From d0e6a01dfd542c5e1f5bfe4870b96dbc8d54aebb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 21 Dec 2018 09:32:25 +0100
Subject: [PATCH] data overlay upload process color schema type properly
---
.../lcsb/mapviewer/common/TextFileUtils.java | 84 ++++-----
.../model/map/layout/ColorSchemaType.java | 19 ++
.../mapviewer/model/map/layout/Layout.java | 15 ++
....20181221__overlay_type_property_added.sql | 1 +
.../configuration/ConfigurationRestImpl.java | 4 +-
.../api/projects/models/ModelRestImpl.java | 4 +-
.../projects/overlays/OverlayController.java | 33 ++--
.../projects/overlays/OverlayRestImpl.java | 2 +-
.../overlays/OverlayRestImplTest.java | 2 +-
.../services/impl/LayoutService.java | 173 +++++++++---------
.../services/interfaces/ILayoutService.java | 2 +-
.../services/utils/ColorSchemaReader.java | 31 +++-
.../utils/data/ColorSchemaColumn.java | 1 +
.../services/utils/data/ColorSchemaType.java | 21 ---
.../services/impl/LayoutServiceTest.java | 29 ++-
.../coloring/gene_variants_without_type.txt | 4 +
16 files changed, 243 insertions(+), 182 deletions(-)
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchemaType.java
create mode 100644 persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181221__overlay_type_property_added.sql
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java
create mode 100644 service/testFiles/coloring/gene_variants_without_type.txt
diff --git a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
index 824ae83c93..3f0b8226e2 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
@@ -15,50 +15,50 @@ import java.util.Map;
*/
public final class TextFileUtils {
- /**
- * Name of the param that contains number of columns.
- */
- public static final String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
+ /**
+ * Name of the param that contains number of columns.
+ */
+ public static final String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
- /**
- * Default constructor that prevents instatiation.
- */
- private TextFileUtils() {
+ /**
+ * Default constructor that prevents instatiation.
+ */
+ private TextFileUtils() {
- }
+ }
- /**
- * Parses input stream to get parameters from header. {@link InputStream}
- * should be a text file. Header parameters are lines at the beginning of the
- * file starting with '#' character.
- *
- * @param is
- * input stream for a file to process
- * @return map with paramteres parsed from input stream
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
- Map<String, String> result = new HashMap<String, String>();
- BufferedReader in = new BufferedReader(new InputStreamReader(is));
- String line = null;
- while ((line = in.readLine()) != null) {
- if (line.startsWith("#")) {
- String tmp = line.substring(1);
- if (tmp.indexOf("=") > 0) {
- String key = tmp.substring(0, tmp.indexOf("=")).trim();
- String value = tmp.substring(tmp.indexOf("=") + 1).trim();
- result.put(key, value);
- }
- } else {
- String key = COLUMN_COUNT_PARAM;
- String value = line.split("\t").length + "";
- result.put(key, value);
- break;
- }
- }
- is.close();
- return result;
- }
+ /**
+ * Parses input stream to get parameters from header. {@link InputStream} should
+ * be a text file. Header parameters are lines at the beginning of the file
+ * starting with '#' character.
+ *
+ * @param is
+ * input stream for a file to process
+ * @return map with parameters parsed from input stream
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
+ Map<String, String> result = new HashMap<>();
+ BufferedReader in = new BufferedReader(new InputStreamReader(is));
+ String line = null;
+ while ((line = in.readLine()) != null) {
+ if (line.startsWith("#")) {
+ String tmp = line.substring(1);
+ if (tmp.indexOf("=") > 0) {
+ String key = tmp.substring(0, tmp.indexOf("=")).trim();
+ String value = tmp.substring(tmp.indexOf("=") + 1).trim();
+ result.put(key, value);
+ }
+ } else {
+ String key = COLUMN_COUNT_PARAM;
+ String value = line.split("\t").length + "";
+ result.put(key, value);
+ break;
+ }
+ }
+ is.close();
+ return result;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchemaType.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchemaType.java
new file mode 100644
index 0000000000..1c0072a4ed
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchemaType.java
@@ -0,0 +1,19 @@
+package lcsb.mapviewer.model.map.layout;
+
+/**
+ * Type of the {@link ColorSchema}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ColorSchemaType {
+ /**
+ * Generic color schema (used for expression levels, etc).
+ */
+ GENERIC,
+
+ /**
+ * Customized color schema used for highlighting genetic variants.
+ */
+ GENETIC_VARIANT
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
index 6e51b69dc6..4e3537e542 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
@@ -91,6 +91,13 @@ public class Layout implements Serializable {
private boolean googleLicenseConsent = false;
+ /**
+ * Data overlay type. It can be null in such case it should be obtained from
+ * {@link #inputData}.
