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-rw-r--r--wqflask/wqflask/__init__.py3
-rw-r--r--wqflask/wqflask/metadata_edits.py147
-rw-r--r--wqflask/wqflask/views.py115
3 files changed, 153 insertions, 112 deletions
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 5b2d05d1..a5097287 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -11,6 +11,8 @@ from utility import formatting
from wqflask.resource_manager import resource_management
+from wqflask.metadata_edits import metadata_edit
+
from wqflask.api.markdown import glossary_blueprint
from wqflask.api.markdown import references_blueprint
from wqflask.api.markdown import links_blueprint
@@ -60,6 +62,7 @@ app.register_blueprint(news_blueprint, url_prefix="/news")
app.register_blueprint(resource_management, url_prefix="/resource-management")
+app.register_blueprint(metadata_edit, url_prefix="/datasets/")
@app.before_request
def before_request():
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
new file mode 100644
index 00000000..94e2710b
--- /dev/null
+++ b/wqflask/wqflask/metadata_edits.py
@@ -0,0 +1,147 @@
+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"),
+ )
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b0da1f21..463b7c3a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -4,7 +4,6 @@ import MySQLdb
import array
import base64
import csv
-import difflib
import datetime
import flask
import io # Todo: Use cStringIO?
@@ -20,8 +19,6 @@ import traceback
import uuid
import xlsxwriter
-from itertools import groupby
-from collections import namedtuple
from zipfile import ZipFile
from zipfile import ZIP_DEFLATED
@@ -30,19 +27,12 @@ from wqflask import app
from gn3.commands import run_cmd
from gn3.computations.gemma import generate_hash_of_string
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.db.traits import get_trait_csv_sample_data
-# from gn3.db.traits import update_sample_data
-
from flask import current_app
from flask import g
@@ -426,106 +416,6 @@ def submit_trait_form():
version=GN_VERSION)
-@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>")
-@edit_access_required
-def edit_phenotype(name, inbredset_id):
- 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"))
- publish_xref = fetchone(
- conn=conn,
- table="PublishXRef",
- where=PublishXRef(id_=name,
- inbred_set_id=inbredset_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 render_template(
- "edit_phenotype.html",
- diff=diff_data_,
- publish_xref=publish_xref,
- phenotype=phenotype_,
- publication=publication_,
- version=GN_VERSION,
- )
-
-
-@app.route("/trait/edit/probeset-name/<dataset_name>")
-@edit_access_required
-def edit_probeset(dataset_name):
- 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"))
- probeset_ = fetchone(conn=conn,
- table="ProbeSet",
- columns=list(probeset_mapping.values()),
- where=Probeset(name=dataset_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 render_template(
- "edit_probeset.html",
- diff=diff_data_,
- probeset=probeset_)
-
-
@app.route("/trait/update", methods=["POST"])
@edit_access_required
def update_phenotype():
@@ -653,7 +543,6 @@ def update_phenotype():
@app.route("/probeset/update", methods=["POST"])
-@edit_access_required
def update_probeset():
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
@@ -691,7 +580,9 @@ def update_probeset():
where=Probeset(id_=data_.get("id")))
diff_data = {}
- author = g.user_session.record.get(b'user_name')
+ author = (g.user_session.record.get(b"user_id",
+ b"").decode("utf-8") or
+ g.user_session.record.get("user_id", ""))
if updated_probeset:
diff_data.update({"Probeset": diff_from_dict(old={
k: data_.get(f"old_{k}") for k, v in probeset_.items()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 21:41:26 +0000