diff options
| -rw-r--r-- | wqflask/base/data_set.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 2 |
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&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}"> <button type="button" class="btn btn-default" title="Find similar expression data">Find</button> |