Merge pull request #9 from broadinstitute/ab_large_import

Added script to allow importing large TSV files into FireCloud

import_large_tsv/README.md

+## Import a TSV that is too large to load directly into FireCloud
+This script imports a TSV file when it is too large to import from the GUI.
+
+Run this as follows (from the main directory):
+```./run.sh import_large_tsv/import_large_tsv.py -p <workspace project> -n <workspace name> -f <tsv file name>```
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import_large_tsv/import_large_tsv.py

+##!/usr/bin/env python
+from common import *
+import tempfile
+
+
+
+
+def main():
+    setup()
+
+    # The main argument parser
+    parser = DefaultArgsParser(description="Imports a TSV file when it is too large to import from FireCloud.")
+
+    # Core application arguments
+    parser.add_argument('-p', '--namespace', dest='ws_namespace', action='store', required=True, help='Workspace namespace')
+    parser.add_argument('-n', '--name', dest='ws_name', action='store', required=True, help='Workspace name')
+    parser.add_argument('-f', '--tsv_file', dest='tsv_file', action='store', required=True, help='TSV file to import.')
+
+    args = parser.parse_args()
+
+    tsv_strings = []
+    with open(args.tsv_file, "r") as tsvfile:
+        headers = tsvfile.readline()
+
+        tsv_data = headers
+        for i, line in enumerate(tsvfile):
+            tsv_data += line
+
+            if i > 0 and i % 200 == 0:
+                tsv_strings.append(tsv_data)
+                tsv_data = headers
+
+        # catch the last lines from the tsv file that aren't caught by the % above
+        tsv_strings.append(tsv_data)
+
+        pb = ProgressBar(0, len(tsv_strings), "Split TSV files uploaded")
+        pb.print_bar()
+        for tsv_string in tsv_strings:
+            request = firecloud_api.upload_entities(args.ws_namespace, args.ws_name, tsv_string)
+            if request.status_code != 200:
+                fail(request.text)
+            pb.increment()
+            pb.print_bar()
+
+
+
+
+
+        # pb = ProgressBar(0, entity_count, "Entities gathered")
+        #
+        #
+        #         pb.increment()
+        #         pb.print_bar()
+if __name__ == "__main__":
+    main()
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