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Commit e984455a authored by David Hoksza's avatar David Hoksza
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functional and tested api

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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!418Formats conversion rest api
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README.md
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......@@ -481,6 +481,55 @@ curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/mine
curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/minerva/api/users/testAdmin
```
### Conversion
Conversion API provides access to MINERVA's ability convert between different systems biology
network formats and to export of layouts to different graphical formats.
* Conversion to systems biology formats
* List available formats
* URL: `/convert/`
* Method: GET or POST
* Example:
* Output: List of input and output format identifiers which can be used as values for the `sourceFormat` and `targetFormat` parameters in other convert API calls
```
curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/minerva/api/convert/
```
* Convert network from an input format to an output format
* URL: `/convert/{sourceFromat}:{tagetFormat}/`
* Method: POST
* Parameters:
* `sourceFromat` - input format (list of available formats be obtained from the `/convert/` API)
* `tagetFormat` - input format (list of available formats be obtained from the `/convert/` API)
* Body: the input file to be converted
* Example:
```
curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" --data @cell_designer.xml -H "Content-Type: text/plain" http://pg-sandbox.uni.lu/minerva/api/convert/CellDesigner_SBML:SBML
```
* Conversion to image
* List available formats
* URL: `/convert/image/`
* Method: GET or POST
* Output: List of input and output format identifiers which can be used as values for the `sourceFormat` and `targetFormat` parameters in other convert API calls
* Example:
```
curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/minerva/api/convert/image/
```
* Convert network from an input format to an output image
* URL: `/convert/image/{sourceFromat}:{tagetFormat}/`
* Method: POST
* Parameters:
* `sourceFromat` - input format (list of available formats be obtained from the `/convert/image/` API)
* `tagetFormat` - input format (list of available formats be obtained from the `/convert/image/` API)
* Body: the input file to be converted
* Example:
```
curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" --data @cell_designer.xml -H "Content-Type: text/plain" http://pg-sandbox.uni.lu/minerva/api/convert/image/CellDesigner_SBML:SVG
```
# JavaScript API. Unstable dev API.
Minerva visualization is created by including `minerva.js` and calling `minerva.create({element:divElement})` method. This method returns a Promise which will resolve to the object that allows custom JS manipulation.
......
rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
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......@@ -320,21 +320,8 @@ public abstract class BaseRestImpl {
*/
public void setProjectService(IProjectService projectService) {
this.projectService = projectService;
}
private String removeWhiteSpaces(String str) {
return str.replace(' ', '_');
}
}
protected IConverter getModelParserByName(String name) throws QueryException {
for (IConverter converter : getModelConverters()) {
if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
return converter;
}
}
throw new QueryException("Unknown parser name: " + name);
}
protected IConverter getModelParser(String handlerClass) throws QueryException {
for (IConverter converter : getModelConverters()) {
if (converter.getClass().getCanonicalName().equals(handlerClass)) {
......
rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
+ 21
− 1
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......@@ -2,6 +2,7 @@ package lcsb.mapviewer.api.convert;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
......@@ -19,6 +20,7 @@ import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.bind.annotation.RestController;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterException;
......@@ -53,7 +55,7 @@ public class ConvertController extends BaseController {
}
@RequestMapping(value = "/convert/{fromFormat}:{toFormat}:img",
@RequestMapping(value = "/convert/image/{fromFormat}:{toFormat}",
method = { RequestMethod.POST })
public @ResponseBody ResponseEntity<byte[]> convertInputToImage(//
@PathVariable(value = "fromFormat") String fromFormat, //
......@@ -73,4 +75,22 @@ public class ConvertController extends BaseController {
.body(os.toByteArray());
}
@RequestMapping(value = "/convert/", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getInformation(
@CookieValue(value = Configuration.AUTH_TOKEN) String token //
) throws SecurityException, ObjectNotFoundException
{
return convertController.getInformation(token);
}
@RequestMapping(value = "/convert/image/", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getInformationImage(
@CookieValue(value = Configuration.AUTH_TOKEN) String token //
) throws SecurityException, ObjectNotFoundException
{
return convertController.getInformationImage(token);
}
}
\ No newline at end of file
rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
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− 5
