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authorzsloan2020-05-07 19:38:27 -0500
committerzsloan2020-05-07 19:38:27 -0500
commitecb0a828de3ba744da82a45e1dc7a55906fd5fb1 (patch)
treec384b40aa8c1fab0e5ad5706a81e3f661dd33323 /wqflask
parent67ecc774ac70c5ba528f0ac1536d8d35f7301dac (diff)
downloadgenenetwork2-blatseq_fix.tar.gz
Fixed blatseq issue and geno correlation issueblatseq_fix
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py3
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py26
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js2
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html2
4 files changed, 16 insertions, 17 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5f08c34c..1457ba8d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -165,12 +165,11 @@ Publish or ProbeSet. E.g.
geno_query = """
SELECT
- GenoFreezeId
+ GenoFreeze.Id
FROM
GenoFreeze
WHERE
GenoFreeze.Name = "{0}"
- {1}
""".format(name)
results = g.db.execute(geno_query).fetchall()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f73079f8..072d7f8c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -73,16 +73,16 @@ class ShowTrait(object):
#ZS: Get verify/rna-seq link URLs
try:
- blatsequence = self.this_trait.blatseq
+ blatsequence = self.this_trait.sequence
if not blatsequence:
#XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
query1 = """SELECT Probe.Sequence, Probe.Name
- FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSet.Name = '%s' AND
- Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
+ FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s' AND
+ Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
seqs = g.db.execute(query1).fetchall()
if not seqs:
raise ValueError
@@ -98,10 +98,10 @@ class ShowTrait(object):
query2 = """SELECT Probe.Sequence, Probe.Name
FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSet.Name = '%s' AND
- Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s' AND
+ Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
seqs = g.db.execute(query2).fetchall()
for seqt in seqs:
@@ -121,8 +121,8 @@ class ShowTrait(object):
self.UCSC_BLAT_URL = ""
self.UTHSC_BLAT_URL = ""
except:
- self.UCSC_BLAT_URL = ""
- self.UTHSC_BLAT_URL = ""
+ self.UCSC_BLAT_URL = ""
+ self.UTHSC_BLAT_URL = ""
if self.dataset.type == "ProbeSet":
self.show_probes = "True"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index d94a2347..785e5332 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -518,7 +518,7 @@ submit_special = function(url) {
return $("#trait_data_form").submit();
};
-var corr_input_list = ['corr_type', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
$(".corr_compute").on("click", (function(_this) {
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 20dee54e..62268a54 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -212,7 +212,7 @@
<a href="#redirect">
<button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
</a>
- {% if this_trait.dataset.type == 'ProbeSet' %}
+ {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
{% if this_trait.symbol != None %}
<a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
<button type="button" class="btn btn-default" title="Find similar expression data">Find</button>