Merge remote-tracking branch 'origin/develop' into r-extractor

Author: robkooper

CHANGELOG.md

@@ -4,7 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/) 
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
-## Unreleased
+## [Unreleased]
+### Changed
+- files.upload_preview and collections.upload_preview does not require section_id for metadata [CATS-935](https://opensource.ncsa.illinois.edu/jira/browse/CATS-935)
 
 ### Added
 - Docker compose file for starting up the Clowder stack [BD-2226](https://opensource.ncsa.illinois.edu/jira/browse/BD-2226)
@@ -38,4 +40,4 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 - Now has onbuild version of pyclowder
 - release.sh will now tag images (e.g. this will be tagged 2.0.3 2.0 and 2)
 - RABBITMQ_URI is now set to amqp://guest:guest@rabbitmq/%2F to allow easy deployment
-  using docker-compose of clowder
+  using docker-compose of clowder

Dockerfile

@@ -4,7 +4,7 @@ FROM ubuntu:16.04
 ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq:5672/%2F" \
     RABBITMQ_EXCHANGE="clowder" \
     RABBITMQ_QUEUE="" \
-    REGISTRATION_ENDPOINTS="https://clowder.ncsa.illinois.edu/extractors" \
+    REGISTRATION_ENDPOINTS="" \
     MAIN_SCRIPT=""
 
 # install python

pyclowder/collections.py

@@ -137,7 +137,7 @@ def upload_preview(connector, host, key, collectionid, previewfile, previewmetad
     logger.debug("preview id = [%s]", previewid)
 
     # associate uploaded preview with original collection
-    if collectionid and not (previewmetadata and previewmetadata['section_id']):
+    if collectionid and not (previewmetadata and 'section_id' in previewmetadata and previewmetadata['section_id']):
         url = '%sapi/collections/%s/previews/%s?key=%s' % (host, collectionid, previewid, key)
         result = requests.post(url, headers=headers, data=json.dumps({}),
                                verify=connector.ssl_verify if connector else True)

pyclowder/extractors.py

@@ -84,7 +84,7 @@ def __init__(self):
         self.parser.add_argument('--pickle', type=file, nargs='*', dest="hpc_picklefile",
                                  default=None, action='append',
                                  help='pickle file that needs to be processed (only needed for HPC)')
-        self.parser.add_argument('--register', '-r', nargs='?', dest="regstration_endpoints",
+        self.parser.add_argument('--register', '-r', nargs='?', dest="registration_endpoints",
                                  default=registration_endpoints,
                                  help='Clowder registration URL (default=%s)' % registration_endpoints)
         self.parser.add_argument('--rabbitmqURI', nargs='?', dest='rabbitmq_uri', default=rabbitmq_uri,
@@ -159,7 +159,7 @@ def start(self):
                                               rabbitmq_key=rabbitmq_key,
                                               mounted_paths=json.loads(self.args.mounted_paths))
                     rconn.connect()
-                    rconn.register_extractor(self.args.regstration_endpoints)
+                    rconn.register_extractor(self.args.registration_endpoints)
                     connectors.append(rconn)
                     threading.Thread(target=rconn.listen, name="Connector-" + str(connum)).start()
             elif self.args.connector == "HPC":
@@ -172,7 +172,7 @@ def start(self):
                                          process_message=self.process_message,
                                          picklefile=self.args.hpc_picklefile,
                                          mounted_paths=json.loads(self.args.mounted_paths))
-                    hconn.register_extractor(self.args.regstration_endpoints)
+                    hconn.register_extractor(self.args.registration_endpoints)
                     connectors.append(hconn)
                     threading.Thread(target=hconn.listen, name="Connector-" + str(connum)).start()
             elif self.args.connector == "Local":

pyclowder/files.py

@@ -222,7 +222,7 @@ def upload_preview(connector, host, key, fileid, previewfile, previewmetadata, p
     logger.debug("preview id = [%s]", previewid)
 
     # associate uploaded preview with orginal file
-    if fileid and not (previewmetadata and previewmetadata['section_id']):
+    if fileid and not (previewmetadata and 'section_id' in previewmetadata and previewmetadata['section_id']):
         url = '%sapi/files/%s/previews/%s?key=%s' % (host, fileid, previewid, key)
         result = connector.post(url, headers=headers, data=json.dumps({}),
                                 verify=connector.ssl_verify if connector else True)