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mikekuceramikekucera
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Start of CyREST command for creating EM network.
Refs #385
1 parent b5f1d36 commit ad3ed03

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5 files changed

+183
-2
lines changed

5 files changed

+183
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lines changed

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,7 @@
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import org.baderlab.csplugins.enrichmentmap.commands.tunables.MannWhitRanksTunableHandlerFactory;
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import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
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import org.baderlab.csplugins.enrichmentmap.model.io.SessionListener;
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import org.baderlab.csplugins.enrichmentmap.rest.BuildResource;
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import org.baderlab.csplugins.enrichmentmap.rest.ExpressionsResource;
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import org.baderlab.csplugins.enrichmentmap.rest.ModelResource;
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import org.baderlab.csplugins.enrichmentmap.style.ChartFactoryManager;
@@ -72,9 +73,10 @@ public void start(BundleContext bc) {
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// commands
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initializeCommands(bc);
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// jax-rs resources
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// jax-rs (CyREST) resources
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registerService(bc, injector.getInstance(ExpressionsResource.class), ExpressionsResource.class);
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registerService(bc, injector.getInstance(ModelResource.class), ModelResource.class);
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registerService(bc, injector.getInstance(BuildResource.class), BuildResource.class);
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// CyProperty
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CyProperty<Properties> cyProperty = injector.getInstance(Key.get(new TypeLiteral<CyProperty<Properties>>(){}));

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/FilterTunables.java‎

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -71,7 +71,7 @@ public class FilterTunables {
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public String attributePrefix = null;
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@Inject private LegacySupport legacySupport;
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private LegacySupport legacySupport;
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public FilterTunables() {
@@ -83,6 +83,11 @@ public FilterTunables() {
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nesFilter = enumNames(NESFilter.values());
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nesFilter.setSelectedValue(NESFilter.ALL.name());
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}
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@Inject
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public void setLegacySupport(LegacySupport legacySupport) {
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this.legacySupport = legacySupport;
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}
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public EMCreationParameters getCreationParameters() throws IllegalArgumentException {

