Revert submission of instance metadata

scripts/grt-submit.py

@@ -5,13 +5,13 @@
 """
 from __future__ import print_function
 
+import argparse
 import os
 import sys
-import json
-import urllib2
-import argparse
+import time
 import yaml
-import re
+import logging
+import urllib2
 
 sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml.sample'))
 default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml'))
@@ -37,9 +37,16 @@ def main(argv):
         with open(sample_config) as handle:
             config = yaml.load(handle)
 
+    REPORT_DIR = args.report_directory
+    CHECK_POINT_FILE = os.path.join(REPORT_DIR, '.checkpoint')
+    ARCHIVE_DIR = os.path.join(REPORT_DIR, 'archives')
+    METADATA_FILE = os.path.join(REPORT_DIR, 'meta.json')
+    REPORT_BASE = os.path.join(ARCHIVE_DIR, REPORT_IDENTIFIER)
+
     GRT_URL = config['grt']['url']
     GRT_INSTANCE_ID = config['grt']['instance_id']
     GRT_API_KEY = config['grt']['api_key']
+    # Contact the server and check auth details.
 
     # TODO: server interaction.
 

scripts/grt.py

@@ -189,7 +189,6 @@ def main(argv):
     REPORT_DIR = args.report_directory
     CHECK_POINT_FILE = os.path.join(REPORT_DIR, '.checkpoint')
     ARCHIVE_DIR = os.path.join(REPORT_DIR, 'archives')
-    METADATA_FILE = os.path.join(REPORT_DIR, 'meta.json')
     REPORT_IDENTIFIER = str(time.time())
     REPORT_BASE = os.path.join(ARCHIVE_DIR, REPORT_IDENTIFIER)
 
@@ -200,7 +199,7 @@ def main(argv):
         last_job_sent = -1
 
     logging.info('Loading Galaxy...')
-    model, object_store, engine, gxconfig, app = _init(config['galaxy_config'], need_app=config['grt']['metadata']['share_toolbox'])
+    model, object_store, engine, gxconfig, app = _init(config['galaxy_config'], need_app=config['grt']['share_toolbox'])
 
     sa_session = model.context.current
     logging.info('Configuration Loaded')
@@ -285,11 +284,6 @@ def main(argv):
     if os.path.exists(REPORT_DIR) and not os.path.exists(ARCHIVE_DIR):
         os.makedirs(ARCHIVE_DIR)
 
-    _times.append(('job_meta_start', time.time() - _start_time))
-    with open(METADATA_FILE, 'w') as handle:
-        json.dump(config['grt']['metadata'], handle, indent=2)
-    _times.append(('job_meta_end', time.time() - _start_time))
-
     with gzip.open(REPORT_BASE + '.tsv.gz', 'w') as handle:
         for job in grt_jobs_data:
             handle.write('\t'.join(job))
@@ -302,7 +296,7 @@ def main(argv):
 
     # Now serialize the individual report data.
     with open(REPORT_BASE + '.json', 'w') as handle:
-        if config['grt']['metadata']['share_toolbox']:
+        if config['grt']['share_toolbox']:
             toolbox = [
                 (tool.id, tool.name, tool.version, tool.tool_shed, tool.repository_id, tool.repository_name)
                 for tool_id, tool in app.toolbox._tools_by_id.items()

scripts/grt.yml.sample

@@ -4,30 +4,16 @@ galaxy_config: config/galaxy.ini
 
 grt:
     # Go to https://telescope.galaxyproject.org to obtain an Instance ID and API key
-    instance_id: None
-    api_key: None
+    instance_id: 5f126e1d-d216-493e-a67a-3d6f20a0f1ac
+    api_key: 9e43e2b9-b54a-418c-9712-36e79f4d9183
     # Galaxy Project offers a public galactic-radio-telescope instance, however
     # you are free to run your own if you need. We would love it if you were
     # willing and able to contribute your data publicly.
-    url: https://telescope.galaxyproject.org/
-    # Some metadata about your galaxy instance
-    metadata:
-        url: https://example.com/galaxy/
-        title: NLP Galaxy
-        description: |
-            This is our Galaxy instance!
-        # Is the instance open to the public?
-        public: False
-        # Optional Location
-        latitude: 0.00
-        longitude: 0.00
-        # Owners (these are the usernames of users registered with the galactic-radio-telescope system.)
-        owners:
-            - jane.doe
-        # Are you willing to share your toolbox? I.e. what tools are installed.
-        # If your instance is public, this can help us direct users to your
-        # instance.
-        share_toolbox: False
+    url: http://localhost:8080
+    # Are you willing to share your toolbox? I.e. what tools are installed.
+    # If your instance is public, this can help us direct users to your
+    # instance.
+    share_toolbox: False
 
 
 blacklist: