Merge pull request #7 from uc-cdis/feat/tsv

TSV export for record / node

Author: cgmeyer

gen3/submission.py

@@ -31,6 +31,14 @@ def __init__(self, endpoint, auth_provider):
         self._auth_provider = auth_provider
         self._endpoint = endpoint
 
+    def __export_file(self, filename, output):
+        """Writes an API response to a file.
+        """
+        outfile = open(filename, "w")
+        outfile.write(output)
+        outfile.close
+        print("\nOutput written to file: "+filename)
+
     def query(self, query_txt, variables=None, max_tries=1):
         """Execute a GraphQL query against a data commons.
 
@@ -69,49 +77,63 @@ def query(self, query_txt, variables=None, max_tries=1):
 
         return data
 
-    def export_node(self, program, project, uuid):
+    def export_record(self, program, project, uuid, fileformat, filename=None):
         """Export a single record into json.
 
         Args:
             program (str): The program the record is under.
             project (str): The project the record is under.
             uuid (str): The UUID of the record to export.
+            fileformat (str): Export data as either 'json' or 'tsv'
+            filename (str): Name of the file to export to; if no filename is provided, prints data to screen
 
         Examples:
             This exports a single record from the sandbox commons.
 
-            >>> Gen3Submission.export_node("DCF", "CCLE", "d70b41b9-6f90-4714-8420-e043ab8b77b9")
+            >>> Gen3Submission.export_record("DCF", "CCLE", "d70b41b9-6f90-4714-8420-e043ab8b77b9", "json", filename="DCF-CCLE_one_record.json")
 
         """
-        api_url = "{}/api/v0/submission/{}/{}/export?ids={}&format=json".format(
-            self._endpoint, program, project, uuid
+        assert fileformat in ["json","tsv"],"File format must be either 'json' or 'tsv'"
+        api_url = "{}/api/v0/submission/{}/{}/export?ids={}&format={}".format(
+            self._endpoint, program, project, uuid, fileformat
         )
         output = requests.get(api_url, auth=self._auth_provider).text
-        data = json.loads(output)
-        return data
+        if filename is None:
+            if fileformat == 'json': output = json.loads(output)
+            return output
+        else:
+            self.__export_file(filename, output)
+            return output
 
-    def export_node_all_type(self, program, project, node_type):
-        """Export all records in a single node.
+    def export_node(self, program, project, node_type, fileformat, filename=None):
+        """Export all records in a single node type of a project.
 
         Args:
             program (str): The program to which records belong.
             project (str): The project to which records belong.
             node_type (str): The name of the node to export.
+            fileformat (str): Export data as either 'json' or 'tsv'
+            filename (str): Name of the file to export to; if no filename is provided, prints data to screen
 
         Examples:
             This exports all records in the "sample" node from the CCLE project in the sandbox commons.
 
-            >>> Gen3Submission.export_node_all_type("DCF", "CCLE", "sample")
+            >>> Gen3Submission.export_node("DCF", "CCLE", "sample", "tsv", filename="DCF-CCLE_sample_node.tsv")
 
         """
-        api_url = "{}/api/v0/submission/{}/{}/export/?node_label={}&format=json".format(
-            self._endpoint, program, project, node_type
+        assert fileformat in ["json","tsv"],"File format must be either 'json' or 'tsv'"
+        api_url = "{}/api/v0/submission/{}/{}/export/?node_label={}&format={}".format(
+            self._endpoint, program, project, node_type, fileformat
         )
         output = requests.get(api_url, auth=self._auth_provider).text
-        data = json.loads(output)
-        return data
+        if filename is None:
+            if fileformat == 'json': output = json.loads(output)
+            return output
+        else:
+            self.__export_file(filename, output)
+            return output
 
-    def submit_node(self, program, project, json):
+    def submit_record(self, program, project, json):
         """Submit record(s) to a project as json.
 
         Args:
@@ -122,14 +144,14 @@ def submit_node(self, program, project, json):
         Examples:
             This submits records to the CCLE project in the sandbox commons.
 
-            >>> Gen3Submission.submit_node("DCF", "CCLE", json)
+            >>> Gen3Submission.submit_record("DCF", "CCLE", json)
 
         """
         api_url = "{}/api/v0/submission/{}/{}".format(self._endpoint, program, project)
         output = requests.put(api_url, auth=self._auth_provider, json=json).text
         return output
 
-    def delete_node(self, program, project, uuid):
+    def delete_record(self, program, project, uuid):
         """Delete a record from a project.
         Args:
             program (str): The program to delete from.
@@ -139,7 +161,7 @@ def delete_node(self, program, project, uuid):
         Examples:
             This deletes a record from the CCLE project in the sandbox commons.
 
-            >>> Gen3Submission.delete_node("DCF", "CCLE", uuid)
+            >>> Gen3Submission.delete_record("DCF", "CCLE", uuid)
         """
         api_url = "{}/api/v0/submission/{}/{}/entities/{}".format(
             self._endpoint, program, project, uuid