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
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 %}
+<!-- Start of body -->
+Edit Trait for Probeset
+Submit Trait | Reset
+
+{% if diff %}
+
+<div class="container">
+ <details class="col-sm-12 col-md-10 col-lg-12">
+ <summary>
+ <h2>Update History</h2>
+ </summary>
+ <table class="table">
+ <tbody>
+ <tr>
+ <th>Timestamp</th>
+ <th>Editor</th>
+ <th>Field</th>
+ <th>Diff</th>
+ </tr>
+ {% set ns = namespace(display_cell=True) %}
+
+ {% for timestamp, group in diff %}
+ {% set ns.display_cell = True %}
+ {% for i in group %}
+ <tr>
+ {% if ns.display_cell and i.timestamp == timestamp %}
+
+ {% set author = i.author %}
+ {% set timestamp_ = i.timestamp %}
+
+ {% else %}
+
+ {% set author = "" %}
+ {% set timestamp_ = "" %}
+
+ {% endif %}
+ <td>{{ timestamp_ }}</td>
+ <td>{{ author }}</td>
+ <td>{{ i.diff.field }}</td>
+ <td><pre>{{ i.diff.diff }}</pre></td>
+ {% set ns.display_cell = False %}
+ </tr>
+ {% endfor %}
+ {% endfor %}
+ </tbody>
+ </table>
+ </details>
+
+</div>
+
+{% endif %}
+
+<form id="edit-form" class="form-horizontal" method="post" action="/probeset/update">
+ <h2 class="text-center">Probeset Information:</h2>
+ <div class="form-group">
+ <label for="symbol" class="col-sm-2 control-label">Symbol:</label>
+ <div class="col-sm-4">
+ <textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea>
+ <input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="description" class="col-sm-2 control-label">Description:</label>
+ <div class="col-sm-5">
+ <textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea>
+ <input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_target_description" class="col-sm-2 control-label">Probe Target Description:</label>
+ <div class="col-sm-4">
+ <textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea>
+ <input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="chr" class="col-sm-2 control-label">Chr:</label>
+ <div class="col-sm-4">
+ <textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea>
+ <input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="mb" class="col-sm-2 control-label">Mb:</label>
+ <div class="col-sm-4">
+ <textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea>
+ <input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="alias" class="col-sm-2 control-label">
+ Alias:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea>
+ <input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="geneid" class="col-sm-2 control-label">
+ Gene Id:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea>
+ <input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="homologeneid" class="col-sm-2 control-label">
+ Homolegene Id:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea>
+ <input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="unigeneid" class="col-sm-2 control-label">
+ Unigene Id:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea>
+ <input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="omim" class="col-sm-2 control-label">OMIM:</label>
+ <div class="col-sm-4">
+ <textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea>
+ <input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="refseq_transcriptid" class="col-sm-2 control-label">
+ Refseq TranscriptId:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea>
+ <input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="blatseq" class="col-sm-2 control-label">BlatSeq:</label>
+ <div class="col-sm-8">
+ <textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea>
+ <input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="targetseq" class="col-sm-2 control-label">TargetSeq:</label>
+ <div class="col-sm-8">
+ <textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea>
+ <input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="strand_probe" class="col-sm-2 control-label">Strand Probe:</label>
+ <div class="col-sm-2">
+ <textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea>
+ <input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_target_region" class="col-sm-2 control-label">Probe Set Target Region:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea>
+ <input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_specificity" class="col-sm-2 control-label">Probeset Specificity:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea>
+ <input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_blat_score" class="col-sm-2 control-label">Probeset Blat Score:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea>
+ <input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_blat_mb_start" class="col-sm-2 control-label">
+ Probeset Blat Mb Start:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea>
+ <input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_blat_mb_end" class="col-sm-2 control-label">Probeset Blat Mb End:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_blat_mb_end" class="form-control" rows="6">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea>
+ <input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_strand" class="col-sm-2 control-label">Probeset Strand:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea>
+ <input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_note_by_rw" class="col-sm-2 control-label">Probeset Strand:</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea>
+ <input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
+ <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+ <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+ <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/>
+ <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change">
+ <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset">
+ </div>
+</form>
+
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+ function MarkAsChanged(){
+ $(this).addClass("changed");
+ }
+ $(":input").blur(MarkAsChanged).change(MarkAsChanged);
+
+ $("input[type=submit]").click(function(){
+ $(":input:not(.changed)").attr("disabled", "disabled");
+ });
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index e1f6dd71..741861e6 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -498,13 +498,40 @@ def edit_probeset(dataset_name):
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",
- probeset=probeset_
- )
+ diff=diff_data_,
+ probeset=probeset_)
@app.route("/trait/update", methods=["POST"])
+@admin_login_required
def update_phenotype():
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
--
cgit v1.2.3