dbUtils
- */
- public DbUtils getDbUtils() {
- return dbUtils;
- }
-
- /**
- * @param dbUtils
- * the dbUtils to set
- * @see #dbUtils
- */
- public void setDbUtils(DbUtils dbUtils) {
- this.dbUtils = dbUtils;
- }
-
- /**
- * @return the projectDao
- * @see #projectDao
- */
- public ProjectDao getProjectDao() {
- return projectDao;
- }
-
- /**
- * @param projectDao
- * the projectDao to set
- * @see #projectDao
- */
- public void setProjectDao(ProjectDao projectDao) {
- this.projectDao = projectDao;
- }
-
- /**
- * @return the dataMiningService
- * @see #dataMiningService
- */
- public IDataMiningService getDataMiningService() {
- return dataMiningService;
- }
-
- /**
- * @param dataMiningService
- * the dataMiningService to set
- * @see #dataMiningService
- */
- public void setDataMiningService(IDataMiningService dataMiningService) {
- this.dataMiningService = dataMiningService;
- }
-
- @Override
- public ProjectView createEmpty() {
- return projectViewFactory.create(null);
- }
-
- /**
- * Analyzes annotation of the model and put information about invalid
- * annotations into the {@link Model#creationWarnings} field.
- *
- * @param originalModel
- * model to analyze
- * @param params
- * parameters used for model generation
- */
- protected void analyzeAnnotations(final Model originalModel, final CreateProjectParams params) {
- logger.debug("Analyze annotations");
- Collection<? extends ProblematicAnnotation> improperAnnotations = modelAnnotator.findImproperAnnotations(originalModel, new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.VALIDATING_MIRIAM, progress, params);
- }
- }, params.getValidAnnotations());
- List<String> res = new ArrayList<>();
- for (ProblematicAnnotation improperAnnotation : improperAnnotations) {
- res.add(improperAnnotation.toString());
- }
- Collections.sort(res);
-
- Collection<? extends ProblematicAnnotation> missingAnnotations = modelAnnotator.findMissingAnnotations(originalModel, params.getRequiredAnnotations());
- for (ProblematicAnnotation improperAnnotation : missingAnnotations) {
- res.add(improperAnnotation.toString());
- }
- for (String message : res) {
- logger.warn(message);
- }
- logger.debug("Analyze finished");
- }
-
- /**
- * Sends notification email that map was removed.
- *
- * @param projectId
- * identifier of the project
- * @param email
- * otification email
- * @throws MessagingException
- * thrown when there is a problem with sending email
- */
- protected void sendSuccesfullRemoveEmail(String projectId, String email) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("Map " + projectId + " was successfully removed.<br/>");
- emailSender.sendEmail("MapViewer notification", content.toString(), email);
- }
-
- @Override
- public TreeNode createClassAnnotatorTree(User user) {
-
- UserAnnotationSchema annotationSchema = prepareUserAnnotationSchema(user);
-
- ElementUtils elementUtils = new ElementUtils();
-
- ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
-
- Class<?> clazz = top.getClazz();
- TreeNode root = new DefaultTreeNode(
- new AnnotatedObjectTreeRow(
- top, modelAnnotator.getAvailableAnnotators(clazz), modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
- annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz)),
- null);
-
- root.setExpanded(true);
-
- Queue<Pair<ClassTreeNode, TreeNode>> nodes = new LinkedList<Pair<ClassTreeNode, TreeNode>>();
- nodes.add(new Pair<ClassTreeNode, TreeNode>(top, root));
- // create children
-
- Queue<TreeNode> expandParents = new LinkedList<TreeNode>();
-
- while (!nodes.isEmpty()) {
- Pair<ClassTreeNode, TreeNode> element = nodes.poll();
-
- for (ClassTreeNode node : element.getLeft().getChildren()) {
-
- clazz = node.getClazz();
- AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(
- node, modelAnnotator.getAvailableAnnotators(clazz), modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
- annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz));
- TreeNode treeNode = new DefaultTreeNode(data, element.getRight());
- nodes.add(new Pair<ClassTreeNode, TreeNode>(node, treeNode));
- if (data.getUsedAnnotators().size() > 0 || data.getValidAnnotators().size() > 0) {
- expandParents.add(treeNode);
- }
- }
- }
- while (!expandParents.isEmpty()) {
- TreeNode node = expandParents.poll();
- if (node.getParent() != null && !node.getParent().isExpanded()) {
- node.getParent().setExpanded(true);
- expandParents.add(node.getParent());
- }
- }
-
- return root;
-
- }
-
- /**
- * Retrieves (or creates) annotation schema for a given user.
- *
- * @param user
- * for this users {@link UserAnnotationSchema} will be prepared
- * @return {@link UserAnnotationSchema} for {@link User}
- */
- public UserAnnotationSchema prepareUserAnnotationSchema(User user) {
- UserAnnotationSchema annotationSchema = null;
- if (user != null) {
- annotationSchema = userDao.getById(user.getId()).getAnnotationSchema();
- }
- if (annotationSchema == null) {
- annotationSchema = new UserAnnotationSchema();
-
- ElementUtils elementUtils = new ElementUtils();
-
- ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
-
- Map<Class<? extends BioEntity>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
- Map<Class<? extends BioEntity>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
-
- Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
- nodes.add(top);
-
- while (!nodes.isEmpty()) {
- ClassTreeNode element = nodes.poll();
- annotationSchema.addClassAnnotator(new UserClassAnnotators(element.getClazz(), modelAnnotator.getAvailableDefaultAnnotatorNames(element.getClazz())));
- annotationSchema.addClassValidAnnotations(new UserClassValidAnnotations(element.getClazz(), validMiriam.get(element.getClazz())));
- annotationSchema.addClassRequiredAnnotations(new UserClassRequiredAnnotations(element.getClazz(), requiredMiriam.get(element.getClazz())));
- for (ClassTreeNode node : element.getChildren()) {
- nodes.add(node);
- }
- }
- User dbUser = userDao.getById(user.getId());
- dbUser.setAnnotationSchema(annotationSchema);
- userDao.update(dbUser);
- }
- return annotationSchema;
- }
-
- @Override
- public void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat, boolean networkLayoutAsDefault) {
- User dbUser = userDao.getById(user.getId());
- if (dbUser.getAnnotationSchema() == null) {
- dbUser.setAnnotationSchema(new UserAnnotationSchema());
- }
- UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
-
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
- for (TreeNode child : node.getChildren()) {
- queue.add(child);
- }
- AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) node.getData();
- annotationSchema.addClassAnnotator(new UserClassAnnotators(data.getClazz(), data.getUsedAnnotators()));
- annotationSchema.addClassRequiredAnnotations(new UserClassRequiredAnnotations(data.getClazz(), data.getRequiredAnnotations()));
- annotationSchema.addClassValidAnnotations(new UserClassValidAnnotations(data.getClazz(), data.getValidAnnotations()));
- }
- annotationSchema.setSbgnFormat(sbgnFormat);
- annotationSchema.setNetworkLayoutAsDefault(networkLayoutAsDefault);
- userService.updateUser(dbUser);
- user.setAnnotationSchema(annotationSchema);
- }
-
- /**
- * Sends email about unsuccessfull project creation.
