-
Values of record {{ this_trait.name }} in the {{ dataset.fullname }}
+
Values of record {{ this_trait.name }} in the {{ this_dataset.fullname }}
dataset were compared to all records in the {{ target_dataset.fullname }}
- dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed.
+ dataset. The top {{ return_results }} correlations ranked by the {{ formatted_corr_type }} are displayed.
You can resort this list by clicking the headers. Select the Record ID to open the trait data
and analysis page.
@@ -30,7 +30,7 @@
{% include 'tool_buttons.html' %}
@@ -43,7 +43,7 @@
-
+
@@ -146,7 +146,7 @@
+{% endblock %}
diff --git a/wqflask/wqflask/templates/edit_trait.html b/wqflask/wqflask/templates/edit_trait.html
deleted file mode 100644
index 7d4c65f8..00000000
--- a/wqflask/wqflask/templates/edit_trait.html
+++ /dev/null
@@ -1,234 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Trait Submission{% endblock %}
-{% block content %}
-
-Edit Trait for Published Database
-Submit Trait | Reset
-
-{% if diff %}
-
-
-
-
- Update History
-
-
-
-
- Timestamp
- Editor
- Field
- Diff
-
- {% set ns = namespace(display_cell=True) %}
-
- {% for timestamp, group in diff %}
- {% set ns.display_cell = True %}
- {% for i in group %}
-
- {% if ns.display_cell and i.timestamp == timestamp %}
-
- {% set author = i.author %}
- {% set timestamp_ = i.timestamp %}
-
- {% else %}
-
- {% set author = "" %}
- {% set timestamp_ = "" %}
-
- {% endif %}
- {{ timestamp_ }}
- {{ author }}
- {{ i.diff.field }}
- {{ i.diff.diff }}
- {% endfor %}
- {% endfor %}
-
-
-
-
-
-
-{% endif %}
-
-
-
-{%endblock%}
-
-{% block js %}
-
-{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index da427bfe..595a0de7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -428,9 +428,9 @@ def submit_trait_form():
version=GN_VERSION)
-@app.route("/trait/
/edit/")
+@app.route("/trait//edit/inbredset-id/")
@admin_login_required
-def edit_trait(name, inbred_set_id):
+def edit_phenotype(name, inbred_set_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"),
@@ -476,7 +476,7 @@ def edit_trait(name, inbred_set_id):
if len(diff_data) > 0:
diff_data_ = groupby(diff_data, lambda x: x.timestamp)
return render_template(
- "edit_trait.html",
+ "edit_phenotype.html",
diff=diff_data_,
publish_xref=publish_xref,
phenotype=phenotype_,
@@ -486,7 +486,7 @@ def edit_trait(name, inbred_set_id):
@app.route("/trait/update", methods=["POST"])
-def update_trait():
+def update_phenotype():
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
passwd=current_app.config.get("DB_PASS"),
@@ -544,7 +544,8 @@ def update_trait():
data=MetadataAudit(dataset_id=data_.get("dataset-name"),
editor=author.decode("utf-8"),
json_data=json.dumps(diff_data)))
- return redirect("/trait/10007/edit/1")
+ return redirect(f"/trait/{data_.get('dataset-name')}"
+ f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
@app.route("/create_temp_trait", methods=('POST',))
--
cgit v1.2.3
From ffa34cc70ad70ab39682e8bdda6b6eb0d46a577d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 9 Jul 2021 13:42:22 +0300
Subject: wqflask: views: Add extra route showing probeset editing form
* wqflask/wqflask/views.py (edit_probeset): New function/ route.
---
wqflask/wqflask/views.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 595a0de7..e1f6dd71 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -34,8 +34,10 @@ 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 flask import current_app
@@ -485,6 +487,23 @@ def edit_phenotype(name, inbred_set_id):
)
+@app.route("/trait/edit/probeset-name/")
+@admin_login_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))
+ return render_template(
+ "edit_probeset.html",
+ probeset=probeset_
+ )
+
+
@app.route("/trait/update", methods=["POST"])
def update_phenotype():
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
--
cgit v1.2.3
From 503ff72502d7bc440450c1c91ac2d5051ca446b9 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 9 Jul 2021 15:23:10 +0300
Subject: templates: edit_probeset: Add template for editing probeset data
* wqflask/wqflask/templates/edit_probeset.html: New file(template).
