From: Diane Trout <diane@ghic.org>
Date: Tue, 31 Mar 2015 22:35:52 +0000 (-0700)
Subject: Add get_accession_name to use collection name to find commonly used spreadsheet acces... 
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=fe1b091216ef9011987352f26839601a7b77f5fb

Add get_accession_name to use collection name to find commonly used spreadsheet accesssion column name
---

diff --git a/htsworkflow/submission/encoded.py b/htsworkflow/submission/encoded.py
index 83f5826..26c07f7 100644
--- a/htsworkflow/submission/encoded.py
+++ b/htsworkflow/submission/encoded.py
@@ -258,6 +258,23 @@ class ENCODED:
 
         return self.prepare_url(ENCODED_SCHEMA_ROOT + object_type + '.json') + '#'
 
+    def get_accession_name(self, collection):
+        """Lookup common object accession name given a collection name.
+        """
+        collection_to_accession_name = {
+            '/experiments/': 'experiment_accession',
+            '/biosamples/': 'biosample_accession',
+            '/libraries/': 'library_accession',
+            '/replicates/': 'uuid',
+        }
+
+        accession_name = collection_to_accession_name.get(collection, None)
+        if accession_name is None:
+            raise RuntimeError("Update list of collection to accession names for %s",
+                               collection)
+
+        return accession_name
+
     def _is_encoded_object(self, obj):
         '''Test to see if an object is a JSON-LD object