Zenodo tests

scripts/zenodo_metadata.json

@@ -3,9 +3,9 @@
 								"upload_type": "dataset",
 								"publication_type": "other",
 								"publication_date": "2018-09-14",
-								"title": "Eljen II Rakoczi Feco",
-								"creators": [ { "name": "Szilveszter, Juhos", "affiliation": "SciLifeLab" }],
-								"description": "This is my first upload",
+								"title": "References and test data for Sarek",
+								"creators": [ { "name": "Maxime Garcia", "affiliation": "SciLifeLab" },{ "name": "Szilveszter, Juhos", "affiliation": "SciLifeLab"}],
+								"description": "Reference files necessary to run somatic/germline variation discovery for https://github.com/SciLifeLab/Sarek",
 								"access_right": "open", 
 								"license": { "id":"cc-by" }
 				}

scripts/zenodo_upload.py

@@ -7,56 +7,75 @@
 import json
 import codecs
 
+# global static header
+headers = {"Content-Type": "application/json"}
+
 @click.command(context_settings = dict( help_option_names = ['-h', '--help'] ))
-@click.option('--filename',   '-f', type=str, help='Files to upload to Zenodo.org', required=True)
+@click.option('--filename',   '-f', type=str, help='Files to upload to Zenodo.org', required=False)
 @click.option('--token',      '-t', type=str, help='Access token', required=True)
-@click.option('--metadata',   '-m', type=str, help='Metadata file', required=True)
+@click.option('--metadata',   '-m', type=str, help='Metadata file', required=False)
 @click.option('--deposition', '-d', type=str, help='Deposition ID', required=False)
 @click.option('--sandbox',    '-s', is_flag=True, help='Use sandbox', required=False, default=True)
-
+# This is the surrogate for main(): everything happens here
 def uploadToZenodo(filename,token,metadata,sandbox,deposition):
     print "Processing file ",filename
     zenodoHost='zenodo.org'
     if sandbox:
         zenodoHost='sandbox.' + zenodoHost
     print "Using host: " + zenodoHost
 
-    # reading metadata:
-    with codecs.open(metadata, 'r', 'utf-8') as f:
+    # The URL for the actual upload and a global 
+    zenodoURL='https://' + zenodoHost + '/api/deposit/depositions'
+
+    # if there is no deposition ID, create one
+    newDeposition = False
+    if not deposition:
+        deposition = new_deposition(zenodoURL, token)
+        newDeposition = True
+    # add file - in some cases we are only updating metadata, but 
+    # to create a new deposition you must have a file
+    if not newDeposition and filename is not None:
+        upload_file(filename, deposition, zenodoURL, token)
+
+    if metadata:
+        print "Uploading metadata %s" % metadata
+        r = upload_metadata(zenodoURL, metadata, deposition, token) 
+
+def new_deposition(zURL,token):
+    r = requests.post( zURL,
+            params={'access_token': token}, 
+            json={}, 
+            headers=headers)
+    depo_id = r.json()['id']
+    print "New deposition created with ID %s at %s" % (depo_id, zURL +"/"+str(depo_id))
+    print "Refer to this at further file uploads"
+    return depo_id
+
+def upload_file(filename, deposition_id, zURL, token):
+    data = {'filename': os.path.basename(filename)}
+    files = {'file': open(filename, 'rb')}
+    r = requests.post(zURL + '/%s/files' % deposition_id,
+            params={'access_token': token}, 
+            data=data,
+            files=files)
+    # TODO: actualy it is not true: if the filename is already there, it is not uploaded, the JSON
+    # returns with a warning and does nothing
+    print "New file %s uploaded" % filename
+
+def upload_metadata(zURL, mdFile, deposition_id, token):
+     # reading metadata:
+    with codecs.open(mdFile, 'r', 'utf-8') as f:
         metadataStr = f.read()
     if not _is_valid_json(metadataStr):
         return
     else:
         metadataJSON = json.loads(metadataStr)
-    print metadataJSON
-
-    zenodoURL='https://' + zenodoHost + '/api/deposit/depositions'
-    headers = {"Content-Type": "application/json"}
-#    r = requests.post( zenodoURL,
-#            params={'access_token': token}, 
-#            json={}, 
-#            headers=headers)
-
-#    deposition_id = r.json()['id']
-#    data = {'filename': os.path.basename(filename)}
-#    files = {'file': open(filename, 'rb')}
-#    r = requests.post(zenodoURL + '/%s/files' % deposition_id,
-#            params={'access_token': token}, 
-#            data=data,
-#            files=files)
 
-#    print r.json()
-
-    deposition_id = deposition
-
-    r = requests.put(zenodoURL + '/%s' % deposition_id, 
+    return requests.put(zURL + '/%s' % deposition_id, 
             params={'access_token': token}, 
             json=metadataJSON, 
             headers=headers)
 
-    print r.json()
-
-
 def _is_valid_json(text):
     try:
         json.loads(text)