+ */
+ @Enumerated(EnumType.STRING)
+ private ColorSchemaType colorSchemaType = null;
+
/**
* If overlay contain hierarchical view then it might be fixed on some specific
* level. This parameter defines the level at which it's fixed or contains null
@@ -421,4 +428,12 @@ public class Layout implements Serializable {
this.dataOverlayImageLayers = dataOverlayImageLayers;
}
+ public ColorSchemaType getColorSchemaType() {
+ return colorSchemaType;
+ }
+
+ public void setColorSchemaType(ColorSchemaType colorSchemaType) {
+ this.colorSchemaType = colorSchemaType;
+ }
+
}
diff --git a/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181221__overlay_type_property_added.sql b/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181221__overlay_type_property_added.sql
new file mode 100644
index 0000000000..dcf1b3feb5
--- /dev/null
+++ b/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181221__overlay_type_property_added.sql
@@ -0,0 +1 @@
+alter table layout_table add column color_schema_type character varying(255);
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index ade1476684..3030964b4d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.api.configuration;
-import java.io.File;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
@@ -28,6 +26,7 @@ import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.model.graphics.MapCanvasType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -39,7 +38,6 @@ import lcsb.mapviewer.modelutils.map.ClassTreeNode;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
@Transactional
@Service
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index e89cc3a92b..98534da8ff 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -238,7 +238,7 @@ public class ModelRestImpl extends BaseRestImpl {
Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(), overlay.getColorSchemaType());
new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
}
@@ -328,7 +328,7 @@ public class ModelRestImpl extends BaseRestImpl {
if (overlay != null) {
if (overlay.getInputData() != null) {
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(), overlay.getColorSchemaType());
new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
} else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index 6fc3eeb591..39de15b080 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
@@ -43,8 +43,8 @@ public class OverlayController extends BaseController {
@CookieValue(value = Configuration.AUTH_TOKEN) String token,
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "creator", defaultValue = "") String creator,
- @RequestParam(value = "publicOverlay", defaultValue = "") String publicOverlay
- ) throws SecurityException, QueryException {
+ @RequestParam(value = "publicOverlay", defaultValue = "") String publicOverlay)
+ throws SecurityException, QueryException {
return overlayRestImp.getOverlayList(token, projectId, creator, publicOverlay);
}
@@ -53,8 +53,7 @@ public class OverlayController extends BaseController {
public Map<String, Object> getOverlayById(
@CookieValue(value = Configuration.AUTH_TOKEN) String token,
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "overlayId") String overlayId
- ) throws SecurityException, QueryException {
+ @PathVariable(value = "overlayId") String overlayId) throws SecurityException, QueryException {
return overlayRestImp.getOverlayById(token, projectId, overlayId);
}
@@ -76,8 +75,7 @@ public class OverlayController extends BaseController {
@PathVariable(value = "modelId") String modelId,
@PathVariable(value = "overlayId") String overlayId,
@PathVariable(value = "reactionId") String reactionId,
- @RequestParam(value = "columns", defaultValue = "") String columns
- ) throws SecurityException, QueryException {
+ @RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
Integer.valueOf(reactionId), "REACTION", columns);
}
@@ -90,8 +88,7 @@ public class OverlayController extends BaseController {
@PathVariable(value = "modelId") String modelId,
@PathVariable(value = "overlayId") String overlayId,
@PathVariable(value = "elementId") String reactionId,
- @RequestParam(value = "columns", defaultValue = "") String columns
- ) throws SecurityException, QueryException {
+ @RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
Integer.valueOf(reactionId), "ALIAS", columns);
}
@@ -106,10 +103,11 @@ public class OverlayController extends BaseController {
@RequestParam(value = "content", defaultValue = "") String content,
@RequestParam(value = "fileId", defaultValue = "") String fileId,
@RequestParam(value = "filename") String filename,
- @RequestParam(value = "googleLicenseConsent") String googleLicenseConsent,
- @RequestParam(value = "type", defaultValue = "") String type
- ) throws SecurityException, QueryException, IOException {
- return overlayRestImp.addOverlay(token, projectId, name, description, content, fileId, filename, type, googleLicenseConsent);
+ @RequestParam(value = "googleLicenseConsent") String googleLicenseConsent,
+ @RequestParam(value = "type", defaultValue = "") String type)
+ throws SecurityException, QueryException, IOException {
+ return overlayRestImp.addOverlay(token, projectId, name, description, content, fileId, filename, type,
+ googleLicenseConsent);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = {
@@ -117,8 +115,7 @@ public class OverlayController extends BaseController {
public Map<String, Object> removeOverlay(
@CookieValue(value = Configuration.AUTH_TOKEN) String token,
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "overlayId") String overlayId
- ) throws SecurityException, QueryException, IOException {
+ @PathVariable(value = "overlayId") String overlayId) throws SecurityException, QueryException, IOException {
return overlayRestImp.removeOverlay(token, projectId, overlayId);
}
@@ -128,8 +125,8 @@ public class OverlayController extends BaseController {
@RequestBody String body,
@PathVariable(value = "projectId") String projectId,
@PathVariable(value = "overlayId") String overlayId,
- @CookieValue(value = Configuration.AUTH_TOKEN) String token
- ) throws SecurityException, QueryException, IOException {
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token)
+ throws SecurityException, QueryException, IOException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "overlay");
return overlayRestImp.updateOverlay(token, projectId, overlayId, data);
@@ -140,8 +137,8 @@ public class OverlayController extends BaseController {
public ResponseEntity<byte[]> getOverlaySource(
@CookieValue(value = Configuration.AUTH_TOKEN) String token,
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "overlayId") String overlayId
- ) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
+ @PathVariable(value = "overlayId") String overlayId)
+ throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
FileEntry file = overlayRestImp.getOverlaySource(token, projectId, overlayId);
MediaType type = MediaType.TEXT_PLAIN;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index 000bbc3e3f..88c1282aa5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -28,6 +28,7 @@ import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.DataOverlayImageLayer;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
@@ -42,7 +43,6 @@ import lcsb.mapviewer.persist.dao.map.LayoutDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
@Transactional
@Service
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java
index 51eef85b9c..7c940c37e3 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java
@@ -11,10 +11,10 @@ import com.google.gson.Gson;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
public class OverlayRestImplTest extends RestTestFunctions {
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 b2d15f2747..54713f147b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -29,6 +29,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.BioEntity;
@@ -392,11 +393,14 @@ public class LayoutService implements ILayoutService {
return topLayout;
}
- @Override
- public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
- TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+ @Override
+ public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
+ if (params.getColorSchemaType() != null) {
+ parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, params.getColorSchemaType().name());
+ }
+ final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(), parameters);
// check if we can color our model using this schema,
// if not then exception will be thrown and passed up
@@ -411,6 +415,7 @@ public class LayoutService implements ILayoutService {
layoutDao.flush();
Layout topLayout = new Layout(params.getName(), false);
+ topLayout.setColorSchemaType(params.getColorSchemaType());
if (params.getUser() == null) {
topLayout.setPublicLayout(true);
} else {
@@ -792,71 +797,76 @@ public class LayoutService implements ILayoutService {
}
}
- @Override
- public List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId, String token)
- throws SecurityException {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
- List<Pair<Element, ColorSchema>> result = new ArrayList<>();
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Element) {
- result.add(new Pair<Element, ColorSchema>((Element) entry.getKey(), entry.getValue()));
- }
- }
- result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
- return result;
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
+ @Override
+ public List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId, String token)
+ throws SecurityException {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId, token);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ List<Pair<Element, ColorSchema>> result = new ArrayList<>();
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Element) {
+ result.add(new Pair<Element, ColorSchema>((Element) entry.getKey(), entry.getValue()));
}
+ }
+ result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
+ return result;
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
}
+ }
- @Override
- public List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId, String token)
- throws SecurityException {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
- List<Pair<Reaction, ColorSchema>> result = new ArrayList<>();
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Reaction) {
- result.add(new Pair<Reaction, ColorSchema>((Reaction) entry.getKey(), entry.getValue()));
- }
- }
- result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
- return result;
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
+ private Collection<ColorSchema> createColorSchemaCollection(int overlayId, String token)
+ throws IOException, InvalidColorSchemaException, SecurityException {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Layout overlay = getLayoutById(overlayId, token);
+ Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(overlayId, token),
+ overlay.getColorSchemaType());
+ return schemas;
+ }
+
+ @Override
+ public List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId, String token)
+ throws SecurityException {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId, token);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ List<Pair<Reaction, ColorSchema>> result = new ArrayList<>();
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Reaction) {
+ result.add(new Pair<Reaction, ColorSchema>((Reaction) entry.getKey(), entry.getValue()));
}
+ }
+ result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
+ return result;
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
}
+ }
- @Override
- public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token)
- throws SecurityException {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
- return command.getModifiedElements();
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
- }
+ @Override
+ public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token)
+ throws SecurityException {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId, token);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ return command.getModifiedElements();
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
}
+ }
@Override
public EmailSender getEmailSender() {
@@ -902,16 +912,15 @@ public class LayoutService implements ILayoutService {
return layout;
}
- @Override
- public Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
- throws SecurityException {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ @Override
+ public Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException {
+ try {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId, token);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
if (entry.getKey() instanceof Element) {
@@ -929,16 +938,14 @@ public class LayoutService implements ILayoutService {
}
}
- @Override
- public Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId, String token)
- throws SecurityException {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ @Override
+ public Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId, token);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
if (entry.getKey() instanceof Reaction) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index 11f129385e..6901b0297a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -11,6 +11,7 @@ import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
@@ -20,7 +21,6 @@ import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.LayoutDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
/**
* Service that manages layouts of the map.
