We have been doing a iRODS to Figshare PoC py plugin.
Feel free to test it ;-)
We are missing : Use the script from the iDROP-Web and maybe have a figshare-button or menu thing. (any got that working ? let me know! )
irods_figshare playground for irods figshare integration.
irods_to_figshare.py script is a PoC for copying files from iRODS to figshare via the figshare API.
Figshare access token
Create a figshare account, login and then access the Apllications section. There you can generate a Personal Access token that can be used to access the figshare API.
Required configuration
Check out irods_figshare.conf.json for some sample values.
Running the script
Requires python-irodsclient available here.
Make sure that the file passed as argument to the script exists in iRODS and that it has associated the following metadata fields: title, description, tags. The script will search for and use these in order to create the figshare article.
Execute the script: python irods_to_figshare.py figshare_test.txt
Code :
file : irods_figshare.conf.json
{
"irods": {
"host": "localhost",
"port": 1247,
"user": "irods",
"passwd": "irods",
"zone": "tempZone",
"collection": "/tempZone/home/irods"
},
"figshare": {
"access_token": "
"api_endpoint": "https://api.figshare.com/v2"
}
}
---- CUT -----
file : irods_to_figshare.py
import argparse
import requests
import json
import hashlib
import os
from irods.session import iRODSSession
#load config
config = json.loads(open('irods_
#argument parser
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('file'
args = arg_parser.parse_args()
#irods stuff
irods_session = iRODSSession(host=config['
port=config['irods']['port'],
user=config['irods']['user'],
password=str(config['irods'][
zone=config['irods']['zone'])
irods_collection = irods_session.collections.get(
#figshare stuff
access_token = config['figshare']['access_
api_endpoint = config['figshare']['api_
#request session
http_session = requests.Session()
api_headers = {
"Authorization": "token {}".format(access_token),
"Content-Type": "application/json"
}
http_session.headers.update(
#lets get the file and associated metadata
file_path = os.path.join(config['irods']['
file_obj = irods_session.data_objects.
file_metadata = file_obj.metadata.items()
#create article
article_metadata = {
"title": "",
"description": "",
"tags": ""
}
for meta in file_metadata:
name = meta.name.lower()
if name == "title":
article_metadata["title"] = meta.value
elif name == "description":
article_metadata["description"
elif name == "tags":
article_metadata["tags"] = meta.value.split(',')
else:
continue
article_create_endpoint = "{}/account/articles".format(
request = http_session.post(article_
article_id = request.headers["Location"].
#Add file to article - upload file
##initiate upload
m = hashlib.md5()
with file_obj.open('r') as fd:
for line in fd:
m.update(line)
fd.seek(0, 0)
md5sum = m.hexdigest()
file_data = {
"name": file_obj.name,
"size": file_obj.size,
"md5": md5sum
}
create_file_endpoint = "{}/account/articles/{}/files"
request = http_session.post(create_file_
file_url = '{location}'.format(**request.
file_id = file_url.split('/')[-1]
file_info = http_session.get(file_url).
file_parts = http_session.get(file_info["
with file_obj.open('r') as fd:
for part in file_parts:
size = part['endOffset'] - part['startOffset'] + 1
address = '{}/{}'.format(file_info['
http_session.put(address, data=fd.read(size))
#complete file
file_completed = http_session.post(file_url)
print "Done!"
print "Check out the article at {}/{}?access_token={}".format(
print "Check out the file at {}/{}/files/{}?access_token={}
