aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorBonfaceKilz2021-11-01 17:39:28 +0300
committerBonfaceKilz2021-11-04 15:22:41 +0300
commit3b8f6eedaa9ca47cdbfdf2a7f87858e58949e8dd (patch)
tree68b000d61110819e1e813d872e56e56fb75d2de6
parentf6a2a07b726dbff09f73bd7e98b155fd90471862 (diff)
downloadgenenetwork2-3b8f6eedaa9ca47cdbfdf2a7f87858e58949e8dd.tar.gz
Move "*/diffs/*" to metadata_edits module
-rw-r--r--wqflask/wqflask/metadata_edits.py162
-rw-r--r--wqflask/wqflask/views.py62
2 files changed, 130 insertions, 94 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index 2be54620..85bd9b08 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -49,6 +49,45 @@ from gn3.db.traits import update_sample_data
metadata_edit = Blueprint('metadata_edit', __name__)
+def _get_diffs(diff_dir: str,
+ user_id: str,
+ redis_conn: redis.Redis,
+ gn_proxy_url: str):
+ def __get_file_metadata(file_name: str) -> Dict:
+ author, resource_id, time_stamp, *_ = file_name.split(".")
+
+ return {
+ "resource_id": resource_id,
+ "file_name": file_name,
+ "author": json.loads(redis_conn.hget("users",
+ author)).get("full_name"),
+ "time_stamp": time_stamp,
+ "roles": get_highest_user_access_role(
+ resource_id=resource_id,
+ user_id=user_id,
+ gn_proxy_url=gn_proxy_url),
+ }
+
+ approved, rejected, waiting = [], [], []
+ if os.path.exists(diff_dir):
+ for name in os.listdir(diff_dir):
+ file_metadata = __get_file_metadata(file_name=name)
+ admin_status = file_metadata["roles"].get("admin")
+ append_p = (user_id in name or
+ admin_status > AdminRole.EDIT_ACCESS)
+ if name.endswith(".rejected") and append_p:
+ rejected.append(__get_file_metadata(file_name=name))
+ elif name.endswith(".approved") and append_p:
+ approved.append(__get_file_metadata(file_name=name))
+ elif append_p: # Normal file
+ waiting.append(__get_file_metadata(file_name=name))
+ return {
+ "approved": approved,
+ "rejected": rejected,
+ "waiting": waiting,
+ }
+
+
def edit_phenotype(conn, name, dataset_id):
publish_xref = fetchone(
conn=conn,
@@ -185,7 +224,7 @@ def update_phenotype(dataset_id: str, name: str):
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 "")
+ or g.user_session.record.get("user_id") or "")
phenotype_id = str(data_.get('phenotype-id'))
if not (file_ := request.files.get("file")):
flash("No sample-data has been uploaded", "warning")
@@ -201,13 +240,13 @@ def update_phenotype(dataset_id: str, name: str):
os.makedirs(os.path.join(SAMPLE_DATADIR,
"updated"))
current_time = str(datetime.datetime.now().isoformat())
- _file_name = (f"{request.args.get('resource-id')}."
- f"{current_time}.csv")
+ _file_name = (f"{author}.{request.args.get('resource-id')}."
+ f"{current_time}")
new_file_name = (os.path.join(TMPDIR,
f"sample-data/updated/{_file_name}.csv"))
uploaded_file_name = (os.path.join(
- TMPDIR, "sample-data/updated/updated.",
- f"{_file_name}.csv"))
+ TMPDIR, "sample-data/updated/",
+ f"{_file_name}.csv.uploaded"))
file_.save(new_file_name)
publishdata_id = ""
lines = []
@@ -331,7 +370,7 @@ def update_probeset(name: str):
}
diff_data = {}
author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
- or g.user_session.record.get("user_id") or "")
+ or g.user_session.record.get("user_id") or "")
if (updated_probeset := update(
conn, "ProbeSet",
data=Probeset(**probeset_),
@@ -371,29 +410,88 @@ def get_sample_data_as_csv(dataset_id: str, phenotype_id: int):
)
-# @metadata_edit.route("/diffs")
-# @login_required
-# def display_diffs_admin():
-# TMPDIR = current_app.config.get("TMPDIR")
-# DIFF_DIR = f"{TMPDIR}/sample-data/diffs"
-# approved_files, rejected_files, files = {}, {}, {}
-# user_id = ((g.user_session.record.get(b"user_id") or
-# b"").decode("utf-8")
-# or g.user_session.record.get("user_id") or "")
-# redis_conn = redis.from_url(current_app.config["REDIS_URL"],
-# decode_responses=True)
-# if os.path.exists(DIFF_DIR):
-# for name in os.listdir(DIFF_DIR):
-# if name.endswith(".approved"):
-
-# approved_file.update{
-
-# }
-# approved_files.add(name)
-# elif name.endswith(".rejected"):
-# approved_files.add(name)
-# else:
-# files.append(name)
-# return render_template("display_files_admin.html",
-# files=files)
-# http://localhost:5004/datasets/diffs/admin
+@metadata_edit.route("/diffs")
+@login_required
+def list_diffs():
+ files = _get_diffs(
+ diff_dir=f"{current_app.config.get('TMPDIR')}/sample-data/diffs",
+ user_id=((g.user_session.record.get(b"user_id") or
+ b"").decode("utf-8")
+ or g.user_session.record.get("user_id") or ""),
+ redis_conn=redis.from_url(current_app.config["REDIS_URL"],
