Changeset 156 for trunk/corelib/src/org/bridgedb/webservice/IDMapperBiomart.java

Timestamp:

08/14/09 21:50:23 (3 years ago)

Author:

jgao

Message:

IDMapperText & IDMapperBiomart driver update,
IDMapperBiomart constructor with mart

Files:

• trunk/corelib/src/org/bridgedb/webservice/IDMapperBiomart.java (modified) (11 diffs)

trunk/corelib/src/org/bridgedb/webservice/IDMapperBiomart.java

@@ -28 +28 @@
 import java.util.Vector;
 
+import javax.xml.parsers.ParserConfigurationException;
+
 import org.bridgedb.AbstractIDMapperCapabilities;
 import org.bridgedb.BridgeDb;
@@ -41 +43 @@
 import org.bridgedb.webservice.biomart.XMLQueryBuilder;
 
+import org.xml.sax.SAXException;
+
 /**
  *
@@ -55 +59 @@
                 private Driver() { } 
 
-        private static final String DATASET_TAG = "dataset=";
-
         /** {@inheritDoc} */
-                public IDMapper connect(String location) throws IDMapperException  {
-            // e.g.: dataset=oanatinus_gene_ensembl
-                        // e.g.: http://www.biomart.org/biomart/martservice?dataset=oanatinus_gene_ensembl
+        public IDMapper connect(String location) throws IDMapperException  {
+            // e.g.: transitivity=false,id-type-filter=true@dataset=oanatinus_gene_ensembl
+            // e.g.: http://www.biomart.org/biomart/martservice?dataset=oanatinus_gene_ensembl
             String baseURL = BiomartStub.defaultBaseURL;
-            String param = location;
-            int idx = location.indexOf('?');
+            boolean transitivity = false;
+            boolean idTypeFilter = true;
+            
+            String config = null;
+            String path = location;
+            int idx = location.indexOf("@");
+            if (idx==0) {
+                path =location.substring(idx+1);
+            } else if (idx>0) {
+                config = location.substring(0, idx);
+                path = location.substring(idx+1);
+            }
+
+            if (config!=null) {
+                String transitivityTag = "transitivity=";
+                idx = config.indexOf(transitivityTag);
+                if (idx!=-1) {
+                    String tran = config.substring(idx+transitivityTag.length());
+                    if (tran.toLowerCase().startsWith("true")) {
+                        transitivity = true;
+                    } else if (tran.toLowerCase().startsWith("false")) {
+                        transitivity = false;
+                    } else {
+                        throw new IDMapperException(
+                                "transivity can only be true or false");
+                    }
+                }
+
+
+                String idTypeFilterTag = "id-type-filter=";
+                idx = config.indexOf(idTypeFilterTag);
+                if (idx!=-1) {
+                    String filter = config.substring(idx+idTypeFilterTag.length());
+                    if (filter.toLowerCase().startsWith("true")) {
+                        idTypeFilter = true;
+                    } else if (filter.toLowerCase().startsWith("false")) {
+                        idTypeFilter = false;
+                    } else {
+                        throw new IDMapperException(
+                                "id-type-filter can only be true or false");
+                    }
+                }
+            }
+
+            String param = path;
+            idx = path.indexOf('?');
             if (idx>-1) {
-                baseURL = location.substring(0,idx);
-                param = location.substring(idx+1);
-            }
-
-            idx = param.indexOf(DATASET_TAG);
-            String datasetName = param.substring(idx+DATASET_TAG.length());
+                baseURL = path.substring(0,idx);
+                param = path.substring(idx+1);
+            }
+
+            String martTag = "mart=";
+            idx = param.indexOf(martTag);
+            String martName = param.substring(idx+martTag.length());
+
+            idx = martName.indexOf("&");
+            if (idx>-1) {
+                martName = martName.substring(0,idx);
+            }
+
+            String datasetTag = "dataset=";
+            idx = param.indexOf(datasetTag);
+            String datasetName = param.substring(idx+datasetTag.length());
 