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/rest/BuildResource.java‎

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@@ -0,0 +1,116 @@
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package org.baderlab.csplugins.enrichmentmap.rest;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.Reader;
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import java.util.Collections;
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import java.util.List;
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import javax.ws.rs.Consumes;
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import javax.ws.rs.POST;
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import javax.ws.rs.Path;
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import javax.ws.rs.core.MediaType;
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import javax.ws.rs.core.Response;
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import org.baderlab.csplugins.enrichmentmap.commands.tunables.FilterTunables;
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import org.baderlab.csplugins.enrichmentmap.model.DataSetParameters;
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import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters;
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import org.baderlab.csplugins.enrichmentmap.model.LegacySupport;
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import org.baderlab.csplugins.enrichmentmap.model.TableParameters;
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import org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory;
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import org.cytoscape.model.CyRow;
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import org.cytoscape.model.CyTable;
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import org.cytoscape.model.CyTableFactory;
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import org.cytoscape.work.SynchronousTaskManager;
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import org.cytoscape.work.TaskIterator;
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import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import com.google.inject.Inject;
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import com.google.inject.Provider;
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import io.swagger.annotations.Api;
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import io.swagger.annotations.ApiOperation;
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import io.swagger.annotations.ApiParam;
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@Api(tags="Apps: EnrichmentMap")
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@Path("/enrichmentmap/build")
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public class BuildResource {
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private static final String
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NAME = "name",
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GENES = "genes",
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PVALUE = "pvalue",
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QVALUE = "qvalue",
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NES = "nes",
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DESC = "description";
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@Inject private SynchronousTaskManager<?> taskManager;
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@Inject private CreateEnrichmentMapTaskFactory.Factory taskFactoryFactory;
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@Inject private CyTableFactory tableFactory;
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@Inject private Provider<LegacySupport> legacySupport;
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@POST
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@Path("/")
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@Consumes(MediaType.APPLICATION_JSON)
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@ApiOperation(value="Create an EnrichmentMap network.",
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notes=""
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)
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public Response createEnrichmentMap(
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@ApiParam(value="Body JSON data.") InputStream is
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) {
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EMJsonData emJson;
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try(Reader reader = new InputStreamReader(is)) {
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Gson gson = new GsonBuilder().create();
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emJson = gson.fromJson(reader, EMJsonData.class);
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} catch(IOException e) {
70+
throw new RuntimeException(e);
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}
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CyTable enrichmentTable = createEnrichmentTable();
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fillEnrichmentTable(enrichmentTable, emJson.enrichments);
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TableParameters tableParams = new TableParameters(enrichmentTable, NAME, GENES, PVALUE, QVALUE, NES, DESC, null);
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DataSetParameters dsParams = new DataSetParameters("DataSet1", tableParams, null);
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List<DataSetParameters> dataSets = Collections.singletonList(dsParams);
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FilterTunables filter = emJson.filter;
82+
filter.setLegacySupport(legacySupport.get());
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84+
EMCreationParameters creationParams = filter.getCreationParameters();
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CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(creationParams, dataSets);
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TaskIterator tasks = taskFactory.createTaskIterator();
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taskManager.execute(tasks);
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return Response.ok().build();
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}
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private CyTable createEnrichmentTable() {
94+
CyTable enrichmentTable = tableFactory.createTable("tempEnrichmentEM", "pk", Long.class, false, false);
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enrichmentTable.createColumn(NAME, String.class, false);
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enrichmentTable.createListColumn(GENES, String.class, false);
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enrichmentTable.createColumn(PVALUE, Double.class, false);
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enrichmentTable.createColumn(QVALUE, Double.class, false);
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enrichmentTable.createColumn(NES, Double.class, false);
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enrichmentTable.createColumn(DESC, String.class, false);
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return enrichmentTable;
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}
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private void fillEnrichmentTable(CyTable table, List<EnrichmentEntry> enrichments) {
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long i = 0;
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for(EnrichmentEntry enrichment : enrichments) {
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CyRow row = table.getRow(i++);
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row.set(NAME, enrichment.name);
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row.set(GENES, enrichment.genes);
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row.set(PVALUE, enrichment.pvalue);
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row.set(QVALUE, enrichment.qvalue);
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row.set(NES, enrichment.nes);
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row.set(DESC, enrichment.description);
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}
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}
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}

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/rest/EMJsonData.java‎

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package org.baderlab.csplugins.enrichmentmap.rest;
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import java.util.List;
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import org.baderlab.csplugins.enrichmentmap.commands.tunables.FilterTunables;
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public class EMJsonData {
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public FilterTunables filter;
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public List<EnrichmentEntry> enrichments;
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@Override
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public String toString() {
15+
StringBuilder builder = new StringBuilder();
16+
builder.append("EMJsonData [filter=");
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builder.append(filter);
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builder.append(", enrichments=");
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builder.append(enrichments);
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builder.append("]");
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return builder.toString();
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}
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}

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/rest/EnrichmentEntry.java‎

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package org.baderlab.csplugins.enrichmentmap.rest;
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import java.util.List;
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public class EnrichmentEntry {
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public String name;
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public List<String> genes;
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public Double pvalue;
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public Double qvalue;
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public Double nes;
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public String description;
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@Override
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public String toString() {
17+
StringBuilder builder = new StringBuilder();
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builder.append("EnrichmentEntry [name=");
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builder.append(name);
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builder.append(", genes=");
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builder.append(genes);
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builder.append(", pvalue=");
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builder.append(pvalue);
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builder.append(", qvalue=");
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builder.append(qvalue);
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builder.append(", nes=");
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builder.append(nes);
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builder.append(", description=");
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builder.append(description);
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builder.append("]");
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return builder.toString();
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}
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}

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