diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index dcea803793f2182a1ad48fbb4514294dd2839b37..b48c8fb71e8b940730073dff2cfb9f6153aa2a83 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -127,8 +127,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
DOMParser parser = new DOMParser();
try {
parser.parse(params.getSource());
- } catch (IOException e) {
- throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
+ } catch (Exception e) {
+ throw new InvalidInputDataExecption("Problem with a file: " + params.getSource().getSystemId(), e);
}
Document doc = parser.getDocument();
try {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 43df7989f4a4f6afa884b26760c8167c2820e9ba..2d31cd35462e43417b2176a5a8c7fe23341bd178 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -115,9 +115,7 @@ public class ComplexZipConverter {
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 model = converter.createModel(new ConverterParams().inputStream(is, entry.getName()));
model.setName(modelEntryFile.getName());
filenameModelMap.put(entry.getName(), model);
nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()).toLowerCase(), model);
@@ -180,7 +178,7 @@ public class ComplexZipConverter {
return true;
} else if (name.isEmpty()) {
return true;
- } else if (name.startsWith(".DS_Store")) {
+ } else if (name.startsWith(".DS_Store") || name.endsWith(".DS_Store")) {
return true;
} else if (name.startsWith("__MACOSX")) {
return true;
@@ -189,7 +187,7 @@ public class ComplexZipConverter {
}
/**
- * Process a single reaction in mapping file (transfomring reaction into
+ * Process a single reaction in mapping file (transforming reaction into
* connection between submodels).
*
* @param mapping
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
index 20400e0c8010baf9e814cc906724f3fb36f8062f..3eb7ff6424d87a561478fe089e042fd577ab1449 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
@@ -11,114 +11,122 @@ import org.apache.xerces.xni.parser.XMLInputSource;
*
* @author Piotr Gawron
*/
-public class ConverterParams {
- /**
- * Input stream for the parser.
- */
- private InputStream inputStream;
-
- /**
- * Name of the file used as a data input. (not obligatory)
- */
- private String filename;
- /**
- * Should the map be autoresized after parsing or not. Autoresizing will equal
- * right with left margin and top with bottom margin.
- */
- private boolean sizeAutoAdjust = true;
-
- /**
- * Should the map be formated as SBGN.
- */
- private boolean sbgnFormat = false;
-
- /**
- * Set file as input source.
- *
- * @param fileName
- * path to a file that should be parsed.
- * @return object with all set parameters
- * @throws FileNotFoundException
- */
- public ConverterParams filename(String fileName) throws FileNotFoundException {
- inputStream = new FileInputStream(fileName);
- this.filename = fileName;
- return this;
- }
-
- /**
- *
- * Set input stream as input source.
- *
- * @param is
- * input stream that should be parsed
- * @return object with all set parameters
- */
- public ConverterParams inputStream(InputStream is) {
- this.inputStream = is;
- return this;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public XMLInputSource getSource() {
- return new XMLInputSource(null, null, null, this.inputStream, null);
- }
-
- /**
- *
- * @param value
- * the sizeAutoAdjust to set
- * @see #sizeAutoAdjust
- * @return object with all parameters
- */
- public ConverterParams sizeAutoAdjust(boolean value) {
- sizeAutoAdjust = value;
- return this;
- }
-
- /**
- * @return the inputStream
- * @see #inputStream
- */
- public InputStream getInputStream() {
- return this.inputStream;
- }
-
- /**
- * @return the sizeAutoAdjust
- * @see #sizeAutoAdjust
- */
- public boolean isSizeAutoAdjust() {
- return sizeAutoAdjust;
- }
-
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return filename;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat the sbgnFormat to set
- * @return ConverterParams object with all parameters
- * @see #sbgnFormat
- */
- public ConverterParams sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- return this;
- }
+public class ConverterParams {
+ /**
+ * Input stream for the parser.
+ */
+ private InputStream inputStream;
+
+ /**
+ * Name of the file used as a data input. (not obligatory)
+ */
+ private String filename;
+ /**
+ * Should the map be autoresized after parsing or not. Autoresizing will equal
+ * right with left margin and top with bottom margin.
+ */
+ private boolean sizeAutoAdjust = true;
+
+ /**
+ * Should the map be formated as SBGN.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * Set file as input source.
+ *
+ * @param fileName
+ * path to a file that should be parsed.
+ * @return object with all set parameters
+ * @throws FileNotFoundException
+ */
+ public ConverterParams filename(String fileName) throws FileNotFoundException {
+ inputStream = new FileInputStream(fileName);
+ this.filename = fileName;
+ return this;
+ }
+
+ /**
+ *
+ * Set input stream as input source.
