Migrated all bio webservices.

PKatGITHUB · Aug 21, 2019 · 7d4bea9 · 7d4bea9
1 parent 2217a27
commit 7d4bea9
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Showing 24 changed files with 653 additions and 510 deletions.
diff --git a/bio/webservices/src/main/java/org/intermine/bio/web/export/BEDExporter.java b/bio/webservices/src/main/java/org/intermine/bio/web/export/BEDExporter.java
@@ -28,15 +28,15 @@
 import org.intermine.util.IntPresentSet;
 import org.intermine.web.logic.export.ExportException;
 import org.intermine.web.logic.export.Exporter;
+import org.intermine.web.logic.export.ExporterSpring;
 
 /**
  * Exports LocatedSequenceFeature objects in UCSC BED format.
  *
  * @author Fengyuan Hu
  */
-public class BEDExporter implements Exporter
+public class BEDExporter extends ExporterSpring
 {
-    PrintWriter out;
     private boolean makeUcscCompatible = true;
     private int writtenResultsCount = 0;
     private boolean headerPrinted = false;
@@ -63,21 +63,19 @@ public class BEDExporter implements Exporter
 
     /**
      * Constructor.
-     * @param out output stream
      * @param featureIndexes index of column with exported sequence
      * @param sourceName name of Mine to put in GFF source column
      * @param organismString a comma separated string of organism short names
      * @param makeUcscCompatible true if chromosome ids should be prefixed by 'chr'
      * @param trackDescription track description in the header
      */
-    public BEDExporter(PrintWriter out, List<Integer> featureIndexes, String sourceName,
+    public BEDExporter(List<Integer> featureIndexes, String sourceName,
             String organismString, boolean makeUcscCompatible, String trackDescription) {
-
-        this.out = out;
         this.featureIndexes = featureIndexes;
         this.sourceName = sourceName;
         this.makeUcscCompatible = makeUcscCompatible;
         this.trackDescription = trackDescription;
+        this.outputString = "";
 
         if ("".equals(trackDescription) || trackDescription == null) {
             this.trackName = "track";
@@ -111,10 +109,8 @@ public void export(Iterator<? extends List<ResultElement>> resultIt,
             finishLastRow();
 
             if (writtenResultsCount == 0) {
-                out.println("Nothing was found for export");
+                outputString = outputString.concat("Nothing was found for export").concat("\n");
             }
-
-            out.flush();
         } catch (Exception ex) {
             throw new ExportException("Export failed", ex);
         }
@@ -217,11 +213,11 @@ private void makeRecord() {
         if (bedRecord != null) {
             // have a chromosome ref and chromosomeLocation ref
             if (!headerPrinted) {
-                out.println(getHeader());
+                outputString = outputString.concat(getHeader()).concat("\n");
                 headerPrinted = true;
             }
 
-            out.println(bedRecord.toBED());
+            outputString = outputString.concat(bedRecord.toBED()).concat("\n");
             exportedIds.add(lastLsf.getId());
             writtenResultsCount++;
         }
@@ -247,11 +243,11 @@ private void finishLastRow() {
         if (bedRecord != null) {
             // have a chromsome ref and chromosomeLocation ref
             if (!headerPrinted) {
-                out.println(getHeader());
+                outputString = outputString.concat(getHeader()).concat("\n");
                 headerPrinted = true;
             }
 
-            out.println(bedRecord.toBED());
+            outputString = outputString.concat(bedRecord.toBED()).concat("\n");
             writtenResultsCount++;
         }
         lastLsfId = null;

diff --git a/bio/webservices/src/main/java/org/intermine/bio/web/export/GFF3Exporter.java b/bio/webservices/src/main/java/org/intermine/bio/web/export/GFF3Exporter.java
@@ -39,13 +39,14 @@
 import org.intermine.util.PropertiesUtil;
 import org.intermine.web.logic.export.ExportException;
 import org.intermine.web.logic.export.Exporter;
+import org.intermine.web.logic.export.ExporterSpring;
 
 /**
  * Exports LocatedSequenceFeature objects in GFF3 format.
  * @author Kim Rutherford
  * @author Jakub Kulaviak
  */
-public class GFF3Exporter implements Exporter
+public class GFF3Exporter extends ExporterSpring
 {
     private static final Logger LOG = Logger.getLogger(GFF3Exporter.class);
     /**
@@ -65,7 +66,6 @@ public class GFF3Exporter implements Exporter
     public static final String FLY_LINK =
         "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7227";
 
-    PrintWriter out;
     private List<Integer> featureIndexes;
     private Map<String, String> soClassNames;
     private int writtenResultsCount = 0;
@@ -82,7 +82,6 @@ public class GFF3Exporter implements Exporter
 