- *
- * @param projectName
- * name of the project
- * @param email
- * email where we want to send information
- * @param e
- * exception that caused problem
- */
- private void sendUnsuccesfullEmail(String projectName, String email, Exception e) {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("");
- content.append("There was a problem with generating " + projectName + " map.<br/>");
- content.append(e.getClass().getName() + ": " + e.getMessage());
- try {
- emailSender.sendEmail("MapViewer notification", content.toString(), email);
- } catch (MessagingException e1) {
- logger.error(e1);
- }
- }
-
- /**
- * Sends email about successfull project creation.
- *
- * @param originalModel
- * model that was created
- * @throws MessagingException
- * exception thrown when there is a problem with sending email
- */
- protected void sendSuccesfullEmail(Model originalModel) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("Your map was generated successfully.<br/>");
- emailSender.sendEmail("MapViewer notification", content.toString(), originalModel.getProject().getNotifyEmail());
- }
-
- @Override
- public void updateProject(Project project) {
- projectDao.update(project);
- }
-
- /**
- * This method handles situation when sever db error appeard during uploading
- * of the project into database.
- *
- * @param params
- * parameters used to create project
- * @param e
- * exception that occured during uploading of the project
- */
- private void handleHibernateExceptionReporting(CreateProjectParams params, HibernateException e) {
- // we need to open separate thread because current one thrown db exception
- // and transaction is corrupetd and will be rolledback
- Thread reportInSeparateThread = new Thread(new Runnable() {
-
- @Override
- public void run() {
- dbUtils.createSessionForCurrentThread();
-
- try {
- Project project = getProjectByProjectId(params.getProjectId(), params.getAuthenticationToken());
- String errorMessage = "Problem with uploading to database. "
- + "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n" + e.getMessage()
- + "\nMore information can be found in log file.";
- project.setErrors(errorMessage);
- project.setStatus(ProjectStatus.FAIL);
- projectDao.update(project);
- } catch (Exception e) {
- logger.error(e, e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- });
- reportInSeparateThread.start();
-
- }
-
- @Override
- public byte[] getInputDataForProject(ProjectView projectView) {
- return getInputDataForProject(projectView.getIdObject());
- }
-
- /**
- * Returns byte array containing data from original input file that was used
- * to create this project.
- *
- * @param projectId
- * identifier of project for which we want to retrieve original file
- * data
- * @return original data file for given layout, if such file is not stored in
- * database (compatibility reasons) then null is returned
- */
- private byte[] getInputDataForProject(int projectId) {
- Project project = projectDao.getById(projectId);
- if (project == null || project.getInputData() == null) {
- return null;
- } else {
- return project.getInputData().getFileContent();
- }
- }
-
- /**
- * Method that handles exception reporting during creation of a project.
- *
- * @param params
- * set of parameters used to create project
- * @param e
- * exception that caused problems
- */
- private void handleCreateProjectException(final CreateProjectParams params, Exception e) {
- Project p = projectDao.getProjectByProjectId(params.getProjectId());
- logger.error(e.getMessage(), e);
- if (p != null) {
- p.setErrors("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
- }
- updateProjectStatus(p, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
-
- String email = params.getNotifyEmail();
- String projectName = params.getProjectId();
-
- LogParams logParams = new LogParams().description("Failed: " + e.getMessage()).type(LogType.MAP_CREATED).object(p);
- logService.log(logParams);
- if (email != null) {
- sendUnsuccesfullEmail(projectName, email, e);
- }
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- public TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
+ /**
+ * Size of the artifitial buffer that will be released when
+ * {@link OutOfMemoryError} is thrown to gain some free memory and report
+ * problem.
+ */
+ private static final int OUT_OF_MEMORY_BACKUP_BUFFER_SIZE = 10000;
+
+ /**
+ * How much time (out of 1.00) is used for creation of the data from file.
+ */
+ private static final double CREATION_OF_DATA = 0.50;
+
+ /**
+ * How much time (out of 1.00) is used for upploading of the data from file.
+ */
+ private static final double UPLOAD_OF_DATA = 0.50;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ProjectService.class);
+
+ /**
+ * Data access object for projects.
+ */
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Data access object for models.
+ */
+ @Autowired
+ private ModelDao modelDao;
+
+ /**
+ * Data access object for users.
+ */
+ @Autowired
+ private UserDao userDao;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @Autowired
+ private IModelService modelService;
+
+ /**
+ * Service that allows to access and manage comments.
+ */
+ @Autowired
+ private ICommentService commentService;
+
+ /**
+ * Service used to access logs.
+ *
+ * @see ILogService
+ */
+ @Autowired
+ private ILogService logService;
+
+ /**
+ * Service that manages and gives access to configuration parameters.
+ */
+ @Autowired
+ private IConfigurationService configurationService;
+
+ /**
+ * Services that manages and gives access to user information.
+ */
+ @Autowired
+ private IUserService userService;
+
+ /**
+ * Services that accessa data about chemicals.
+ */
+ @Autowired
+ private IChemicalService chemicalService;
+
+ /**
+ * Services that accessa data about drugs.
+ */
+ @Autowired
+ private IDrugService drugService;
+
+ /**
+ * Services that accessa data about mirna.
+ */
+ @Autowired
+ private IMiRNAService mirnaService;
+
+ /**
+ * Service that manages data mining information.
+ */
+ @Autowired
+ private IDataMiningService dataMiningService;
+
+ /**
+ * Data access object for comments.
+ */
+ @Autowired
+ private CommentDao commentDao;
+
+ /**
+ * Service that provides password encoding.
+ */
+ @Autowired
+ private PasswordEncoder passwordEncoder;
+
+ /**
+ * Module that allows to annotate maps.
+ */
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Factory object for {@link ProjectView} elements.
+ */
+ @Autowired
+ private ProjectViewFactory projectViewFactory;
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private MeSHParser meshParser;
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ /**
+ * Class that helps to generate images for google maps API.
