def authenticate(auth_code, orcid_id):
user_data = mongo.get_user(orcid_id)
if 'figshare_token' not in user_data and auth_code is not None:
params = {
'client_id': config.get('DEFAULT', 'FIGSHARE_CLIENT_ID'),
'client_secret': config.get('DEFAULT', 'FIGSHARE_SECRET'),
'grant_type': 'authorization_code',
'code': auth_code
}
data = urllib.parse.urlencode(params)
data = data.encode('ascii')
req = urllib.request.Request(config.get('DEFAULT',
'FIGSHARE_TOKEN_URL'),
data=data,
headers={'Accept': 'application/json'})
req.get_method = lambda: "POST"
response = urllib.request.urlopen(req).read()
figshare_token = json.loads(response)
user_data['figshare_token'] = figshare_token
mongo.update_user(orcid_id, user_data)
elif 'figshare_token' in user_data:
figshare_token = user_data['figshare_token']
else:
figshare_token = None
return figshare_token['access_token']
def get_works(user_token, orcid_id):
api = orcid.PublicAPI(config.get("DEFAULT", "ORCID_CLIENT_ID"),
config.get("DEFAULT", "ORCID_SECRET"))
summary = api.read_record_public(orcid_id, "works", user_token)
metadata = []
for work in summary["group"]:
work_summary = work["work-summary"][0]
work_metadata = dict()
work_metadata["id"] = work_summary["put-code"]
work_metadata["title"] = work_summary["title"]["title"]["value"]
work_metadata["last-modified-date"] = work_summary[
"last-modified-date"]["value"]
work_metadata["type"] = work_summary["type"]
work_metadata["publication-year"] = work_summary["publication-date"][
"year"]["value"]
work_metadata["owner"] = orcid_id
for ext_id in work_summary["external-ids"]["external-id"]:
if ext_id["external-id-type"] == "doi":
work_metadata["doi"] = ext_id["external-id-value"]
if ext_id["external-id-type"] == "pmid":
work_metadata["pmid"] = ext_id["external-id-value"]
if ext_id["external-id-type"] == "pmc":
work_metadata["pmcid"] = ext_id["external-id-value"]
metadata.append(work_metadata)
return metadata
def harvest_file(user, research_object):
tmp_dir = config.get("DEFAULT", "TMP_DIR")
file_name = research_object["source"] + "_" + research_object["name"]
logger.info(f"Harvesting files for research object: ${file_name}")
if research_object["source"] == "github":
downloads_url = research_object["ro"]["archive_url"]
downloads_url = downloads_url.replace("{archive_format}", "zipball")
downloads_url = downloads_url.replace("{/ref}", "/master")
logger.info(
f"Downloading Github zip files for research object: ${file_name}")
ro_content = github.download_zip_file(
downloads_url, user["github_token"]["access_token"])
file_name += ".zip"
with open(tmp_dir + file_name, "wb") as f:
f.write(ro_content)
elif research_object["source"] == "figshare":
file_name += ".zip"
logger.info(
f"Downloading Figshare files for research object: ${file_name}")
figshare.download_files(
research_object["ro"],
user["figshare_token"]["access_token"],
tmp_dir + file_name,
)
else:
logger.info(
f"Generating Orcid JSON file for research object: ${file_name}")
ro_content = str(research_object["ro"]).encode("utf-8")
file_name += ".json"
with open(tmp_dir + file_name, "wb") as f:
f.write(ro_content)
return file_name
def authenticate(auth_code, orcid_id):
user_data = mongo.get_user(orcid_id)
if 'github_token' not in user_data:
params = {'client_id': config.get('DEFAULT', 'GITHUB_CLIENT_ID'),
'client_secret': config.get('DEFAULT', 'GITHUB_SECRET'),
'code': auth_code
}
data = urllib.parse.urlencode(params)
data = data.encode('ascii')
req = urllib.request.Request('https://github.com/login/oauth/access_token', data,
headers={'Accept': 'application/json'})
response = urllib.request.urlopen(req).read()
github_token = json.loads(response)
user_data['github_token'] = github_token
mongo.update_user(orcid_id, user_data)
else:
github_token = user_data['github_token']
return github_token['access_token']
def research_object_exist(source, research_object):
composer_url = config.get("DEFAULT", "HYPERLEDGER_COMPOSER_URL")
research_object_url = (research_object[SOURCE_URL_FIELD_MAP[source]]
if SOURCE_URL_FIELD_MAP[source] in research_object
else research_object["id"])
req = requests.get(f"{composer_url}/ResearchOJ/{research_object_url}")
if req.status_code == 404:
return False
return True
