Changeset 16239

Timestamp:

16/07/08 14:16:08 (1 month ago)

Author:

julie

Message:

in anoph-expr, create synonyms for genes

Files:

• trunk/bio/sources/anoph-expr/main/src/org/intermine/bio/dataconversion/AnophExprConverter.java (modified) (5 diffs)
• trunk/bio/sources/anoph-expr/resources/anoph-expr_keys.properties (modified) (1 diff)

trunk/bio/sources/anoph-expr/main/src/org/intermine/bio/dataconversion/AnophExprConverter.java

@@ -11 +11 @@
- */
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.intermine.dataconversion.ItemWriter;
-import org.intermine.metadata.Model;
-import org.intermine.objectstore.ObjectStoreException;
-import org.intermine.util.StringUtil;
-import org.intermine.xml.full.Attribute;
-import org.intermine.xml.full.Item;
-import org.intermine.xml.full.ReferenceList;
-
-import java.io.BufferedReader;
-import java.io.File;
@@ -29 +16 @@
-import java.io.IOException;
-import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.intermine.dataconversion.ItemWriter;
+import org.intermine.metadata.Model;
+import org.intermine.objectstore.ObjectStoreException;
+import org.intermine.util.StringUtil;
+import org.intermine.xml.full.Item;
+import org.intermine.xml.full.ReferenceList;
-
-/**
@@ -44 +41 @@
-    private Map<String, Item> genes = new HashMap<String, Item>();
-    private Map<String, Item> assays = new HashMap<String, Item>();
+    private Map<String, Item> synonyms = new HashMap<String, Item>();
-    private static final String TYPE = "Geometric mean of ratios";
-    Item org;
@@ -245 +243 @@
-            store(item);
-        }
+        for (Item item : synonyms.values()) {
+            store(item);
+        }
-    }
-
@@ -255 +256 @@
-        gene.setReference("organism", org.getIdentifier());
-        genes.put(geneCG, gene);
+        createSynonym(gene.getIdentifier(), "identifier", geneCG);
-        return gene;
-    }
+
+    private Item createSynonym(String subjectId, String type, String value) {
+        String key = subjectId + type + value;
+        if (StringUtils.isEmpty(value)) {
+            return null;
+        }
+        if (!synonyms.containsKey(key)) {
+            Item syn = createItem("Synonym");
+            syn.setReference("subject", subjectId);
+            syn.setAttribute("type", type);
+            syn.setAttribute("value", value);
+            synonyms.put(key, syn);
+            return syn;
+        }
+        return null;
+    }
-}
-

trunk/bio/sources/anoph-expr/resources/anoph-expr_keys.properties

@@ -3 +3 @@
-Publication=key_pubmed
-DataSource=key_name
+Synonym=key_synonym