+ */
+ private MapGenerator generator = new MapGenerator();
+
+ @Override
+ public Project getProjectByProjectId(String name, AuthenticationToken token) throws UserAccessException {
+ Project result = projectDao.getProjectByProjectId(name);
+ if (result == null) {
+ return result;
+ }
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, result)) {
+ return result;
+ } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return result;
+ }
+ throw new UserAccessException("User cannot access project");
+ }
+
+ @Override
+ public boolean projectExists(String projectName) {
+ if (projectName == null || projectName.equals("")) {
+ return false;
+ }
+ return projectDao.isProjectExistsByName(projectName);
+ }
+
+ @Override
+ public List<Project> getAllProjects(AuthenticationToken token) {
+ List<Project> projects = projectDao.getAll();
+ if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return projects;
+ }
+ List<Project> result = new ArrayList<>();
+ for (Project project : projects) {
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
+ result.add(project);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public List<ProjectView> getAllProjectViews(AuthenticationToken token) {
+ List<ProjectView> result = new ArrayList<>();
+ List<Project> projects = getAllProjects(token);
+ for (Project project : projects) {
+ result.add(projectViewFactory.create(project));
+ }
+ return result;
+ }
+
+ @Override
+ public void updateProject(ProjectView selectedProject) {
+ Project project = projectDao.getById(selectedProject.getIdObject());
+ project.setProjectId(selectedProject.getProjectId());
+ project.setName(selectedProject.getProjectName());
+ project.setVersion(selectedProject.getVersion());
+ project.setNotifyEmail(selectedProject.getNotifyEmail());
+ MiriamData disease = null;
+ MiriamData organism = null;
+ if (selectedProject.getNewDiseaseName() != null && !selectedProject.getNewDiseaseName().isEmpty()) {
+ disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
+ }
+ if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
+ }
+ try {
+ if (meshParser.isValidMeshId(disease)) {
+ project.setDisease(disease);
+ } else {
+ project.setDisease(null);
+ selectedProject.setNewDiseaseName(null);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing mesh", e);
+ project.setDisease(null);
+ selectedProject.setNewDiseaseName(null);
+ }
+ try {
+ if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
+ project.setOrganism(organism);
+ } else {
+ project.setOrganism(null);
+ selectedProject.setNewOrganismName(null);
+ }
+ } catch (TaxonomySearchException e) {
+ logger.error("Problem with accessing taxonomy db", e);
+ project.setOrganism(null);
+ selectedProject.setNewOrganismName(null);
+ }
+ for (ModelData model : project.getModels()) {
+ if (model.getId().equals(selectedProject.getModelId())) {
+ modelService.updateModel(model, selectedProject);
+ }
+ }
+ projectDao.update(project);
+ }
+
+ @Override
+ public void removeProject(ProjectView selectedProject, String homeDir, boolean async, AuthenticationToken token)
+ throws UserAccessException {
+ Project project = projectDao.getById(selectedProject.getIdObject());
+ removeProject(project, homeDir, async, token);
+ }
+
+ /**
+ * Removes all types of privileges from every user to the project given in the
+ * parameter.
+ *
+ * @param project
+ * from which project we remove privileges
+ */
+ private void removePrivilegesForProject(Project project) {
+ for (PrivilegeType type : PrivilegeType.values()) {
+ if (type.getPrivilegeObjectType() == Project.class) {
+ userService.dropPrivilegesForObjectType(type, project.getId());
+ }
+ }
+ }
+
+ @Override
+ public ProjectView getProjectViewByProjectId(String name, AuthenticationToken token) throws UserAccessException {
+ Project project = getProjectByProjectId(name, token);
+ return projectViewFactory.create(project);
+ }
+
+ @Override
+ public void removeProject(final Project p, final String dir, final boolean async, AuthenticationToken token)
+ throws UserAccessException {
+ if (!userService.userHasPrivilege(userService.getUserByToken(token), PrivilegeType.PROJECT_MANAGEMENT)) {
+ throw new UserAccessException("User cannot remove project");
+ }
+
+ final String homeDir;
+ if (dir != null) {
+ if (p.getDirectory() != null) {
+ homeDir = dir + "/../map_images/" + p.getDirectory() + "/";
+ } else {
+ homeDir = dir + "/../map_images/";
+ }
+ } else {
+ if (p.getDirectory() != null) {
+ homeDir = p.getDirectory() + "/";
+ } else {
+ homeDir = null;
+ }
+ }
+ removePrivilegesForProject(p);
+ updateProjectStatus(p, ProjectStatus.REMOVING, 0, new CreateProjectParams());
+ Thread computations = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ if (async) {
+ // because we are running this in separate thread we need to open a
+ // new
+ // session for db connection
+ dbUtils.createSessionForCurrentThread();
+ }
+
+ Project project = projectDao.getById(p.getId());
+
+ try {
+ String email = null;
+ MapGenerator mapGenerator = new MapGenerator();
+ for (ModelData originalModel : project.getModels()) {
+ List<ModelData> models = new ArrayList<ModelData>();
+ models.add(originalModel);
+ for (ModelSubmodelConnection connection : originalModel.getSubmodels()) {
+ models.add(connection.getSubmodel());
+ }
+ modelService.removeModelFromCache(originalModel);
+ for (ModelData model : models) {
+ logger.debug("Remove model: " + model.getId());
+ commentService.removeCommentsForModel(model);
+
+ for (Layout layout : model.getLayouts()) {
+ try {
+ mapGenerator.removeLayout(layout, homeDir);
+ } catch (IOException e) {
+ logger.error("Problem with removing directory: " + layout.getDirectory(), e);
+ }
+ }
+ }
+ email = project.getNotifyEmail();
+ }
+ projectDao.delete(project);
+ if (async) {
+ projectDao.commit();
+ }
+
+ LogParams params = new LogParams().type(LogType.MAP_REMOVED).object(project);
+ logService.log(params);
+
+ if (email != null) {
+ try {
+ sendSuccesfullRemoveEmail(project.getProjectId(), email);
+ } catch (MessagingException e) {
+ logger.error("Problem with sending remove email.", e);
+ }
+ }
+ modelService.removeModelFromCacheByProjectId(p.getProjectId());
+
+ } catch (HibernateException e) {
+ logger.error("Problem with database", e);
+ handleHibernateExceptionRemovingReporting(project, e, token);
+ } finally {
+ if (async) {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+ if (homeDir != null) {
+ File homeDirFile = new File(homeDir);
+ if (homeDirFile.exists()) {
+ logger.debug("Removing project directory: " + homeDirFile.getAbsolutePath());
+ try {
+ FileUtils.deleteDirectory(homeDirFile);
+ } catch (IOException e) {
+ logger.error("Problem with removing diriectory", e);
+ }
+ }
+ }
+
+ }
+ });
+
+ if (async) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+
+ }
+
+ /**
+ * When we encountered hibernate exception we need to handle error reporting
+ * differently (hibernate session is broken). This method handles such case when
+ * hibernate excedption occured when removing project.