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 983d3f3b82..9b77d4d774 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -8,7 +8,6 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
@@ -31,6 +30,7 @@ import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.GeneVariation;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -38,7 +38,6 @@ import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
/**
* Class that reads information about set of {@link ColorSchema color schemas}
@@ -726,9 +725,19 @@ public class ColorSchemaReader {
* @throws InvalidColorSchemaException
* thrown when color schema is invalid
*/
- public Collection<ColorSchema> readColorSchema(String filename) throws IOException, InvalidColorSchemaException {
- return readColorSchema(new FileInputStream(filename),
- TextFileUtils.getHeaderParametersFromFile(new FileInputStream(filename)));
+ public Collection<ColorSchema> readColorSchema(String filename, ColorSchemaType colorSchemaType)
+ throws IOException, InvalidColorSchemaException {
+ Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new FileInputStream(filename));
+ if (colorSchemaType != null) {
+ params.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, colorSchemaType.name());
+ }
+
+ return readColorSchema(new FileInputStream(filename), params);
+ }
+
+ Collection<ColorSchema> readColorSchema(String filename)
+ throws IOException, InvalidColorSchemaException {
+ return readColorSchema(filename, null);
}
/**
@@ -740,7 +749,7 @@ public class ColorSchemaReader {
* schemas)
*/
public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
+ Set<ColorSchemaColumn> result = new HashSet<>();
for (ColorSchema schema : schemas) {
if (schema.getColor() != null) {
result.add(ColorSchemaColumn.COLOR);
@@ -788,8 +797,12 @@ public class ColorSchemaReader {
* @throws InvalidColorSchemaException
* thrown when color schema is invalid
*/
- public Collection<ColorSchema> readColorSchema(byte[] inputData) throws IOException, InvalidColorSchemaException {
- return readColorSchema(new ByteArrayInputStream(inputData),
- TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(inputData)));
+ public Collection<ColorSchema> readColorSchema(byte[] inputData, ColorSchemaType colorSchemaType)
+ throws IOException, InvalidColorSchemaException {
+ Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(inputData));
+ if (colorSchemaType != null) {
+ params.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, colorSchemaType.name());
+ }
+ return readColorSchema(new ByteArrayInputStream(inputData), params);
}
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 6e593c9bf2..838eeda5fe 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.services.utils.data;
import java.util.HashSet;
import java.util.Set;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java
deleted file mode 100644
index 108a4ce7b1..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package lcsb.mapviewer.services.utils.data;
-
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-
-/**
- * Type of the {@link ColorSchema}.
- *
- * @author Piotr Gawron
- *
- */
-public enum ColorSchemaType {
- /**
- * Generic color schema (used for expression levels, etc).
- */
- GENERIC,
-
- /**
- * Customized color schema used for highlightig genetic variants.
- */
- GENETIC_VARIANT
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index 30aec7f828..9e2a8022b3 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -13,6 +13,7 @@ import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
+import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
@@ -28,6 +29,8 @@ import lcsb.mapviewer.common.TextFileUtils;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.ColorSchemaType;
import lcsb.mapviewer.model.map.layout.DataOverlayImageLayer;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
@@ -441,7 +444,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
Model model = new CellDesignerXmlParser()
.createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
-
+
project.addModel(model);
projectService.addProject(project);
@@ -497,4 +500,28 @@ public class LayoutServiceTest extends ServiceTestFunctions {
}
+ @Test
+ public void testDataOverlayWithType() throws Exception {
+ try {
+ String layoutId = "Test";
+ userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+ CreateLayoutParams params = new CreateLayoutParams().name(layoutId).
+ directory("testDir").
+ project(project).
+ colorInputStream(new FileInputStream("testFiles/coloring/gene_variants_without_type.txt")).
+ user(user).colorSchemaType(ColorSchemaType.GENETIC_VARIANT);
+
+ Layout layout = layoutService.createLayout(params);
+ Map<Object, ColorSchema> result = layoutService.getElementsForLayout(model, layout.getId(), token);
+ assertNotNull(result);
+ layoutService.removeLayout(layout, null);
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
}
diff --git a/service/testFiles/coloring/gene_variants_without_type.txt b/service/testFiles/coloring/gene_variants_without_type.txt
new file mode 100644
index 0000000000..b58ad1bb26
--- /dev/null
+++ b/service/testFiles/coloring/gene_variants_without_type.txt
@@ -0,0 +1,4 @@
+#GENOME_TYPE=UCSC
+#GENOME_VERSION=hg38
+position original_dna alternative_dna name description color contig
+10146 AC A DDX11L1 upstream #ff0000 chr1
--
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