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import MySQLdb
import os
import json
import datetime
import difflib
from collections import namedtuple
from flask import (Blueprint, current_app, redirect,
flash, g, render_template, request)
from itertools import groupby
from wqflask.decorators import edit_access_required
from gn3.db import diff_from_dict
from gn3.db import fetchall
from gn3.db import fetchone
from gn3.db import insert
from gn3.db import update
from gn3.db.metadata_audit import MetadataAudit
from gn3.db.phenotypes import Phenotype
from gn3.db.phenotypes import Probeset
from gn3.db.phenotypes import Publication
from gn3.db.phenotypes import PublishXRef
from gn3.db.phenotypes import probeset_mapping
from gn3.commands import run_cmd
from gn3.db.traits import get_trait_csv_sample_data
from gn3.db.traits import update_sample_data
metadata_edit = Blueprint('metadata_edit', __name__)
def edit_phenotype(conn, name, dataset_id):
publish_xref = fetchone(
conn=conn,
table="PublishXRef",
where=PublishXRef(id_=name,
inbred_set_id=dataset_id))
phenotype_ = fetchone(
conn=conn,
table="Phenotype",
where=Phenotype(id_=publish_xref.phenotype_id))
publication_ = fetchone(
conn=conn,
table="Publication",
where=Publication(id_=publish_xref.publication_id))
json_data = fetchall(
conn,
"metadata_audit",
where=MetadataAudit(dataset_id=publish_xref.id_))
Edit = namedtuple("Edit", ["field", "old", "new", "diff"])
Diff = namedtuple("Diff", ["author", "diff", "timestamp"])
diff_data = []
for data in json_data:
json_ = json.loads(data.json_data)
timestamp = json_.get("timestamp")
author = json_.get("author")
for key, value in json_.items():
if isinstance(value, dict):
for field, data_ in value.items():
diff_data.append(
Diff(author=author,
diff=Edit(field,
data_.get("old"),
data_.get("new"),
"\n".join(difflib.ndiff(
[data_.get("old")],
[data_.get("new")]))),
timestamp=timestamp))
diff_data_ = None
if len(diff_data) > 0:
diff_data_ = groupby(diff_data, lambda x: x.timestamp)
return {
"diff": diff_data_,
"publish_xref": publish_xref,
"phenotype": phenotype_,
"publication": publication_,
}
def edit_probeset(conn, name):
probeset_ = fetchone(conn=conn,
table="ProbeSet",
columns=list(probeset_mapping.values()),
where=Probeset(name=name))
json_data = fetchall(
conn,
"metadata_audit",
where=MetadataAudit(dataset_id=probeset_.id_))
Edit = namedtuple("Edit", ["field", "old", "new", "diff"])
Diff = namedtuple("Diff", ["author", "diff", "timestamp"])
diff_data = []
for data in json_data:
json_ = json.loads(data.json_data)
timestamp = json_.get("timestamp")
author = json_.get("author")
for key, value in json_.items():
if isinstance(value, dict):
for field, data_ in value.items():
diff_data.append(
Diff(author=author,
diff=Edit(field,
data_.get("old"),
data_.get("new"),
"\n".join(difflib.ndiff(
[data_.get("old")],
[data_.get("new")]))),
timestamp=timestamp))
diff_data_ = None
if len(diff_data) > 0:
diff_data_ = groupby(diff_data, lambda x: x.timestamp)
return {
"diff": diff_data_,
"probeset": probeset_,
}
@metadata_edit.route("/<dataset_id>/traits/<name>")
@edit_access_required
def display_phenotype_metadata(dataset_id: str, name: str):
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
passwd=current_app.config.get("DB_PASS"),
host=current_app.config.get("DB_HOST"))
_d = edit_phenotype(conn=conn, name=name, dataset_id=dataset_id)
return render_template(
"edit_phenotype.html",
diff=_d.get("diff"),
publish_xref=_d.get("publish_xref"),
phenotype=_d.get("phenotype"),
publication=_d.get("publication"),
dataset_id=dataset_id,
resource_id=request.args.get("resource-id"),
version=os.environ.get("GN_VERSION"),
)
@metadata_edit.route("/traits/<name>")
@edit_access_required
def display_probeset_metadata(name: str):
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
passwd=current_app.config.get("DB_PASS"),
host=current_app.config.get("DB_HOST"))
_d = edit_probeset(conn=conn, name=name)
return render_template(
"edit_probeset.html",
diff=_d.get("diff"),
probeset=_d.get("probeset"),
resource_id=request.args.get("resource-id"),
version=os.environ.get("GN_VERSION"),
)
@metadata_edit.route("/<dataset_id>/traits/<name>", methods=("POST",))
@edit_access_required
def update_phenotype(dataset_id: str, name: str):
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
passwd=current_app.config.get("DB_PASS"),
host=current_app.config.get("DB_HOST"))
data_ = request.form.to_dict()
TMPDIR = current_app.config.get("TMPDIR")
author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
or g.user_session.record.get("user_id") or "")
phenotype_id = str(data_.get('phenotype-id'))
if 'file' not in request.files:
flash("No sample-data has been uploaded", "warning")
else:
file_ = request.files['file']
SAMPLE_DATADIR = os.path.join(TMPDIR, "sample-data")
if not os.path.exists(SAMPLE_DATADIR):
os.makedirs(SAMPLE_DATADIR)
if not os.path.exists(os.path.join(SAMPLE_DATADIR,
"diffs")):
os.makedirs(os.path.join(SAMPLE_DATADIR,
"diffs"))
if not os.path.exists(os.path.join(SAMPLE_DATADIR,
"updated")):
os.makedirs(os.path.join(SAMPLE_DATADIR,
"updated"))
current_time = str(datetime.datetime.now().isoformat())
new_file_name = (os.path.join(TMPDIR,
"sample-data/updated/",
(f"{author}."