+ *
+ * @param originalProject
+ * project that was beining removed
+ * @param exception
+ * hibernate exception that caused problems
+ */
+ protected void handleHibernateExceptionRemovingReporting(Project originalProject, HibernateException exception,
+ AuthenticationToken token) {
+ // we need to open separate thread because current one thrown db exception
+ // and transaction is corrupetd and will be rolledback
+ Thread reportInSeparateThread = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ dbUtils.createSessionForCurrentThread();
+ try {
+ // we need to get the project from db, because session where
+ // originalProject was retrieved is broken
+ Project project = getProjectByProjectId(originalProject.getProjectId(), token);
+ String errorMessage = "Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
+ + "\nMore information can be found in log file.";
+ project.setErrors(errorMessage + "\n" + project.getErrors());
+ project.setStatus(ProjectStatus.FAIL);
+ projectDao.update(project);
+ } catch (UserAccessException e) {
+ logger.error(e, e);
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ });
+ reportInSeparateThread.start();
+ }
+
+ @Override
+ public void addProject(Project project) {
+ projectDao.add(project);
+
+ }
+
+ @Override
+ public ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException {
+ Project project = projectDao.getById(id);
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
+ return projectViewFactory.create(project);
+ } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return projectViewFactory.create(project);
+ } else {
+ throw new UserAccessException("User cannot access project");
+ }
+ }
+
+ /**
+ * This methods add privileges for the users listed in params to the project.
+ *
+ * @param project
+ * to which project we add privileges
+ * @param params
+ * which users should be included to have privileges to the project
+ */
+ private void addUsers(Project project, CreateProjectParams params) {
+ if (project == null) {
+ logger.warn("Users won't be added. Project not defined");
+ return;
+ }
+ List<String[]> users = params.getUsers();
+ String[][] newUsers = new String[users.size() + 1][2];
+ for (int i = 0; i < users.size(); i++) {
+ for (int j = 0; j < 2; j++) {
+ newUsers[i][j] = users.get(i)[j];
+ }
+ }
+ newUsers[users.size()][0] = "anonymous";
+ newUsers[users.size()][1] = "";
+ for (int i = 0; i < newUsers.length; i++) {
+ boolean admin = (users.size() != i);
+ String login = newUsers[i][0];
+ String passwd = newUsers[i][1];
+ User user = userService.getUserByLogin(login);
+ if (userService.getUserByLogin(login) == null) {
+ logger.debug("User " + login + " does not exist. Creating");
+ user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(passwd));
+ user.setLogin(login);
+ userService.addUser(user);
+ }
+ if (project != null) {
+ logger.debug("Privileges for " + login + " for project " + project.getProjectId());
+ ObjectPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user);
+ userService.setUserPrivilege(user, privilege);
+ if (admin) {
+ privilege = new ObjectPrivilege(project, 1, PrivilegeType.LAYOUT_MANAGEMENT, user);
+ userService.setUserPrivilege(user, privilege);
+ privilege = new ObjectPrivilege(project, 1, PrivilegeType.EDIT_COMMENTS_PROJECT, user);
+ userService.setUserPrivilege(user, privilege);
+ }
+
+ }
+ }
+ }
+
+ /**
+ * This method creates set of images for the model layouts.
+ *
+ * @param originalModel
+ * model for which we create layout images
+ * @param params
+ * configuration parameters including set of layouts to generate
+ * @throws IOException
+ * thrown when there are problems with generating files
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ * @throws CommandExecutionException
+ * thrown when one of the files describing layouts is invalid
+ */
+ protected void createImages(final Model originalModel, final CreateProjectParams params)
+ throws IOException, DrawingException, CommandExecutionException {
+ if (!params.isImages()) {
+ return;
+ }
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES, 0, params);
+
+ List<Model> models = new ArrayList<Model>();
+ models.add(originalModel);
+ int size = originalModel.getLayouts().size();
+ for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
+ models.add(connection.getSubmodel().getModel());
+ size += connection.getSubmodel().getModel().getLayouts().size();
+ }
+ int counter = 0;
+ for (final Model model : models) {
+ for (int i = 0; i < model.getLayouts().size(); i++) {
+ Layout layout = model.getLayouts().get(i);
+ if (layout.getInputData() == null) {
+ final double imgCounter = counter;
+ final double finalSize = size;
+ IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES,
+ IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize, params);
+ }
+ };
+
+ generateImagesForBuiltInOverlay(params, model, layout, updater);
+ }
+ counter++;
+ }
+ }
+ }
+
+ private void generateImagesForBuiltInOverlay(final CreateProjectParams params, final Model model, Layout layout,
+ IProgressUpdater updater) throws CommandExecutionException, IOException, DrawingException {
+ String directory = layout.getDirectory();
+ Model output = model;
+ if (layout.isHierarchicalView()) {
+ output = new CopyCommand(model).execute();
+ new SetFixedHierarchyLevelCommand(output, layout.getHierarchyViewLevel()).execute();
+ }
+ if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
+ output = new CopyCommand(model).execute();
+ new ClearColorModelCommand(output).execute();
+ }
+
+ MapGeneratorParams imgParams = generator.new MapGeneratorParams().directory(directory).sbgn(params.isSbgnFormat())
+ .nested(layout.isHierarchicalView()).updater(updater);
+ imgParams.model(output);
+ generator.generateMapImages(imgParams);
+ }
+
+ /**
+ * Creates project. Loads model from the input and run PostLoadModification.
