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-rw-r--r--gn2/wqflask/edit.py100
1 files changed, 47 insertions, 53 deletions
diff --git a/gn2/wqflask/edit.py b/gn2/wqflask/edit.py
index ebf8449d..e7a58bc0 100644
--- a/gn2/wqflask/edit.py
+++ b/gn2/wqflask/edit.py
@@ -1,9 +1,14 @@
+import uuid
import requests
import subprocess
+import time
from urllib.parse import urljoin
from pathlib import Path
+
+from gn2.wqflask.oauth2.client import oauth2_get
from gn2.wqflask.oauth2.session import session_info
+from gn2.wqflask.oauth2.tokens import JWTToken
from pymonad.either import Either, Left, Right
@@ -66,8 +71,7 @@ def save_dataset_metadata(
f'{msg}', f"--author='{author}'", "--no-gpg-sign"
]))
.then(lambda _: __run_cmd__(f"git -C {git_dir} \
-push origin master --dry-run".split(" ")))
- )
+push origin master --dry-run".split(" "))))
@metadata.route("/edit")
@@ -94,9 +98,7 @@ def metadata_edit():
edit=_metadata.get(_section),
)
case _:
- return redirect(
- f"/datasets/{_name}"
- )
+ return redirect(f"/datasets/{_name}")
@metadata.route("/save", methods=["POST"])
@@ -105,55 +107,47 @@ def metadata_edit():
def save():
"""Save dataset edits in git."""
from gn2.utility.tools import get_setting
- _gn_docs = Path(
- get_setting("DATA_DIR"),
- "gn-docs"
- )
- # This maps the form elements to the actual path in the git
- # repository
- _map = {
- "description": "summary.rtf",
- "tissueInfo": "tissue.rtf",
- "specifics": "specifics.rtf",
- "caseInfo": "cases.rtf",
- "platformInfo": "platform.rtf",
- "processingInfo": "processing.rtf",
- "notes": "notes.rtf",
- "experimentDesignInfo": "experiment-design.rtf",
- "acknowledgement": "acknowledgement.rtf",
- "citation": "citation.rtf",
- "experimentType": "experiment-type.rtf",
- "contributors": "contributors.rtf"
- }
- _output = Path(
- _gn_docs,
- "general/datasets/",
- request.form.get("id").split("/")[-1],
- f"{_map.get(request.form.get('section'))}"
- )
- match request.form.get("type"):
- case "dcat:Dataset":
- _session = session_info()["user"]
- _author = f"{_session['name']} <{_session['email']}>"
- save_dataset_metadata(
- git_dir=_gn_docs,
- output=_output,
- author=_author,
- content=request.form.get("editor"),
- msg=request.form.get("edit-summary")
+ from gn2.utility.tools import GN3_LOCAL_URL
+ # Call an endpoint to GN3 with special headers
+ name = request.form.get('label')
+ metadata = requests.get(
+ urljoin(
+ GN3_LOCAL_URL,
+ f"api/metadata/datasets/{name}")).json()
+ _session = session_info()["user"]
+ outgoing_url = urljoin(
+ GN3_LOCAL_URL,
+ "api/metadata/datasets/edit")
+ iat = int(time.time())
+ exp = iat + 300 # Expire after 300 seconds
+ token = JWTToken(
+ key=get_setting("JWT_SECRET_KEY"),
+ registered_claims={
+ "iat": iat,
+ "iss": request.url,
+ "sub": request.form.get("label"),
+ "aud": outgoing_url,
+ "exp": exp,
+ "jti": str(uuid.uuid4())},
+ private_claims={
+ "account-name": _session["name"],
+ "email": _session['email'],
+ "account-roles": oauth2_get(
+ f"auth/resource/authorisation\
+/{metadata.get('id', '').split('/')[-1]}"
).either(
- lambda error: flash(
- f"{error=}",
- "error"
- ),
- lambda x: flash(
- "Successfully updated data.",
- "success"
- )
- )
- return redirect(
- f"/datasets/{request.form.get('label')}"
- )
+ lambda err: {"roles": []},
+ lambda val: val)})
+ response = requests.post(
+ outgoing_url,
+ data=request.form,
+ headers=token.bearer_token)
+ if response.status_code == 201:
+ flash("Unable to update data", "alert-danger")
+ else:
+ flash("Successfully updated data", "success")
+ # Make a request to GN3 save endpoint
+ return redirect(f"/datasets/{name}")
def __fetch_dataset_git_history__(