+ decode_responses=True),
+ gn_proxy_url=current_app.config.get("GN2_PROXY"))
+ return render_template(
+ "display_files.html",
+ approved=files.get("approved"),
+ rejected=files.get("rejected"),
+ waiting=files.get("waiting"))
+
+
+@metadata_edit.route("/diffs/<name>")
+def show_diff(name):
+ TMPDIR = current_app.config.get("TMPDIR")
+ with open(os.path.join(f"{TMPDIR}/sample-data/diffs",
+ name), 'r') as myfile:
+ content = myfile.read()
+ return Response(content, mimetype='text/json')
+
+# http://localhost:5004/datasets/diffs
+@metadata_edit.route("<resource_id>/diffs/<file_name>/reject")
+@edit_admins_access_required
+@login_required
+def reject_data(resource_id: str, file_name: str):
+ TMPDIR = current_app.config.get("TMPDIR")
+ os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name),
+ os.path.join(f"{TMPDIR}/sample-data/diffs",
+ f"{file_name}.rejected"))
+ flash(f"{file_name} has been rejected!", "success")
+ return redirect(url_for('metadata_edit.list_diffs'))
+
+
+@metadata_edit.route("<resource_id>/diffs/<file_name>/approve")
+@edit_admins_access_required
+@login_required
+def approve_data(resource_id:str, file_name: str):
+ sample_data = {file_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"))
+ TMPDIR = current_app.config.get("TMPDIR")
+ with open(os.path.join(f"{TMPDIR}/sample-data/diffs",
+ file_name), 'r') as myfile:
+ sample_data = json.load(myfile)
+ PUBLISH_ID = sample_data.get("publishdata_id")
+ modifications = [d for d in sample_data.get("Modifications")]
+ row_counts = len(modifications)
+ for modification in modifications:
+ if modification.get("Current"):
+ (strain_id,
+ strain_name,
+ value, se, count) = modification.get("Current").split(",")
+ update_sample_data(
+ conn=conn,
+ strain_name=strain_name,
+ strain_id=int(strain_id),
+ publish_data_id=int(PUBLISH_ID),
+ value=value,
+ error=se,
+ count=count
+ )
+ insert(conn,
+ table="metadata_audit",
+ data=MetadataAudit(
+ dataset_id=name.split(".")[0], # use the dataset name
+ editor=sample_data.get("author"),
+ json_data=json.dumps(sample_data)))
+ if modifications:
+ # Once data is approved, rename it!
+ os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name),
+ os.path.join(f"{TMPDIR}/sample-data/diffs",
+ f"{file_name}.approved"))
+ flash((f"Just updated data from: {file_name}; {row_counts} "
+ "row(s) modified!"),
+ "success")
+ return redirect(url_for('metadata_edit.list_diffs'))
+
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3e53e4c5..2cbaffd6 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1084,65 +1084,3 @@ def display_diffs_users():
files=files)
-@app.route("/data-samples/approve/<name>")
-def approve_data(name):
- sample_data = {}
- 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"))
- TMPDIR = current_app.config.get("TMPDIR")
- with open(os.path.join(f"{TMPDIR}/sample-data/diffs",
- name), 'r') as myfile:
- sample_data = json.load(myfile)
- PUBLISH_ID = sample_data.get("publishdata_id")
- modifications = [d for d in sample_data.get("Modifications")]
- row_counts = len(modifications)
- for modification in modifications:
- if modification.get("Current"):
- (strain_id,
- strain_name,
- value, se, count) = modification.get("Current").split(",")
- update_sample_data(
- conn=conn,
- strain_name=strain_name,
- strain_id=int(strain_id),
- publish_data_id=int(PUBLISH_ID),
- value=value,
- error=se,
- count=count
- )
- insert(conn,
- table="metadata_audit",
- data=MetadataAudit(
- dataset_id=name.split(".")[0], # use the dataset name
- editor=sample_data.get("author"),
- json_data=json.dumps(sample_data)))
- if modifications:
- # Once data is approved, rename it!
- os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name),
- os.path.join(f"{TMPDIR}/sample-data/diffs",
- f"{name}.approved"))
- flash((f"Just updated data from: {name}; {row_counts} "
- "row(s) modified!"),
- "success")
- return redirect("/admin/data-sample/diffs/")
-
-
-@app.route("/data-samples/reject/<name>")
-def reject_data(name):
- TMPDIR = current_app.config.get("TMPDIR")
- os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name),
- os.path.join(f"{TMPDIR}/sample-data/diffs",
- f"{name}.rejected"))
- flash(f"{name} has been rejected!", "success")
- return redirect("/admin/data-sample/diffs/")
-
-
-@app.route("/display-file/<name>")
-def display_file(name):
- TMPDIR = current_app.config.get("TMPDIR")
- with open(os.path.join(f"{TMPDIR}/sample-data/diffs",
- name), 'r') as myfile:
- content = myfile.read()
- return Response(content, mimetype='text/json')