+ *
+ * @param params
+ * params used to create model
+ * @param dbProject
+ * project where the model should be placed
+ * @throws InvalidInputDataExecption
+ * thrown when there is a problem with input file
+ */
+ protected void createModel(final CreateProjectParams params, Project dbProject) throws InvalidInputDataExecption {
+ ModelData modelData = modelDao.getLastModelForProjectIdentifier(params.getProjectId(), false);
+ if (modelData != null) {
+ throw new InvalidArgumentException("Model with the given name already exists");
+ }
+
+ final Project project = dbProject;
+ updateProjectStatus(project, ProjectStatus.PARSING_DATA, 0.0, params);
+
+ if (params.isComplex()) {
+ try {
+ Class<? extends IConverter> clazz = CellDesignerXmlParser.class;
+ if (params.getParser() != null) {
+ clazz = params.getParser().getClass();
+ }
+ ComplexZipConverter parser = new ComplexZipConverter(clazz);
+ ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
+ complexParams.visualizationDir(params.getProjectDir());
+ for (ZipEntryFile entry : params.getZipEntries()) {
+ complexParams.entry(entry);
+ }
+ ProjectFactory projectFactory = new ProjectFactory(parser);
+ projectFactory.create(complexParams, dbProject);
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+ } else {
+ IConverter parser;
+ if (params.getParser() != null) {
+ parser = params.getParser();
+ } else if (params.getProjectFile().endsWith("sbgn")) {
+ parser = new SbgnmlXmlConverter();
+ } else {
+ parser = new CellDesignerXmlParser();
+ }
+ try {
+ Model model = parser.createModel(new ConverterParams().filename(params.getProjectFile())
+ .sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
+ model.setName(params.getProjectName());
+ project.addModel(model);
+ } catch (FileNotFoundException ex) {
+ throw new InvalidInputDataExecption(ex);
+ }
+ }
+ Model topModel = project.getModels().iterator().next().getModel();
+ topModel.setZoomLevels(generator.computeZoomLevels(topModel));
+ topModel.setTileSize(MapGenerator.TILE_SIZE);
+ dbProject.setNotifyEmail(params.getNotifyEmail());
+
+ updateProjectStatus(project, ProjectStatus.UPLOADING_TO_DB, 0.0, params);
+ dbUtils.setAutoFlush(false);
+ projectDao.update(project);
+ dbUtils.setAutoFlush(true);
+ projectDao.flush();
+
+ List<BuildInLayout> buildInLayouts = new ArrayList<>();
+ BuildInLayout nested = null;
+ if (params.isSemanticZoom()) {
+ nested = BuildInLayout.SEMANTIC;
+ } else {
+ nested = BuildInLayout.NESTED;
+ }
+ if (params.isNetworkLayoutAsDefault()) {
+ buildInLayouts.add(BuildInLayout.NORMAL);
+ buildInLayouts.add(nested);
+ } else {
+ buildInLayouts.add(nested);
+ buildInLayouts.add(BuildInLayout.NORMAL);
+ }
+ buildInLayouts.add(BuildInLayout.CLEAN);
+
+ // reverse the order of build in layouts, so we can insert them at the
+ // beginning of list of layouts (the order will be the same)
+ Collections.reverse(buildInLayouts);
+
+ for (BuildInLayout buildInLayout : buildInLayouts) {
+ Layout topLayout = new Layout(buildInLayout.getTitle(),
+ params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + topModel.getId() + "/", true);
+ topLayout.setStatus(LayoutStatus.NA);
+ topLayout.setProgress(0.0);
+ topLayout.setHierarchicalView(buildInLayout.isNested());
+ topModel.addLayout(0, topLayout);
+ int submodelId = 1;
+ List<Layout> semanticLevelOverlays = new ArrayList<>();
+ if (buildInLayout.equals(BuildInLayout.SEMANTIC)) {
+ for (int i = 0; i <= topModel.getZoomLevels(); i++) {
+ String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ + topModel.getId() + "/";
+ Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
+ semanticOverlay.setStatus(LayoutStatus.NA);
+ semanticOverlay.setProgress(0.0);
+ semanticOverlay.setHierarchicalView(buildInLayout.isNested());
+ semanticOverlay.setHierarchyViewLevel(i);
+ semanticLevelOverlays.add(semanticOverlay);
+ topModel.addLayout(1, semanticOverlay);
+ }
+ }
+ for (ModelSubmodelConnection connection : topModel.getSubmodelConnections()) {
+ Layout layout = new Layout(buildInLayout.getTitle(),
+ params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + submodelId + "/", true);
+ layout.setStatus(LayoutStatus.NA);
+ layout.setProgress(0.0);
+ layout.setHierarchicalView(buildInLayout.isNested());
+ layout.setParentLayout(topLayout);
+ connection.getSubmodel().addLayout(0, layout);
+
+ connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
+ connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
+ if (buildInLayout.equals(BuildInLayout.SEMANTIC)) {
+ for (int i = 0; i <= topModel.getZoomLevels(); i++) {
+ String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ + submodelId + "/";
+ Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
+ semanticOverlay.setStatus(LayoutStatus.NA);
+ semanticOverlay.setProgress(0.0);
+ semanticOverlay.setHierarchicalView(buildInLayout.isNested());
+ semanticOverlay.setParentLayout(semanticLevelOverlays.get(i));
+ semanticOverlay.setHierarchyViewLevel(i);
+ connection.getSubmodel().addLayout(1, semanticOverlay);
+ }
+ }
+ submodelId++;
+ }
+ }
+
+ if (params.isUpdateAnnotations()) {
+ Map<Class<?>, List<ElementAnnotator>> annotators = null;
+ if (params.getAnnotatorsMap() != null) {
+ annotators = new HashMap<Class<?>, List<ElementAnnotator>>();
+ for (Class<?> clazz : params.getAnnotatorsMap().keySet()) {
+ annotators.put(clazz, modelAnnotator.getAnnotatorsFromCommonNames(params.getAnnotatorsMap().get(clazz)));
+ }
+ }
+ logger.debug("Updating annotations");
+ modelAnnotator.performAnnotations(topModel, new IProgressUpdater() {
+
+ @Override
+ public void setProgress(final double progress) {
+ updateProjectStatus(project, ProjectStatus.ANNOTATING, progress, params);
+ }
+ }, annotators);
+ logger.debug("Annotations updated");
+ }
+ updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, 0.0, params);
+ processDataMining(topModel, topModel.getDataMiningSets(), new IProgressUpdater() {
+
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, progress, params);
+ }
+
+ });
+ updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, IProgressUpdater.MAX_PROGRESS, params);
+ logger.debug("Model created");
+
+ }
+
+ /**
+ * Process data mining files and assign suggested connections to the model.
+ *
+ * @param model
+ * model where the suggested connections will be added
+ * @param dataMiningSets
+ * set of files to process
+ * @param progressUpdater
+ * callback function informing higher layer about progress
+ * @throws InvalidDataMiningInputFile
+ * thrown when one of the files is invalid
+ */
+ private void processDataMining(Model model, List<DataMiningSet> dataMiningSets,
+ final IProgressUpdater progressUpdater) throws InvalidDataMiningInputFile {
+ Set<Element> nodes = new HashSet<>();
+ nodes.addAll(model.getElements());
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ nodes.addAll(connection.getSubmodel().getElements());
+ }
+ Set<Reaction> reactions = new HashSet<Reaction>();
+ reactions.addAll(model.getReactions());
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ reactions.addAll(connection.getSubmodel().getReactions());
+ }
+
+ int fileCounter = 0;
+ final int filesCount = dataMiningSets.size();
+ for (DataMiningSet dmSet : dataMiningSets) {
+
+ final double offset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount;
+ IProgressUpdater secondPartUpdater = new IProgressUpdater() {
+
+ @Override
+ public void setProgress(double progress) {
+ progressUpdater.setProgress((progress * CREATION_OF_DATA) / ((double) filesCount) + offset);
+ }
+ };
+ Set<DataMining> result = dataMiningService.parseData(dmSet, nodes, reactions, secondPartUpdater);
+ double size = result.size();
+ double count = 0;
+
+ double updateOffset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount
+ + CREATION_OF_DATA / ((double) filesCount);
+ for (DataMining missingConnection : result) {
+ missingConnection.setType(dmSet.getType());
+ missingConnection.getElement().addDataMining(missingConnection);
+ count++;
+ progressUpdater.setProgress(updateOffset + IProgressUpdater.MAX_PROGRESS * count / size * UPLOAD_OF_DATA);
+ }
+ }
+ }
+
+ /**
+ * Updates status of the generating project.