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......@@ -6,6 +6,10 @@ import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
......@@ -61,6 +65,48 @@ public class ConvertRestImpl extends BaseRestImpl {
return os;
}
public Map<String, Object> getInformation(String token){
Map<String, Object> info = new LinkedHashMap<>();
List<Object> converters = new ArrayList<>();
for (IConverter converter: getModelConverters()) {
List<String> names = new ArrayList<>();
names.add(removeWhiteSpaces(converter.getCommonName()));
names.add(converter.getClass().getCanonicalName());
Map<String, Object> names_item = new LinkedHashMap<>();
names_item.put("available_names", names);
converters.add(names_item);
}
info.put("inputs", converters);
info.put("outputs", converters);
return info;
}
public Map<String, Object> getInformationImage(String token){
Map<String, Object> info = getInformation(token);
List<Object> generators = new ArrayList<>();
ImageGenerators igs = new ImageGenerators();
for (Pair<String, Class<? extends AbstractImageGenerator>> generator: igs.getAvailableImageGenerators()) {
List<String> names = new ArrayList<>();
names.add(igs.getExtension(generator.getRight()));
names.add(generator.getRight().getCanonicalName());
Map<String, Object> names_item = new LinkedHashMap<>();
names_item.put("available_names", names);
generators.add(names_item);
}
info.remove("outputs");
info.put("outputs", generators);
return info;
}
private IConverter getModelParserByNameOrClass(String id) throws QueryException {
try {
return getModelParserByName(id);
......@@ -69,25 +115,40 @@ public class ConvertRestImpl extends BaseRestImpl {
}
}
private AbstractImageGenerator getImageGenerator(String extension, AbstractImageGenerator.Params params) throws QueryException{
private String removeWhiteSpaces(String str) {
return str.replace(' ', '_');
}
private IConverter getModelParserByName(String name) throws QueryException {
for (IConverter converter : getModelConverters()) {
if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
return converter;
}
}
throw new QueryException("Unknown parser name: " + name);
}
private AbstractImageGenerator getImageGenerator(String extOrClass, AbstractImageGenerator.Params params) throws QueryException
{
for (Pair<String, Class<? extends AbstractImageGenerator>> element : new ImageGenerators().getAvailableImageGenerators()) {
try {
Constructor<?> ctor = element.getRight().getConstructor(AbstractImageGenerator.Params.class);
Class<? extends AbstractImageGenerator> clazz = element.getRight();
Constructor<?> ctor = clazz.getConstructor(AbstractImageGenerator.Params.class);
AbstractImageGenerator generator = (AbstractImageGenerator) ctor.newInstance(params);
if (extension.equals(generator.getFileExtension())) {
if (extOrClass.equals(clazz.getCanonicalName()) || extOrClass.equals(generator.getFileExtension())) {
return generator;
}
} catch (NoSuchMethodException | java.lang.SecurityException | InstantiationException
| IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
logger.error("Creation of image generator class for '" + element.getLeft() + "' failed.");
throw new QueryException("Issue with obtaining image generator for extension " + extension + ".");
throw new QueryException("Issue with obtaining image generator for extension " + extOrClass + ".");
}
}
throw new QueryException("Image generator for extension " + extension + " not available.");
throw new QueryException("Image generator for extension " + extOrClass + " not available.");
}
private AbstractImageGenerator.Params createImageParams(Model model){
......
rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
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package lcsb.mapviewer.api.convert;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
......@@ -11,9 +17,17 @@ import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.sbml.jsbml.SBMLException;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.services.SecurityException;
public class ConvertRestImplTest extends RestTestFunctions {
......@@ -34,50 +48,192 @@ public class ConvertRestImplTest extends RestTestFunctions {
@After
public void tearDown() throws Exception {
}
@SuppressWarnings("unchecked")
@Test
public void testGetInformation() throws Exception {
try {
Map<String, Object> result = convertRestImpl.getInformationImage(token);
assertTrue(result.keySet().size() == 2);
assertNotNull(result.get("inputs"));
assertNotNull(result.get("outputs"));
List<Object> inputs = (List<Object>) result.get("inputs");
List<Object> outputs = (List<Object>) result.get("outputs");
assertTrue(inputs.size() > 0);
assertTrue(outputs.size() > 0);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@SuppressWarnings("unchecked")
@Test
public void testGetInformationImage() throws Exception {
try {
Map<String, Object> result = convertRestImpl.getInformationImage(token);
assertTrue(result.keySet().size() == 2);
assertNotNull(result.get("inputs"));
assertNotNull(result.get("outputs"));
List<Object> inputs = (List<Object>) result.get("inputs");
List<Object> outputs = (List<Object>) result.get("outputs");
assertTrue(inputs.size() > 0);
assertTrue(outputs.size() > 0);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testCelDesigner2Sbml() throws Exception {
public void testCelDesigner2Sbml1() throws Exception {
try {
File file = new File("testFiles/convert/sample-cd.xml");
String content = FileUtils.readFileToString(file);
String result = convertRestImpl.convert(token, "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