def create_researcher(user):
composer_url = config.get("DEFAULT", "HYPERLEDGER_COMPOSER_URL")
researcher = {
"$class": "org.bforos.Researcher",
"researcherId": f"{user['orcid']}",
"firstName": user["first_name"],
"lastName": user["last_name"],
"email": f"{user['orcid']}@b4os.com",
}
req = requests.post(f"{composer_url}/api/Researcher", researcher)
return True
def claim_research_object(orcid_id, source, research_object):
composer_url = config.get("DEFAULT", "HYPERLEDGER_COMPOSER_URL")
research_object_url = (research_object[SOURCE_URL_FIELD_MAP[source]]
if SOURCE_URL_FIELD_MAP[source] in research_object
else research_object["id"])
claim_op = {
"$class": "org.bforos.ClaimRO",
"researchObjId":
f"resource:org.bforos.ResearchOJ#{research_object_url}",
"claimer": f"resource:org.bforos.Researcher#{orcid_id}",
}
req = requests.post(f"{composer_url}/api/CreateResearchOJ", claim_op)
return True
def update_disco(orcid_id, disco_id, disco_name, research_object_urls):
composer_url = config.get("DEFAULT", "HYPERLEDGER_COMPOSER_URL")
bforos_ros = [
f"resource:org.bforos.ResearchOJ#{url}" for url in research_object_urls
]
create_disco_op = {
"$class": "org.bforos.Disco",
"discoId": disco_id,
"title": disco_name,
"researchObjs": bforos_ros,
"owner": f"org.bforos.Researcher#{orcid_id}",
}
req = requests.put(f"{composer_url}/api/Disco", create_disco_op)
return True
def create_reaserch_object(orcid_id, source, research_object):
ro_type = SOURCE_TYPE_MAP[source] if source in SOURCE_TYPE_MAP else "OTHER"
research_object_url = (research_object[SOURCE_URL_FIELD_MAP[source]]
if SOURCE_URL_FIELD_MAP[source] in research_object
else research_object["id"])
composer_url = config.get("DEFAULT", "HYPERLEDGER_COMPOSER_URL")
create_op = {
"$class": "org.bforos.CreateResearchOJ",
"typeRO": ro_type,
"uri": research_object_url,
"creator": f"org.bforos.Researcher#{orcid_id}",
"researchObjId": research_object_url,
}
req = requests.post(f"{composer_url}/api/CreateResearchOJ", create_op)
return True
def create_disco(orcid_id, disco_id, disco_name, research_object_urls):
composer_url = config.get("DEFAULT", "HYPERLEDGER_COMPOSER_URL")
bforos_ros = [
f"resource:org.bforos.ResearchOJ#{url}" for url in research_object_urls
]
create_disco_op = {
"$class": "org.bforos.Disco",
"discoId": disco_id,
"title": disco_name,
"researchObjs": bforos_ros,
"owner": f"org.bforos.Researcher#{orcid_id}",
"collectors": [f"org.bforos.Researcher#{orcid_id}"],
}
logger.info(create_disco_op)
headers = {"Content-Type": "application/json"}
req = requests.post(f"{composer_url}/api/Disco",
json.dumps(create_disco_op),
headers=headers)
logger.info(req.text)
return True
from scholarly_wallet import config
from scholarly_wallet import mongo_access as mongo, github_api as github
from scholarly_wallet import figshare_api as figshare
from scholarly_wallet import zenodo_api as zenodo
from flask_jwt_extended import (
JWTManager,
jwt_required,
create_access_token,
get_jwt_identity,
)
from scholarly_wallet import hyperledger_api as hyperledger
from threading import Thread
app = Flask(__name__)
app.config["JWT_SECRET_KEY"] = config.get("DEFAULT", "JWT_SECRET")
app.config["JWT_ACCESS_TOKEN_EXPIRES"] = int(config.get("DEFAULT", "JWT_EXPIRES"))
jwt = JWTManager(app)
DEFAULT_SORT = {"orcid": "title", "github": "full_name", "figshare": "title"}
@app.route("/api/auth/orcid", methods=["GET", "OPTIONS"])
def signin():
auth_code = request.args.get("orcid_auth_code")
user_data = orcid.authenticate(auth_code)
if user_data is None:
return jsonify({"msg": "Failed authetication with Orcid"}), 403
access_token = create_access_token(identity=user_data)
return jsonify(access_token=access_token), 200
def publish_to_zenodo(author, disco):
turtle = get_rmap_rdf(author, disco)
zenodo_url = config.get("DEFAULT", "ZENODO_REPOSITIONS_URL")
zenodo_token = config.get("DEFAULT", "ZENODO_ACCESS_TOKEN")
headers = {"Content-Type": "application/json"}
r = requests.post(zenodo_url,
params={"access_token": zenodo_token},
json={},
headers=headers)
r = r.json()
deposition_id = r["id"]
deposition_doi = r["metadata"]["prereserve_doi"]["doi"]
file_name_base = deposition_doi.replace("/", "_")
tmp_dir = config.get("DEFAULT", "TMP_DIR")