+ *
+ * @param project
+ * project that is generated
+ * @param status
+ * what is the current status
+ * @param progress
+ * what is the progress
+ * @param params
+ * parameters used for project creation
+ */
+ private void updateProjectStatus(Project project, ProjectStatus status, double progress, CreateProjectParams params) {
+ if (project != null) {
+ if (!status.equals(project.getStatus())
+ || (Math.abs(progress - project.getProgress()) > IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION)) {
+ project.setStatus(status);
+ project.setProgress(progress);
+ projectDao.update(project);
+ if (params.isAsync()) {
+ projectDao.commit();
+ }
+ }
+ } else {
+ logger.debug("status: " + status + ", " + progress);
+ }
+ }
+
+ @Override
+ public void createProject(final CreateProjectParams params) throws SecurityException {
+ if (!userService.userHasPrivilege(params.getAuthenticationToken(), PrivilegeType.ADD_MAP)) {
+ throw new SecurityException("Adding projects not allowed.");
+ }
+
+ // this count down is used to wait for asynchronous thread to initialize
+ // data in the db (probably it would be better to move the initialization to
+ // main thread)
+ final CountDownLatch waitForInitialData = new CountDownLatch(1);
+
+ Thread computations = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ if (params.isAsync()) {
+ // because we are running this in separate thread we need to open a
+ // new session for db connection
+ dbUtils.createSessionForCurrentThread();
+ }
+
+ Project project = new Project();
+ project.setProjectId(params.getProjectId());
+ project.setName(params.getProjectName());
+ if (params.getProjectDir() == null) {
+ logger.warn("Project directory not set");
+ project.setDirectory(null);
+ } else {
+ project.setDirectory(new File(params.getProjectDir()).getName());
+ }
+ project.setSbgnFormat(params.isSbgnFormat());
+
+ MiriamData disease = null;
+ if (params.getDisease() != null && !params.getDisease().isEmpty()) {
+ disease = new MiriamData(MiriamType.MESH_2012, params.getDisease());
+ }
+ MiriamData organism = null;
+ if (params.getOrganism() != null && !params.getOrganism().isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, params.getOrganism());
+ }
+ project.setVersion(params.getVersion());
+ projectDao.add(project);
+ if (params.isAsync()) {
+ projectDao.commit();
+ }
+ waitForInitialData.countDown();
+ double[] outOfMemoryBuffer;
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ logger.debug("Running: " + params.getProjectId() + "; " + params.getProjectFile());
+ outOfMemoryBuffer = new double[OUT_OF_MEMORY_BACKUP_BUFFER_SIZE];
+ for (int i = 0; i < OUT_OF_MEMORY_BACKUP_BUFFER_SIZE; i++) {
+ outOfMemoryBuffer[i] = Math.random() * OUT_OF_MEMORY_BACKUP_BUFFER_SIZE;
+ }
+
+ File inputFile = new File(params.getProjectFile());
+ if (inputFile.exists()) {
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setFileContent(IOUtils.toByteArray(new FileInputStream(inputFile)));
+ file.setOriginalFileName(FilenameUtils.getName(params.getProjectFile()));
+ file.setLength(file.getFileContent().length);
+ User owner = null;
+ for (String[] userRow : params.getUsers()) {
+ User user = userService.getUserByLogin(userRow[0]);
+ if (user != null) {
+ owner = user;
+ }
+ }
+ file.setOwner(owner);
+ project.setInputData(file);
+ }
+
+ createModel(params, project);
+ Model originalModel = project.getModels().iterator().next().getModel();
+ if (!params.isSemanticZoom()) {
+ new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel),
+ generator.computeZoomFactor(originalModel)).execute();
+ }
+
+ addUsers(project, params);
+ createImages(originalModel, params);
+
+ for (Layout layout : originalModel.getLayouts()) {
+ String[] tmp = layout.getDirectory().split("[\\\\/]");
+ layout.setDirectory(tmp[tmp.length - 1]);
+ }
+ for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
+ for (Layout layout : connection.getSubmodel().getLayouts()) {
+ String[] tmp = layout.getDirectory().split("[\\\\/]");
+ layout.setDirectory(tmp[tmp.length - 1]);
+ }
+ }
+
+ try {
+ if (meshParser.isValidMeshId(disease)) {
+ project.setDisease(disease);
+ } else {
+ logger.warn("No valid disease is provided for project:" + project.getName());
+ }
+ } catch (AnnotatorException e1) {
+ logger.warn("Problem with accessing mesh db. More info in logs.");
+ }
+
+ if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
+ project.setOrganism(organism);
+ } else {
+ logger.warn("No valid organism is provided for project:" + project.getName());
+ }
+
+ modelDao.update(originalModel);
+
+ if (params.isCacheModel()) {
+ cacheData(originalModel, params);
+ }
+
+ if (params.isAnalyzeAnnotations()) {
+ analyzeAnnotations(originalModel, params);
+ }
+ Logger.getRootLogger().removeAppender(appender);
+ project.addLoggingInfo(appender);
+ updateProjectStatus(project, ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS, params);
+ if (project.getNotifyEmail() != null && !project.getNotifyEmail().equals("")) {
+ try {
+ sendSuccesfullEmail(originalModel);
+ } catch (MessagingException e) {
+ logger.error(e, e);
+ }
+ }
+
+ LogParams params = new LogParams().description("Created successfully").type(LogType.MAP_CREATED)
+ .object(originalModel);
+ logService.log(params);
+
+ } catch (HibernateException e) {
+ outOfMemoryBuffer = null;
+ logger.error("Problem with database", e);
+ handleHibernateExceptionReporting(params, e);
+ } catch (Exception e) {
+ outOfMemoryBuffer = null;
+ handleCreateProjectException(params, e);
+ } catch (OutOfMemoryError oome) {
+ // release some memory
+ outOfMemoryBuffer = null;
+ logger.error("Out of memory", oome);
+ if (project != null) {
+ project.setErrors("Out of memory: " + oome.getMessage());
+ }
+ updateProjectStatus(project, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
+ } finally {
+ if (params.isAsync()) {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ }
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+ });
+ if (params.isAsync()) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+
+ try {
+ waitForInitialData.await();
+ } catch (InterruptedException e1) {
+ logger.error(e1, e1);
+ }
+
+ }
+
+ /**
+ * Cache pubmed data for the model.
+ *
+ * @param originalModel
+ * model for which we want to cache data.