     /**
      * Constructor.
-     * @param out output stream
      * @param indexes index of column with exported sequence
      * @param soClassNames mapping
      * @param attributesNames names of attributes that are printed in record,
@@ -92,16 +91,16 @@ public class GFF3Exporter implements Exporter
      * @param organisms taxon id of the organisms
      * @param makeUcscCompatible true if chromosome ids should be prefixed by 'chr'
      */
-    public GFF3Exporter(PrintWriter out, List<Integer> indexes, Map<String, String> soClassNames,
+    public GFF3Exporter(List<Integer> indexes, Map<String, String> soClassNames,
             List<String> attributesNames, String sourceName, Set<String> organisms,
             boolean makeUcscCompatible) {
-        this.out = out;
         this.featureIndexes = indexes;
         this.soClassNames = soClassNames;
         this.attributesNames = attributesNames;
         this.sourceName = sourceName;
         this.organisms = organisms;
         this.makeUcscCompatible = makeUcscCompatible;
+        this.outputString = "";
 
         for (String s : soClassNames.keySet()) {
             this.cNames.add(s.toLowerCase());
@@ -110,7 +109,6 @@ public GFF3Exporter(PrintWriter out, List<Integer> indexes, Map<String, String>
 
     /**
      * Constructor.
-     * @param out output stream
      * @param indexes index of column with exported sequence
      * @param soClassNames mapping
      * @param attributesNames names of attributes that are printed in record,
@@ -121,10 +119,9 @@ public GFF3Exporter(PrintWriter out, List<Integer> indexes, Map<String, String>
      * @param makeUcscCompatible true if chromosome ids should be prefixed by 'chr'
      * @param paths paths
      */
-    public GFF3Exporter(PrintWriter out, List<Integer> indexes, Map<String, String> soClassNames,
+    public GFF3Exporter(List<Integer> indexes, Map<String, String> soClassNames,
             List<String> attributesNames, String sourceName, Set<String> organisms,
             boolean makeUcscCompatible, List<Path> paths) {
-        this.out = out;
         this.featureIndexes = indexes;
         this.soClassNames = soClassNames;
         this.attributesNames = attributesNames;
@@ -199,11 +196,9 @@ public void export(Iterator<? extends List<ResultElement>> resultIt,
             }
 
             if (writtenResultsCount == 0) {
-                out.println("Nothing to export. Sequence features might miss some information, "
+                outputString = outputString.concat("Nothing to export. Sequence features might miss some information, "
                         + "e.g. chromosome location, etc.");
             }
-
-            out.flush();
         } catch (Exception ex) {
             throw new ExportException("Export failed", ex);
         }
@@ -442,11 +437,11 @@ private void makeRecord() {
         if (gff3Record != null) {
             // have a chromosome ref and chromosomeLocation ref
             if (!headerPrinted) {
-                out.println(getHeader());
+                outputString = outputString.concat(getHeader()).concat("\n");
                 headerPrinted = true;
             }
 
-            out.println(gff3Record.toGFF3());
+            outputString = outputString.concat(gff3Record.toGFF3()).concat("\n");
             exportedIds.add(lastLsf.getId());
             writtenResultsCount++;
         }

diff --git a/bio/webservices/src/main/java/org/intermine/bio/web/export/SequenceExporter.java b/bio/webservices/src/main/java/org/intermine/bio/web/export/SequenceExporter.java
@@ -50,6 +50,7 @@
 import org.intermine.util.IntPresentSet;
 import org.intermine.web.logic.export.ExportException;
 import org.intermine.web.logic.export.Exporter;
+import org.intermine.web.logic.export.ExporterSpring;
 
 /**
  * Export data in FASTA format. Select cell in each row that can be exported as
@@ -58,11 +59,10 @@
  * @author Kim Rutherford
  * @author Jakub Kulaviak
  **/
-public class SequenceExporter implements Exporter
+public class SequenceExporter extends ExporterSpring
 {
 
     private ObjectStore os;
-    private OutputStream out;
     private int featureIndex;
     private int writtenResultsCount = 0;
     private final Map<String, List<FieldDescriptor>> classKeys;
@@ -79,40 +79,35 @@ public class SequenceExporter implements Exporter
      *
      * @param os
      *            object store used for fetching sequence for exported object
-     * @param outputStream
-     *            output stream
      * @param featureIndex
      *            index of cell in row that contains object to be exported
      * @param classKeys for the model
      * @param extension extension
      */
-    public SequenceExporter(ObjectStore os, OutputStream outputStream,
+    public SequenceExporter(ObjectStore os,
             int featureIndex, Map<String, List<FieldDescriptor>> classKeys, int extension) {
         this.os = os;
-        this.out = outputStream;
         this.featureIndex = featureIndex;
         this.classKeys = classKeys;
         this.extension = extension;
+        this.outputString = "";
     }
 