with open(tmp_dir + file_name_base + ".rdf", "w+") as t_file:
t_file.write(turtle.decode("utf-8"))
turtle_file = open(tmp_dir + deposition_doi.replace("/", "_") + ".rdf",
"rb")
data = {"filename": deposition_doi + ".rdf"}
files = {"file": turtle_file}
r = requests.post(
f"{zenodo_url}/{deposition_id}/files",
params={"access_token": zenodo_token},
data=data,
files=files,
)
img_data = base64.b64decode(disco["thumb"].split(",")[1])
png_file = f"{file_name_base}.png"
with open(tmp_dir + png_file, "wb") as f:
f.write(img_data)
png_file = open(tmp_dir + png_file, "rb")
data = {"filename": deposition_doi.replace("/", "_") + ".png"}
files = {"file": png_file}
r = requests.post(
f"{zenodo_url}/{deposition_id}/files",
params={"access_token": zenodo_token},
data=data,
files=files,
)
for research_object in disco["diagram"]["elements"]["nodes"]:
research_object = research_object["data"]
file_name = harvest_file(author, research_object)
ro_file = open(tmp_dir + file_name, "rb")
data = {"filename": file_name}
files = {"file": ro_file}
logger.info(f"Uploading ${file_name} to Zenodo")
r = requests.post(
f"{zenodo_url}/{deposition_id}/files",
params={"access_token": zenodo_token},
data=data,
files=files,
)
notes = ""
# TODO Design a implement a queue for publication2zenodo
data = {
"metadata": {
"title":
disco["name"],
"upload_type":
"dataset",
"publication_type":
"milestone",
"description":
disco["description"] if disco["description"] else disco["name"],
"creators": [{
"name": author["name"],
"orcid": author["orcid"]
}],
"keywords": ["disco", "scholarly wallet", "bundle"],
"notes":
notes,
"access_right":
"open",
"communities": [{
"identifier": "b4ossw"
}],
}
}
r = requests.put(
f"{zenodo_url}/{deposition_id}",
params={"access_token": zenodo_token},
data=json.dumps(data),
headers=headers,
)
r = requests.post(
f"{zenodo_url}/{deposition_id}/actions/publish",
params={"access_token": zenodo_token},
)
mongo.update_disco(
author["orcid"],
disco["_id"],
{
"doi": deposition_doi,
"zenodo_id": deposition_id,
"status": "published"
},
)
return dumps({"doi": deposition_doi, "zenodo_id": deposition_id})
def authenticate(auth_code):
params = {
"client_id": config.get("DEFAULT", "ORCID_CLIENT_ID"),
"client_secret": config.get("DEFAULT", "ORCID_SECRET"),
"grant_type": "authorization_code",
"code": auth_code,
"redirect_uri": config.get("DEFAULT", "CLIENT_URL"),
}
data = urllib.parse.urlencode(params)
data = data.encode("ascii")
req = urllib.request.Request(
config.get("DEFAULT", "ORCID_AUTH_URL"),
data,
headers={"Accept": "application/json"},
)
try:
response = urllib.request.urlopen(req).read()
user_data: Dict = json.loads(response)
orcid_token = {
"access_token": user_data.pop("access_token"),
"token_type": user_data.pop("token_type"),
"refresh_token": user_data.pop("refresh_token"),
"expires_in": user_data.pop("expires_in"),
"scope": user_data.pop("scope"),
}
user_data["orcid_token"] = orcid_token
if not mongo.user_exists(user_data["orcid"]):
req = urllib.request.Request(
config.get("DEFAULT", "ORCID_API_URL") + "/" +
user_data["orcid"] + "/person",
data,
headers={
"Accept": "application/json",
"Authorization": f'Bearer {orcid_token["access_token"]}',
},
)
response = urllib.request.urlopen(req).read()
user_profile_data: Dict = json.loads(response)
first_name = user_profile_data["name"]["given-names"]["value"]
last_name = user_profile_data["name"]["family-name"]["value"]
user_data["first_name"] = first_name
user_data["last_name"] = last_name
mongo.create_user(user_data)
thread_user = Thread(target=hyperledger.create_researcher,
args=(user_data, ))
thread_user.start()
user_data.pop("_id")
else:
mongo.update_user(user_data["orcid"], user_data)
works = get_works(user_data["orcid_token"]["access_token"],
user_data["orcid"])
for work in works:
if not mongo.work_exists(work["id"], user_data["orcid"]):
mongo.save_ros([work], "orcid")
thread_works = Thread(target=hyperledger.claim_ros,
args=(user_data["orcid"], "orcid", works))
thread_works.start()
for field_name in user_data.keys():
if field_name.endswith("_token"):
user_data[field_name.replace("_token", "_access")] = True
user_data.pop(field_name)
return user_data
except urllib.error.HTTPError as e:
return None