             idx = datasetName.indexOf("&");
@@ -77 +133 @@
             }
 
-            return new IDMapperBiomart(datasetName, baseURL);
-                }
-        }
-
+            return new IDMapperBiomart(martName, datasetName, baseURL, 
+                    idTypeFilter, transitivity);
+        }
+    }
+
+    private String martName;
     private String datasetName;
     private BiomartStub stub;
@@ -94 +152 @@
      * Transitivity is unsupported.ID only. ID only for target data sources.
      * Use default url of BiMart.
+     * @param martName name of mart
      * @param datasetName name of dataset
      * @throws IDMapperException if failed to link to the dataset
      */
-    public IDMapperBiomart(String datasetName) throws IDMapperException {
-        this(datasetName, null);
+    public IDMapperBiomart(String martName, String datasetName) throws IDMapperException {
+        this(martName, datasetName, null);
     }
 
     /**
      * Use default url of BiMart.
+     * @param martName name of mart
      * @param datasetName name of dataset
      * @param idOnlyForTgtDataSource id-only option, filter data source ends
@@ -109 +169 @@
      * @throws IDMapperException if failed to link to the dataset
      */
-    public IDMapperBiomart(String datasetName, boolean idOnlyForTgtDataSource,
+    public IDMapperBiomart(String martName, String datasetName, boolean idOnlyForTgtDataSource,
                 boolean transitivity) throws IDMapperException {
-        this(datasetName, null, idOnlyForTgtDataSource, transitivity);
+        this(martName, datasetName, null, idOnlyForTgtDataSource, transitivity);
     }
 
     /**
      * Transitivity is unsupported.ID only. ID only for target data sources.
+     * @param martName name of mart
      * @param datasetName name of dataset
      * @param baseURL base url of BioMart
      * @throws IDMapperException if failed to link to the dataset
      */
-    public IDMapperBiomart(String datasetName, String baseURL)
+    public IDMapperBiomart(String martName, String datasetName, String baseURL)
                 throws IDMapperException {
-        this(datasetName, baseURL, true);
+        this(martName, datasetName, baseURL, true);
     }
 
     /**
      * Transitivity is unsupported.
+     * @param martName name of mart
      * @param datasetName name of dataset
      * @param baseURL base url of BioMart
@@ -133 +195 @@
      * @throws IDMapperException if failed to link to the dataset
      */
-    public IDMapperBiomart(String datasetName, String baseURL,
+    public IDMapperBiomart(String martName, String datasetName, String baseURL,
             boolean idOnlyForTgtDataSource) throws IDMapperException {
-        this(datasetName, baseURL, idOnlyForTgtDataSource, false);
+        this(martName, datasetName, baseURL, idOnlyForTgtDataSource, false);
     }
 
@@ -141 +203 @@
      * Construct from a dataset, a database, id-only option and transitivity
      * option.
+     * @param martName name of mart
      * @param datasetName name of dataset
      * @param baseURL base url of BioMart
@@ -148 +211 @@
      * @throws IDMapperException if failed to link to the dataset
      */
-    public IDMapperBiomart(String datasetName, String baseURL, 
+    public IDMapperBiomart(String martName, String datasetName, String baseURL,
             boolean idOnlyForTgtDataSource, boolean transitivity) throws IDMapperException {
+        this.martName = martName;
         this.datasetName = datasetName;
         if (baseURL!=null) {
@@ -162 +226 @@
             throw new IDMapperException(e);
         }
+
+        try {
+            if (!stub.getRegistry().containsKey(martName)) {
+                throw new IDMapperException("Mart not exist.");
+            }
+
+            if (!stub.getAvailableDatasets(martName).contains(stub.getDataset(datasetName))) {
+                throw new IDMapperException("dataset not exist.");
+            }
+        } catch (IOException e) {
+            throw new IDMapperException(e);
+        } catch (ParserConfigurationException e) {
+            throw new IDMapperException(e);
+        } catch (SAXException e) {
+            throw new IDMapperException(e);
+        }
         
         setIDOnlyForTgtDataSource(idOnlyForTgtDataSource);
@@ -224 +304 @@
     public String getBaseURL() {
         return baseURL;
+    }
+
+    /**
+     *
+     * @param mart mart name
+     */
+    public void setMart(final String mart) {
+        this.martName = mart;
+    }
+
+    /**
+     *
+     * @return mart name
+     */
+    public String getMart() {
+        return martName;
     }