+ * @param params
+ * parameters used for model generation
+ */
+ private void cacheData(final Model originalModel, final CreateProjectParams params) {
+ modelService.cacheAllPubmedIds(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING, progress, params);
+ }
+ });
+ modelService.cacheAllMiriamLinks(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MIRIAM, progress, params);
+ }
+ });
+
+ chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
+ }
+ });
+
+ drugService.cacheDataForModel(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_DRUG, progress, params);
+ }
+ });
+
+ mirnaService.cacheDataForModel(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MI_RNA, progress, params);
+ }
+ });
+
+ }
+
+ /**
+ * @return the modelDao
+ * @see #modelDao
+ */
+ public ModelDao getModelDao() {
+ return modelDao;
+ }
+
+ /**
+ * @param modelDao
+ * the modelDao to set
+ * @see #modelDao
+ */
+ public void setModelDao(ModelDao modelDao) {
+ this.modelDao = modelDao;
+ }
+
+ /**
+ * @return the commentService
+ * @see #commentService
+ */
+ public ICommentService getCommentService() {
+ return commentService;
+ }
+
+ /**
+ * @param commentService
+ * the commentService to set
+ * @see #commentService
+ */
+ public void setCommentService(ICommentService commentService) {
+ this.commentService = commentService;
+ }
+
+ /**
+ * @return the passwordEncoder
+ * @see #passwordEncoder
+ */
+ public PasswordEncoder getPasswordEncoder() {
+ return passwordEncoder;
+ }
+
+ /**
+ * @param passwordEncoder
+ * the passwordEncoder to set
+ * @see #passwordEncoder
+ */
+ public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
+ this.passwordEncoder = passwordEncoder;
+ }
+
+ /**
+ * @return the commentDao
+ * @see #commentDao
+ */
+ public CommentDao getCommentDao() {
+ return commentDao;
+ }
+
+ /**
+ * @param commentDao
+ * the commentDao to set
+ * @see #commentDao
+ */
+ public void setCommentDao(CommentDao commentDao) {
+ this.commentDao = commentDao;
+ }
+
+ /**
+ * @return the modelAnnotator
+ * @see #modelAnnotator
+ */
+ public ModelAnnotator getModelAnnotator() {
+ return modelAnnotator;
+ }
+
+ /**
+ * @param modelAnnotator
+ * the modelAnnotator to set
+ * @see #modelAnnotator
+ */
+ public void setModelAnnotator(ModelAnnotator modelAnnotator) {
+ this.modelAnnotator = modelAnnotator;
+ }
+
+ /**
+ * @return the dbUtils
+ * @see #dbUtils
+ */
+ public DbUtils getDbUtils() {
+ return dbUtils;
+ }
+
+ /**
+ * @param dbUtils
+ * the dbUtils to set
+ * @see #dbUtils
+ */
+ public void setDbUtils(DbUtils dbUtils) {
+ this.dbUtils = dbUtils;
+ }
+
+ /**
+ * @return the projectDao
+ * @see #projectDao
+ */
+ public ProjectDao getProjectDao() {
+ return projectDao;
+ }
+
+ /**
+ * @param projectDao
+ * the projectDao to set
+ * @see #projectDao
+ */
+ public void setProjectDao(ProjectDao projectDao) {
+ this.projectDao = projectDao;
+ }
+
+ /**
+ * @return the dataMiningService
+ * @see #dataMiningService
+ */
+ public IDataMiningService getDataMiningService() {
+ return dataMiningService;
+ }
+
+ /**
+ * @param dataMiningService
+ * the dataMiningService to set
+ * @see #dataMiningService
+ */
+ public void setDataMiningService(IDataMiningService dataMiningService) {
+ this.dataMiningService = dataMiningService;
+ }
+
+ @Override
+ public ProjectView createEmpty() {
+ return projectViewFactory.create(null);
+ }
+
+ /**
+ * Analyzes annotation of the model and put information about invalid
+ * annotations into the {@link Model#creationWarnings} field.
+ *
+ * @param originalModel
+ * model to analyze
+ * @param params
+ * parameters used for model generation
+ */
+ protected void analyzeAnnotations(final Model originalModel, final CreateProjectParams params) {
+ logger.debug("Analyze annotations");
+ Collection<? extends ProblematicAnnotation> improperAnnotations = modelAnnotator
+ .findImproperAnnotations(originalModel, new IProgressUpdater() {
+
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.VALIDATING_MIRIAM, progress, params);
+ }
+ }, params.getValidAnnotations());
+ List<String> res = new ArrayList<>();
+ for (ProblematicAnnotation improperAnnotation : improperAnnotations) {
+ res.add(improperAnnotation.toString());
+ }
+ Collections.sort(res);
+
+ Collection<? extends ProblematicAnnotation> missingAnnotations = modelAnnotator
+ .findMissingAnnotations(originalModel, params.getRequiredAnnotations());
+ for (ProblematicAnnotation improperAnnotation : missingAnnotations) {
+ res.add(improperAnnotation.toString());
+ }
+ for (String message : res) {
+ logger.warn(message);
+ }
+ logger.debug("Analyze finished");
+ }
+
+ /**
+ * Sends notification email that map was removed.
+ *
+ * @param projectId
+ * identifier of the project
+ * @param email
+ * otification email
+ * @throws MessagingException
+ * thrown when there is a problem with sending email
+ */
+ protected void sendSuccesfullRemoveEmail(String projectId, String email) throws MessagingException {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("Map " + projectId + " was successfully removed.<br/>");
+ emailSender.sendEmail("MapViewer notification", content.toString(), email);
+ }
+
+ @Override
+ public TreeNode createClassAnnotatorTree(User user) {
+
+ UserAnnotationSchema annotationSchema = prepareUserAnnotationSchema(user);
+
+ ElementUtils elementUtils = new ElementUtils();
+
+ ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+
+ Class<?> clazz = top.getClazz();
+ TreeNode root = new DefaultTreeNode(new AnnotatedObjectTreeRow(top, modelAnnotator.getAvailableAnnotators(clazz),
+ modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
+ annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz)), null);
+
+ root.setExpanded(true);
+
+ Queue<Pair<ClassTreeNode, TreeNode>> nodes = new LinkedList<Pair<ClassTreeNode, TreeNode>>();
+ nodes.add(new Pair<ClassTreeNode, TreeNode>(top, root));
+ // create children
+
+ Queue<TreeNode> expandParents = new LinkedList<TreeNode>();
+
+ while (!nodes.isEmpty()) {
+ Pair<ClassTreeNode, TreeNode> element = nodes.poll();
+
+ for (ClassTreeNode node : element.getLeft().getChildren()) {
+
+ clazz = node.getClazz();
+ AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(node, modelAnnotator.getAvailableAnnotators(clazz),
+ modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
+ annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz));
+ TreeNode treeNode = new DefaultTreeNode(data, element.getRight());
+ nodes.add(new Pair<ClassTreeNode, TreeNode>(node, treeNode));
+ if (data.getUsedAnnotators().size() > 0 || data.getValidAnnotators().size() > 0) {
+ expandParents.add(treeNode);
+ }
+ }
+ }
+ while (!expandParents.isEmpty()) {
+ TreeNode node = expandParents.poll();
+ if (node.getParent() != null && !node.getParent().isExpanded()) {
+ node.getParent().setExpanded(true);
+ expandParents.add(node.getParent());
+ }
+ }
+
+ return root;
+
+ }
+
+ /**
+ * Retrieves (or creates) annotation schema for a given user.