+ *
+ * @param is
+ * input stream that should be parsed
+ * @return object with all set parameters
+ */
+ public ConverterParams inputStream(InputStream is) {
+ return this.inputStream(is, null);
+ }
+
+ public ConverterParams inputStream(InputStream is, String filename) {
+ this.inputStream = is;
+ if (filename != null) {
+ this.filename = filename;
+ }
+ return this;
+ }
+
+ /**
+ * @return the source
+ * @see #source
+ */
+ public XMLInputSource getSource() {
+ return new XMLInputSource(null, this.filename, null, this.inputStream, null);
+ }
+
+ /**
+ *
+ * @param value
+ * the sizeAutoAdjust to set
+ * @see #sizeAutoAdjust
+ * @return object with all parameters
+ */
+ public ConverterParams sizeAutoAdjust(boolean value) {
+ sizeAutoAdjust = value;
+ return this;
+ }
+
+ /**
+ * @return the inputStream
+ * @see #inputStream
+ */
+ public InputStream getInputStream() {
+ return this.inputStream;
+ }
+
+ /**
+ * @return the sizeAutoAdjust
+ * @see #sizeAutoAdjust
+ */
+ public boolean isSizeAutoAdjust() {
+ return sizeAutoAdjust;
+ }
+
+ /**
+ * @return the filename
+ * @see #filename
+ */
+ public String getFilename() {
+ return filename;
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @return ConverterParams object with all parameters
+ * @see #sbgnFormat
+ */
+ public ConverterParams sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ return this;
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
index f1e0095ad6ce099c86fbc1ca9f1dc774032a9719..21cb52fd18a194468b10bbfd9c943110299d54fc 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
@@ -18,11 +18,11 @@ import lcsb.mapviewer.model.map.model.Model;
public interface IConverter {
/**
- * Parse input source and transformes it into a model object.
+ * Parse input source and transforms it into a model object.
*
* @param params
* input params used for reading data
- * @return model obtained from inut source
+ * @return model obtained from input source
* @throws InvalidInputDataExecption
* thrown when input parameters are invalid
*/
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index b57e65f20ba639aacf7037da8b2a32e01f239c46..5b2ffadb63d79afbe80ce87dd6fea06cc1c587c4 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -504,6 +504,10 @@ public class ComplexZipConverterTest {
try {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertTrue(converter.isIgnoredFile("__MACOSX/.desc"));
+ assertTrue(converter.isIgnoredFile(".DS_Store"));
+ assertTrue(converter.isIgnoredFile("images/.DS_Store"));
+ assertTrue(converter.isIgnoredFile("layouts/.DS_Store"));
+ assertTrue(converter.isIgnoredFile("submaps/.DS_Store"));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 85621deee6444c15c125e59854c7b6914daebea9..089c8cdb4f963b12c8ca151be05a8ebe9127dbe7 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -1295,7 +1295,9 @@ AddProjectDialog.prototype.createZipEntry = function (jsZipEntry, zipObject) {
var type;
var data = {};
var processingPromise = Promise.resolve();
- if (filename.indexOf("submaps") === 0) {
+ if (this.isIgnoredZipEntry(filename)) {
+ type = undefined;
+ } else if (filename.indexOf("submaps") === 0) {
type = "MAP";
if (filename.endsWith("mapping.xml")) {
data.mapping = true;
@@ -1318,8 +1320,6 @@ AddProjectDialog.prototype.createZipEntry = function (jsZipEntry, zipObject) {
data.description = "";
}
});
- } else if (this.isIgnoredZipEntry(filename)) {
- type = undefined;
} else if (filename.indexOf("\\") === -1 && filename.indexOf("/") === -1) {
type = "MAP";
data.root = true;
@@ -1392,7 +1392,7 @@ AddProjectDialog.prototype.isIgnoredZipEntry = function (filename) {
// noinspection SpellCheckingInspection
if (lowercaseString.indexOf("__macosx") === 0) {
return true;
- } else if (lowercaseString.indexOf(".ds_store") === 0) {
+ } else if (lowercaseString.indexOf(".ds_store") === 0 || lowercaseString.endsWith(".ds_store")) {
return true;
}
return false;
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 a83943d8057db13e978ca78523d1d612fd0342cd..65a5fcdffd86b1e16f2602fc7742bcf3f69960c6 100644
--- a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
@@ -258,6 +258,7 @@ describe('AddProjectDialog', function () {
assert.ok(dialog.isIgnoredZipEntry(".DS_Store/.desc"));
assert.ok(dialog.isIgnoredZipEntry(".ds_store/.desc"));
+ assert.ok(dialog.isIgnoredZipEntry("images/.ds_store"));
return dialog.destroy();
});
});