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import MySQLdb
import os
import json
import difflib
from collections import namedtuple
from flask import Blueprint, current_app, 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
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")
@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"),
resource_id=request.args.get("resource-id"),
version=os.environ.get("GN_VERSION"),
)
@metadata_edit.route("/traits/<name>/edit")
@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"),
)
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