searchPGS = c.get('resource/search', {
'q': 'Phylogenetic signal',
'types': '["item"]'
})
if len(searchPGS['item']) == 0:
uploadPGS = True
# Read our analyses into Python dictionaries and upload them to girder.
if uploadACR:
ACR = {}
with open("%s/ancestral-state/aceArbor.json" % arborWebAppsPath,
"r") as acrFile:
acrStr = acrFile.read()
ACR['analysis'] = json.loads(acrStr)
item = c.createItem(folderId, 'aceArbor', 'Ancestral state reconstruction')
c.addMetadataToItem(item['_id'], ACR)
print "aceArbor successfully uploaded"
else:
print "aceArbor already exists"
if uploadPGS:
PGS = {}
with open(
"%s/phylogenetic-signal/Phylogenetic_signal.json" %
arborWebAppsPath, "r") as pgsFile:
pgsStr = pgsFile.read()
PGS['analysis'] = json.loads(pgsStr)
item = c.createItem(folderId, 'Phylogenetic signal', 'Phylogenetic signal')
c.addMetadataToItem(item['_id'], PGS)
print "Phylogenetic signal successfully uploaded"
'name': 'Data',
'description': 'Data Folder',
'public': 'true'
})
c.post('folder', parameters={
'parentType': 'collection',
'parentId': collection['_id'],
'name': 'Analyses',
'description': 'Analysis folder',
'public': 'true'
})
else:
collection = collection_search['collection'][0]
# Get the 'Analyses' folder for this collection.
analysis_folder = c.load_or_create_folder('Analyses', collection['_id'], 'collection')
folder_id = analysis_folder['_id']
# Read this analysis into a Python dictionary and upload it to Girder.
analysis = {}
with open (fullpath, "r") as analysis_file:
analysis_str = analysis_file.read()
try:
analysis['analysis'] = json.loads(analysis_str)
except ValueError:
print "Could not read valid JSON from %s" % analysis_filename
continue
item = c.createItem(folder_id, analysis_name, analysis_name)
c.addMetadataToItem(item['_id'], analysis)
print "%s successfully uploaded to %s" % (analysis_filename, collection_name)
uploadACR = True
searchPGS = c.get('resource/search', {
'q': 'Phylogenetic signal',
'types': '["item"]'
})
if len(searchPGS['item']) == 0:
uploadPGS = True
# Read our analyses into Python dictionaries and upload them to girder.
if uploadACR:
ACR = {}
with open ("%s/ancestral-state/aceArbor.json" % args.path, "r") as acrFile:
acrStr = acrFile.read()
ACR['analysis'] = json.loads(acrStr)
item = c.createItem(folderId, 'aceArbor', 'Ancestral state reconstruction')
c.addMetadataToItem(item['_id'], ACR)
print "aceArbor successfully uploaded"
else:
print "aceArbor already exists"
if uploadPGS:
PGS = {}
with open ("%s/phylogenetic-signal/Phylogenetic_signal.json" % args.path, "r") as pgsFile:
pgsStr = pgsFile.read()
PGS['analysis'] = json.loads(pgsStr)
item = c.createItem(folderId, 'Phylogenetic signal', 'Phylogenetic signal')
c.addMetadataToItem(item['_id'], PGS)
print "Phylogenetic signal successfully uploaded"
else:
print "Phylogenetic signal already exists"
output_file_name = input_file_name.replace('.nc', '.json')
try:
# Now download the dataset
(fd, filepath) = tempfile.mkstemp()
os.close(fd)
client.downloadFile(fileId, filepath)
# Create temp file and convert to GeoJs contour JSON format
output_dir = tempfile.mkdtemp()
output_filepath = os.path.join(output_dir, output_file_name)
with open(output_filepath, 'w') as fp:
fp.write(json_util.dumps(convert(filepath, variable, timestep)))
# Create an item for this file
output_item = client.createItem(dataset_folder_id, output_file_name, output_file_name)
# Now upload the result
client.uploadFileToItem(output_item['_id'], output_filepath)
output_item_id = output_item['_id']
# Finally promote item to dataset
client.post('minerva_dataset/%s/dataset' % output_item_id)
finally:
if filepath and os.path.exists(filepath):
os.remove(filepath)
if output_dir and os.path.exists(output_dir):
shutil.rmtree(output_dir)