f"{name}.{phenotype_id}."
f"{current_time}.csv")))
uploaded_file_name = (os.path.join(
TMPDIR,
"sample-data/updated/",
(f"updated.{author}."
f"{request.args.get('resource-id')}."
f"{current_time}.csv")))
file_.save(new_file_name)
publishdata_id = ""
lines = []
with open(new_file_name, "r") as f:
lines = f.read()
first_line = lines.split('\n', 1)[0]
publishdata_id = first_line.split("Id:")[-1].strip()
with open(new_file_name, "w") as f:
f.write(lines.split("\n\n")[-1])
csv_ = get_trait_csv_sample_data(conn=conn,
trait_name=str(name),
phenotype_id=str(phenotype_id))
with open(uploaded_file_name, "w") as f_:
f_.write(csv_.split("\n\n")[-1])
r = run_cmd(cmd=("csvdiff "
f"'{uploaded_file_name}' '{new_file_name}' "
"--format json"))
diff_output = (f"{TMPDIR}/sample-data/diffs/"
f"{author}.{request.args.get('resource-id')}."
f"{current_time}.json")
with open(diff_output, "w") as f:
dict_ = json.loads(r.get("output"))
dict_.update({
"author": author,
"publishdata_id": publishdata_id,
"dataset_id": data_.get("dataset-name"),
"timestamp": datetime.datetime.now().strftime(
"%Y-%m-%d %H:%M:%S")
})
f.write(json.dumps(dict_))
flash("Sample-data has been successfully uploaded", "success")
# Run updates:
phenotype_ = {
"pre_pub_description": data_.get("pre-pub-desc"),
"post_pub_description": data_.get("post-pub-desc"),
"original_description": data_.get("orig-desc"),
"units": data_.get("units"),
"pre_pub_abbreviation": data_.get("pre-pub-abbrev"),
"post_pub_abbreviation": data_.get("post-pub-abbrev"),
"lab_code": data_.get("labcode"),
"submitter": data_.get("submitter"),
"owner": data_.get("owner"),
"authorized_users": data_.get("authorized-users"),
}
updated_phenotypes = update(
conn, "Phenotype",
data=Phenotype(**phenotype_),
where=Phenotype(id_=data_.get("phenotype-id")))
diff_data = {}
if updated_phenotypes:
diff_data.update({"Phenotype": diff_from_dict(old={
k: data_.get(f"old_{k}") for k, v in phenotype_.items()
if v is not None}, new=phenotype_)})
publication_ = {
"abstract": data_.get("abstract"),
"authors": data_.get("authors"),
"title": data_.get("title"),
"journal": data_.get("journal"),
"volume": data_.get("volume"),
"pages": data_.get("pages"),
"month": data_.get("month"),
"year": data_.get("year")
}
updated_publications = update(
conn, "Publication",
data=Publication(**publication_),
where=Publication(id_=data_.get("pubmed-id",
data_.get("old_id_"))))
if updated_publications:
diff_data.update({"Publication": diff_from_dict(old={
k: data_.get(f"old_{k}") for k, v in publication_.items()
if v is not None}, new=publication_)})
if diff_data:
diff_data.update({"dataset_id": name})
diff_data.update({"resource_id": request.args.get('resource-id')})
diff_data.update({"author": author})
diff_data.update({"timestamp": datetime.datetime.now().strftime(
"%Y-%m-%d %H:%M:%S")})
insert(conn,
table="metadata_audit",
data=MetadataAudit(dataset_id=name,
editor=author,
json_data=json.dumps(diff_data)))
flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success")
return redirect(f"/datasets/{dataset_id}/traits/{name}"
f"?resource-id={request.args.get('resource-id')}")
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