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import requests
import subprocess
from urllib.parse import urljoin
from pathlib import Path
from gn2.wqflask.oauth2.session import session_info
from pymonad.either import Either, Left, Right
from flask import (Blueprint,
flash,
redirect,
render_template,
request)
from gn2.wqflask.oauth2.checks import require_oauth2
from gn2.wqflask.oauth2.checks import require_oauth2_edit_resource_access
metadata = Blueprint("metadata", __name__)
def __run_cmd__(cmd) -> Either:
"""Run a given command and return it's results as an Either monad"""
_result = ""
try:
_result = subprocess.run(
cmd, capture_output=True
)
except Exception as e_:
return Left({
"command": cmd,
"error": str(e_),
})
if _result.stderr:
return Left({
"command": cmd,
"error": _result.stderr.decode()
})
return Right(_result.stdout)
def save_dataset_metadata(
git_dir: str, output: str,
author: str, content: str, msg: str
) -> Either:
"""Save dataset metadata to git"""
def __write__():
try:
with Path(output).open(mode="w") as f_:
f_.write(content)
return Right(0)
except Exception as e_:
return Left({
"command": "Writing to File",
"error": str(e_)
})
return (
__run_cmd__(f"git -C {git_dir} reset --hard origin".split(" "))
.then(lambda _: __run_cmd__(f"git -C {git_dir} pull".split(" ")))
.then(lambda _: __write__())
.then(lambda _: __run_cmd__(f"git -C {git_dir} add .".split(" ")))
.then(lambda _: __run_cmd__(
f"git -C {git_dir} commit -m".split(" ") + [
f'{msg}', f"--author='{author}'", "--no-gpg-sign"
]))
.then(lambda _: __run_cmd__(f"git -C {git_dir} \
push origin master --dry-run".split(" ")))
)
@metadata.route("/edit")
@require_oauth2_edit_resource_access
@require_oauth2
def metadata_edit():
"""Endpoint that provides editing functionality for datasets."""
from gn2.utility.tools import GN3_LOCAL_URL
_name = request.args.get("name")
match request.args.get("type"):
case "dcat:Dataset":
_metadata = requests.get(
urljoin(
GN3_LOCAL_URL,
f"api/metadata/datasets/{ _name }"
)
).json()
_section = request.args.get("section")
return render_template(
"metadata/editor.html",
name=_name,
metadata=_metadata,
section=_section,
edit=_metadata.get(_section),
)
case _:
return redirect(
f"/datasets/{_name}"
)
@metadata.route("/save", methods=["POST"])
@require_oauth2_edit_resource_access
@require_oauth2
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")
).either(
lambda error: flash(
f"{error=}",
"error"
),
lambda x: flash(
"Successfully updated data.",
"success"
)
)
return redirect(
f"/datasets/{request.form.get('label')}"
)
def __fetch_dataset_git_history__(
git_dir:str , dataset_name: str
) -> Either:
"""Fetch the git history of a given dataset."""
# Age, Commit, Message, Author
dataset_path = Path(git_dir) / "general/datasets/" / dataset_name
format_ = "<tr><td><i>%cr</i></td>\
<td>\
<a style='color:green;' href='https://git.genenetwork.org/gn-docs/commit/general?id=%H' \
target='_blank'>%h</a></td>\
<td>%s</td><td>%an</td></tr>"
args = [
"git", "-C", str(dataset_path), "log",
f"--pretty=format:{format_}"
]
results = __run_cmd__(
args
)
return results
@metadata.route("<id_>/history")
def view_history(id_):
"""View a datasets history"""
from gn2.utility.tools import get_setting
data = __fetch_dataset_git_history__(
Path(get_setting("DATA_DIR"), "gn-docs"), id_
).either(
lambda error: flash(f"{error=}", error),
lambda x: x
)
return render_template(
"dataset_history.html",
name=request.args.get("name",""),
data=data.decode()
)
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