"lcsb.mapviewer.converter.model.sbml.SbmlParser", content);
System.out.print(result);
assertTrue(result.length() > 0);
assertTrue(result.contains("</layout:speciesReferenceGlyph>"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
/*
* this test does not work because the generator is not deterministic
@Test
public void testCelDesigner2Sbml2() throws Exception {
try {
File file = new File("testFiles/convert/sample-cd.xml");
String content = FileUtils.readFileToString(file);
String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
//String result2 = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
String result2 = convertRestImpl.convert(token, "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
"lcsb.mapviewer.converter.model.sbml.SbmlParser", content);
assertTrue(result.equals(result2));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
*/
@Test
public void testCelDesigner2Svg() throws Exception {
try {
File file = new File("testFiles/convert/sample-cd.xml");
String content = FileUtils.readFileToString(file);
String result = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content).toString();
assertTrue(result.contains("<rect"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
/*
* this test does not work because the generator is not deterministic
@Test
public void testCelDesigner2Svg2() throws Exception {
try {
File file = new File("testFiles/convert/sample-cd.xml");
String content = FileUtils.readFileToString(file);
String result = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content).toString();
String result2 = convertRestImpl.converToImage(token, "CellDesigner_SBML",
"lcsb.mapviewer.converter.graphics.SvgImageGenerator", content).toString();
assertTrue(result.equals(result2));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
*/
@SuppressWarnings("unchecked")
private List<String> extractIdsFromOutputs(Map<String, Object> infoObject) {
List<String> ids = new ArrayList<>();
for (Map<String, List<String>> o : (List<Map<String, List<String>>>) infoObject.get("outputs")) {
ids.add(o.get("available_names").get(0));
}
return ids;
}
private void test2All(String content, String converter)
throws SBMLException, SecurityException, InvalidInputDataExecption, InconsistentModelException,
IOException, ConverterException, XMLStreamException, DrawingException, QueryException
{
Map<String, Object> info = convertRestImpl.getInformation(token);
Map<String, Object> infoImage = convertRestImpl.getInformationImage(token);
List<String> targets = new ArrayList<>();
targets.addAll(extractIdsFromOutputs(info));
for (String target: targets) {
String result = convertRestImpl.convert(token, converter, target, content).toString();
assertTrue(result.length() > 0);
}
targets.clear();
targets.addAll(extractIdsFromOutputs(infoImage));
for (String target: targets) {
String result = convertRestImpl.converToImage(token, converter, target, content).toString();
assertTrue(result.length() > 0);
}
}
@Test
public void testCelDesigner2Sbml_2() throws Exception {
try {
public void testCelDesigner2All() throws Exception {
try {
File file = new File("testFiles/convert/sample-cd.xml");
String content = FileUtils.readFileToString(file);
String result = convertRestImpl.convert(token, "CellDesigner_SBML",
"SBGN-ML", content);
System.out.print(result);
assertTrue(result.length() > 0);
test2All(content, "CellDesigner_SBML");
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
@Test
public void testCelDesigner2Svg() throws Exception {
try {
File file = new File("testFiles/convert/sample-cd.xml");
public void testSbml2All() throws Exception {
try {
File file = new File("testFiles/convert/sample-sbml.xml");
String content = FileUtils.readFileToString(file);
ByteArrayOutputStream os = convertRestImpl.converToImage(token, "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
"svg", content);
System.out.print(os.toString());
test2All(content, "SBML");
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
@Test
public void testSbgn2All() throws Exception {
try {
File file = new File("testFiles/convert/sample.sbgn");
String content = FileUtils.readFileToString(file);
test2All(content, "SBGN-ML");
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
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web/.settings/org.eclipse.wst.common.component
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......@@ -34,10 +34,10 @@
<dependent-module archiveName="converter-graphics-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-converter-graphics/MapViewer-converter-graphics">
<dependency-type>uses</dependency-type>
</dependent-module>
<dependent-module archiveName="rest-api-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-rest-api/MapViewer-rest-api">
<dependent-module archiveName="converter-sbml-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-sbml/converter-sbml">
<dependency-type>uses</dependency-type>
</dependent-module>
<dependent-module archiveName="converter-sbml-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-sbml/converter-sbml">
<dependent-module archiveName="rest-api-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-rest-api/MapViewer-rest-api">
<dependency-type>uses</dependency-type>
</dependent-module>
<dependent-module archiveName="frontend-js-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/frontend-js/frontend-js">
......
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