     /**
      * Constructor.
      *
      * @param os
      *            object store used for fetching sequence for exported object
-     * @param outputStream
-     *            output stream
      * @param featureIndex
      *            index of cell in row that contains object to be exported
      * @param classKeys for the model
      * @param extension extension
      * @param paths paths to include
      */
-    public SequenceExporter(ObjectStore os, OutputStream outputStream,
+    public SequenceExporter(ObjectStore os,
             int featureIndex, Map<String, List<FieldDescriptor>> classKeys, int extension,
             List<Path> paths) {
         this.os = os;
-        this.out = outputStream;
         this.featureIndex = featureIndex;
         this.classKeys = classKeys;
         this.extension = extension;
@@ -204,16 +199,17 @@ public void export(Iterator<? extends List<ResultElement>> resultIt,
                     }
                 }
 
-                FastaWriterHelper.writeSequence(out, bioSequence);
+                //FastaWriterHelper.writeSequence(out, bioSequence);
+                outputString = outputString.concat(bioSequence.getSequenceAsString()).concat("\n");
+
                 writtenResultsCount++;
                 exportedIDs.add(objectId);
             }
 
             if (writtenResultsCount == 0) {
-                out.write("Nothing was found for export".getBytes(Charset.forName("UTF-8")));
+                outputString = outputString.concat("Nothing was found for export");
             }
 
-            out.flush();
         } catch (Exception e) {
             throw new ExportException("Export failed.", e);
         }

diff --git a/bio/webservices/src/main/java/org/intermine/bio/webservice/AbstractRegionExportService.java b/bio/webservices/src/main/java/org/intermine/bio/webservice/AbstractRegionExportService.java
@@ -34,6 +34,7 @@
 import org.intermine.pathquery.PathQuery;
 import org.intermine.metadata.StringUtil;
 import org.intermine.web.logic.export.Exporter;
+import org.intermine.web.logic.export.ExporterSpring;
 import org.intermine.web.logic.export.ResponseUtil;
 import org.intermine.webservice.server.Format;
 import org.intermine.webservice.server.WebServiceRequestParser;
@@ -51,12 +52,19 @@
  */
 public abstract class AbstractRegionExportService extends GenomicRegionSearchService
 {
+    public String getOutputString() {
+        return outputString;
+    }
+
+    protected String outputString;
+
     /**
      * Constructor.
      * @param im The InterMine API settings object.
      */
     public AbstractRegionExportService(InterMineAPI im, Format format) {
         super(im, format);
+        this.outputString = "";
     }
 
     @Override
@@ -123,15 +131,15 @@ protected void checkPathQuery(PathQuery pq) throws Exception {
      * @param pq pathquery
      * @return the exporter
      */
-    protected abstract Exporter getExporter(PathQuery pq);
+    protected abstract ExporterSpring getExporter(PathQuery pq);
 
     /**
      * Method that carries out the logic for this exporter.
      * @param pq The pathquery.
      * @param profile A profile to lookup saved bags in.
      */
     protected void export(PathQuery pq, Profile profile) {
-        Exporter exporter = getExporter(pq);
+        ExporterSpring exporter = getExporter(pq);
         ExportResultsIterator iter = null;
         try {
             PathQueryExecutor executor = this.im.getPathQueryExecutor(profile);
@@ -147,62 +155,9 @@ protected void export(PathQuery pq, Profile profile) {
                 iter.releaseGoFaster();
             }
         }
+        outputString = exporter.getOutputString();
     }
 
-    /**
-     * @return The suffix for the file name.
-     */
-    protected abstract String getSuffix();
-
-    /*@Override
-    protected String getDefaultFileName() {
-        return "results" + StringUtil.uniqueString() + getSuffix();
-    }*/
-
-    private PrintWriter pw;
-    private OutputStream os;
-
-    /**
-     * @return printwriter
-     */
-    protected PrintWriter getPrintWriter() {
-        return pw;
-    }
-
-    /**
-     * @return outputstream
-     */
-    protected OutputStream getOutputStream() {
-        return os;
-    }
-
-    /**
-     * @return content type
-     */
-    protected abstract String getContentType();
 
-    /**
-     * @return formatter
-     */
-    protected Formatter getFormatter() {
-        return new PlainFormatter();
-    }
-
-    /*@Override
-    protected Output getDefaultOutput(PrintWriter out, OutputStream outputstream,
-            String separator) {
-        this.pw = out;
-        this.os = outputstream;
-        output = new StreamedOutput(out, getFormatter(), separator);
-        if (isUncompressed()) {
-            ResponseUtil.setCustomTypeHeader(response, getDefaultFileName(), getContentType());
-        }
-        return output;
-    }*/
-
-    @Override
-    public Format getDefaultFormat() {
-        return Format.UNKNOWN;
-    }
 
 }