+ *
+ * @param user
+ * for this users {@link UserAnnotationSchema} will be prepared
+ * @return {@link UserAnnotationSchema} for {@link User}
+ */
+ public UserAnnotationSchema prepareUserAnnotationSchema(User user) {
+ UserAnnotationSchema annotationSchema = null;
+ if (user != null) {
+ annotationSchema = userDao.getById(user.getId()).getAnnotationSchema();
+ }
+ if (annotationSchema == null) {
+ annotationSchema = new UserAnnotationSchema();
+
+ ElementUtils elementUtils = new ElementUtils();
+
+ ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+
+ Map<Class<? extends BioEntity>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
+
+ Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
+ nodes.add(top);
+
+ while (!nodes.isEmpty()) {
+ ClassTreeNode element = nodes.poll();
+ annotationSchema.addClassAnnotator(new UserClassAnnotators(element.getClazz(),
+ modelAnnotator.getAvailableDefaultAnnotatorNames(element.getClazz())));
+ annotationSchema.addClassValidAnnotations(
+ new UserClassValidAnnotations(element.getClazz(), validMiriam.get(element.getClazz())));
+ annotationSchema.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(element.getClazz(), requiredMiriam.get(element.getClazz())));
+ for (ClassTreeNode node : element.getChildren()) {
+ nodes.add(node);
+ }
+ }
+ User dbUser = userDao.getById(user.getId());
+ dbUser.setAnnotationSchema(annotationSchema);
+ userDao.update(dbUser);
+ }
+ return annotationSchema;
+ }
+
+ @Override
+ public void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat,
+ boolean networkLayoutAsDefault) {
+ User dbUser = userDao.getById(user.getId());
+ if (dbUser.getAnnotationSchema() == null) {
+ dbUser.setAnnotationSchema(new UserAnnotationSchema());
+ }
+ UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
+
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+ for (TreeNode child : node.getChildren()) {
+ queue.add(child);
+ }
+ AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) node.getData();
+ annotationSchema.addClassAnnotator(new UserClassAnnotators(data.getClazz(), data.getUsedAnnotators()));
+ annotationSchema.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(data.getClazz(), data.getRequiredAnnotations()));
+ annotationSchema
+ .addClassValidAnnotations(new UserClassValidAnnotations(data.getClazz(), data.getValidAnnotations()));
+ }
+ annotationSchema.setSbgnFormat(sbgnFormat);
+ annotationSchema.setNetworkLayoutAsDefault(networkLayoutAsDefault);
+ userService.updateUser(dbUser);
+ user.setAnnotationSchema(annotationSchema);
+ }
+
+ /**
+ * Sends email about unsuccessfull project creation.
+ *
+ * @param projectName
+ * name of the project
+ * @param email
+ * email where we want to send information
+ * @param e
+ * exception that caused problem
+ */
+ private void sendUnsuccesfullEmail(String projectName, String email, Exception e) {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("");
+ content.append("There was a problem with generating " + projectName + " map.<br/>");
+ content.append(e.getClass().getName() + ": " + e.getMessage());
+ try {
+ emailSender.sendEmail("MapViewer notification", content.toString(), email);
+ } catch (MessagingException e1) {
+ logger.error(e1);
+ }
+ }
+
+ /**
+ * Sends email about successfull project creation.
+ *
+ * @param originalModel
+ * model that was created
+ * @throws MessagingException
+ * exception thrown when there is a problem with sending email
+ */
+ protected void sendSuccesfullEmail(Model originalModel) throws MessagingException {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("Your map was generated successfully.<br/>");
+ emailSender.sendEmail("MapViewer notification", content.toString(), originalModel.getProject().getNotifyEmail());
+ }
+
+ @Override
+ public void updateProject(Project project) {
+ projectDao.update(project);
+ }
+
+ /**
+ * This method handles situation when sever db error appeard during uploading of
+ * the project into database.
+ *
+ * @param params
+ * parameters used to create project
+ * @param e
+ * exception that occured during uploading of the project
+ */
+ private void handleHibernateExceptionReporting(CreateProjectParams params, HibernateException e) {
+ // we need to open separate thread because current one thrown db exception
+ // and transaction is corrupetd and will be rolledback
+ Thread reportInSeparateThread = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ dbUtils.createSessionForCurrentThread();
+
+ try {
+ Project project = getProjectByProjectId(params.getProjectId(), params.getAuthenticationToken());
+ String errorMessage = "Problem with uploading to database. "
+ + "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n"
+ + e.getMessage() + "\nMore information can be found in log file.";
+ project.setErrors(errorMessage);
+ project.setStatus(ProjectStatus.FAIL);
+ projectDao.update(project);
+ } catch (Exception e) {
+ logger.error(e, e);
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ });
+ reportInSeparateThread.start();
+
+ }
+
+ @Override
+ public byte[] getInputDataForProject(ProjectView projectView) {
+ return getInputDataForProject(projectView.getIdObject());
+ }
+
+ /**
+ * Returns byte array containing data from original input file that was used to
+ * create this project.
+ *
+ * @param projectId
+ * identifier of project for which we want to retrieve original file
+ * data
+ * @return original data file for given layout, if such file is not stored in
+ * database (compatibility reasons) then null is returned
+ */
+ private byte[] getInputDataForProject(int projectId) {
+ Project project = projectDao.getById(projectId);
+ if (project == null || project.getInputData() == null) {
+ return null;
+ } else {
+ return project.getInputData().getFileContent();
+ }
+ }
+
+ /**
+ * Method that handles exception reporting during creation of a project.
+ *
+ * @param params
+ * set of parameters used to create project
+ * @param e
+ * exception that caused problems
+ */
+ private void handleCreateProjectException(final CreateProjectParams params, Exception e) {
+ Project p = projectDao.getProjectByProjectId(params.getProjectId());
+ logger.error(e.getMessage(), e);
+ if (p != null) {
+ p.setErrors("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
+ }
+ updateProjectStatus(p, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
+
+ String email = params.getNotifyEmail();
+ String projectName = params.getProjectId();
+
+ LogParams logParams = new LogParams().description("Failed: " + e.getMessage()).type(LogType.MAP_CREATED).object(p);
+ logService.log(logParams);
+ if (email != null) {
+ sendUnsuccesfullEmail(projectName, email, e);
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
}
--
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