---
wqflask/wqflask/templates/edit_probeset.html | 239 +++++++++++++++++++++++++++
wqflask/wqflask/views.py | 31 +++-
2 files changed, 268 insertions(+), 2 deletions(-)
create mode 100644 wqflask/wqflask/templates/edit_probeset.html
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/edit_probeset.html b/wqflask/wqflask/templates/edit_probeset.html
new file mode 100644
index 00000000..85d49561
--- /dev/null
+++ b/wqflask/wqflask/templates/edit_probeset.html
@@ -0,0 +1,239 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+
+Edit Trait for Probeset
+Submit Trait | Reset
+
+{% if diff %}
+
+
+
+
+ Update History
+
+
+
+
+ Timestamp
+ Editor
+ Field
+ Diff
+
+ {% set ns = namespace(display_cell=True) %}
+
+ {% for timestamp, group in diff %}
+ {% set ns.display_cell = True %}
+ {% for i in group %}
+
+ {% if ns.display_cell and i.timestamp == timestamp %}
+
+ {% set author = i.author %}
+ {% set timestamp_ = i.timestamp %}
+
+ {% else %}
+
+ {% set author = "" %}
+ {% set timestamp_ = "" %}
+
+ {% endif %}
+ {{ timestamp_ }}
+ {{ author }}
+ {{ i.diff.field }}
+ {{ i.diff.diff }}
+ {% endfor %}
+ {% endfor %}
+
+
+
+
+
")
-@admin_login_required
+# @admin_login_required
def edit_probeset(dataset_name):
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
@@ -594,6 +594,63 @@ def update_phenotype():
f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
+@app.route("/probeset/update", methods=["POST"])
+@admin_login_required
+def update_probeset():
+ 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()
+ probeset_ = {
+ "id_": data_.get("id"),
+ "symbol": data_.get("symbol"),
+ "description": data_.get("description"),
+ "probe_target_description": data_.get("probe_target_description"),
+ "chr_": data_.get("chr"),
+ "mb": data_.get("mb"),
+ "alias": data_.get("alias"),
+ "geneid": data_.get("geneid"),
+ "homologeneid": data_.get("homologeneid"),
+ "unigeneid": data_.get("unigeneid"),
+ "omim": data_.get("OMIM"),
+ "refseq_transcriptid": data_.get("refseq_transcriptid"),
+ "blatseq": data_.get("blatseq"),
+ "targetseq": data_.get("targetseq"),
+ "strand_probe": data_.get("Strand_Probe"),
+ "probe_set_target_region": data_.get("probe_set_target_region"),
+ "probe_set_specificity": data_.get("probe_set_specificity"),
+ "probe_set_blat_score": data_.get("probe_set_blat_score"),
+ "probe_set_blat_mb_start": data_.get("probe_set_blat_mb_start"),
+ "probe_set_blat_mb_end": data_.get("probe_set_blat_mb_end"),
+ "probe_set_strand": data_.get("probe_set_strand"),
+ "probe_set_note_by_rw": data_.get("probe_set_note_by_rw"),
+ "flag": data_.get("flag")
+ }
+ updated_probeset = update(
+ conn, "ProbeSet",
+ data=Probeset(**probeset_),
+ where=Probeset(id_=data_.get("id")))
+
+ diff_data = {}
+ author = g.user_session.record.get(b'user_name')
+ if updated_probeset:
+ diff_data.update({"Probeset": diff_from_dict(old={
+ k: data_.get(f"old_{k}") for k, v in probeset_.items()
+ if v is not None}, new=probeset_)})
+ if diff_data:
+ diff_data.update({"probeset_name": data_.get("probeset_name")})
+ diff_data.update({"author": author.decode('utf-8')})
+ diff_data.update({"timestamp": datetime.datetime.now().strftime(
+ "%Y-%m-%d %H:%M:%S")})
+ insert(conn,
+ table="metadata_audit",
+ data=MetadataAudit(dataset_id=data_.get("id"),
+ editor=author.decode("utf-8"),
+ json_data=json.dumps(diff_data)))
+ return redirect(f"/trait/edit/probeset-name/{data_.get('probeset_name')}")
+
+
@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
logger.info(request.url)
--
cgit v1.2.3
From d01b1aadcd3604e4f592f64ce7d9eb010d4c7230 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Sat, 10 Jul 2021 09:55:12 +0300
Subject: templates: show_trait_details: Show edit buttons conditionally
* wqflask/wqflask/templates/show_trait_details.html: Check the data
type, and load different edit buttons.
---
wqflask/wqflask/templates/show_trait_details.html | 6 ++++++
1 file changed, 6 insertions(+)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 83f7b0ac..bb30c54c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -235,8 +235,14 @@
{% endif %}
Go to GN1
{% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+ {% if this_trait.dataset.type == 'Publish' %}
Edit
{% endif %}
+
+ {% if this_trait.dataset.type == 'ProbeSet' %}
+ Edit
+ {% endif %}
+ {% endif %}