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-rw-r--r--scripts/add_missing_columns.sh3
-rw-r--r--wqflask/.DS_Storebin6148 -> 0 bytes
-rw-r--r--wqflask/base/data_set.py12
-rw-r--r--wqflask/runserver.py3
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py3
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html2
-rw-r--r--wqflask/wqflask/views.py36
-rw-r--r--wqflask/wsgi.py4
8 files changed, 14 insertions, 49 deletions
diff --git a/scripts/add_missing_columns.sh b/scripts/add_missing_columns.sh
index 70d5fdeb..611e2dd6 100644
--- a/scripts/add_missing_columns.sh
+++ b/scripts/add_missing_columns.sh
@@ -13,6 +13,9 @@
ALTER TABLE PublishXRef
ADD mean double AFTER DataId;
+ ALTER TABLE CaseAttribute
+ ADD Description varchar(255) AFTER Name;
+
-- This takes some time
ALTER TABLE ProbeSet
ADD UniProtID varchar(20) AFTER ProteinName;
diff --git a/wqflask/.DS_Store b/wqflask/.DS_Store
deleted file mode 100644
index d992942f..00000000
--- a/wqflask/.DS_Store
+++ /dev/null
Binary files differ
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 0ea61faa..8906ab69 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -277,7 +277,6 @@ class Markers:
filtered_markers = []
for marker in self.markers:
if marker['name'] in p_values:
- # logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -298,7 +297,6 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- # logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -746,7 +744,6 @@ class DataSet:
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
- logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
@@ -917,7 +914,6 @@ class PhenotypeDataSet(DataSet):
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -947,7 +943,6 @@ class PhenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -1014,7 +1009,6 @@ class GenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
@@ -1135,8 +1129,6 @@ class MrnaAssayDataSet(DataSet):
ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
-
- logger.sql(query)
result = g.db.execute(query).fetchone()
mean = result[0] if result else 0
@@ -1156,7 +1148,6 @@ class MrnaAssayDataSet(DataSet):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -1188,7 +1179,6 @@ class MrnaAssayDataSet(DataSet):
Order BY
Strain.Name
""" % (escape(trait), escape(self.name))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return results
@@ -1199,7 +1189,6 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return dict(results)
@@ -1233,7 +1222,6 @@ def geno_mrna_confidentiality(ob):
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
- logger.sql(query)
result = g.db.execute(query)
(dataset_id,
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index df957bd9..8198b921 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -23,6 +23,9 @@ app_config()
werkzeug_logger = logging.getLogger('werkzeug')
if WEBSERVER_MODE == 'DEBUG':
+ from flask_debugtoolbar import DebugToolbarExtension
+ app.debug = True
+ toolbar = DebugToolbarExtension(app)
app.run(host='0.0.0.0',
port=SERVER_PORT,
debug=True,
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index bc97d417..4120c801 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -523,6 +523,9 @@ class ShowTrait:
sample_group_type='primary',
header="%s Only" % (self.dataset.group.name))
self.sample_groups = (primary_samples,)
+ print("\nttttttttttttttttttttttttttttttttttttttttttttt\n")
+ print(self.sample_groups)
+ print("\nttttttttttttttttttttttttttttttttttttttttttttt\n")
self.primary_sample_names = primary_sample_names
self.dataset.group.allsamples = all_samples_ordered
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index bb30c54c..53e16aa0 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -236,7 +236,7 @@
<button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
{% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
{% if this_trait.dataset.type == 'Publish' %}
- <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
+ <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
{% endif %}
{% if this_trait.dataset.type == 'ProbeSet' %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 44560427..7095c392 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -365,20 +365,6 @@ def wcgna_setup():
return render_template("wgcna_setup.html", **request.form)
-# @app.route("/wgcna_results", methods=('POST',))
-# def wcgna_results():
-# logger.info("In wgcna, request.form is:", request.form)
-# logger.info(request.url)
-# # Start R, load the package and pointers and create the analysis
-# wgcna = wgcna_analysis.WGCNA()
-# # Start the analysis, a wgcnaA object should be a separate long running thread
-# wgcnaA = wgcna.run_analysis(request.form)
-# # After the analysis is finished store the result
-# result = wgcna.process_results(wgcnaA)
-# # Display them using the template
-# return render_template("wgcna_results.html", **result)
-
-
@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
# We are going to get additional user input for the analysis
@@ -388,20 +374,6 @@ def ctl_setup():
return render_template("ctl_setup.html", **request.form)
-# @app.route("/ctl_results", methods=('POST',))
-# def ctl_results():
-# logger.info("In ctl, request.form is:", request.form)
-# logger.info(request.url)
-# # Start R, load the package and pointers and create the analysis
-# ctl = ctl_analysis.CTL()
-# # Start the analysis, a ctlA object should be a separate long running thread
-# ctlA = ctl.run_analysis(request.form)
-# # After the analysis is finished store the result
-# result = ctl.process_results(ctlA)
-# # Display them using the template
-# return render_template("ctl_results.html", **result)
-
-
@app.route("/intro")
def intro():
doc = Docs("intro", request.args)
@@ -436,9 +408,9 @@ def submit_trait_form():
version=GN_VERSION)
-@app.route("/trait/<name>/edit/phenotype-id/<phenotype_id>")
+@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>")
@admin_login_required
-def edit_phenotype(name, phenotype_id):
+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"),
@@ -447,7 +419,7 @@ def edit_phenotype(name, phenotype_id):
conn=conn,
table="PublishXRef",
where=PublishXRef(id_=name,
- phenotype_id=phenotype_id))
+ inbred_set_id=inbredset_id))
phenotype_ = fetchone(
conn=conn,
table="Phenotype",
@@ -494,7 +466,7 @@ def edit_phenotype(name, phenotype_id):
@app.route("/trait/edit/probeset-name/<dataset_name>")
-# @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"),
diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
deleted file mode 100644
index 755da333..00000000
--- a/wqflask/wsgi.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from run_gunicorn import app as application # expect application as a name
-
-if __name__ == "__main__":
- application.run()
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 19:08:11 +0000