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-rw-r--r--genotype_files/genotypes/.gitattributes1
-rw-r--r--genotype_files/new_genotypes/.gitattributes1
-rw-r--r--web/images/edit.pngbin4322 -> 0 bytes
-rwxr-xr-xwqflask/base/trait.py3
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py41
5 files changed, 12 insertions, 34 deletions
diff --git a/genotype_files/genotypes/.gitattributes b/genotype_files/genotypes/.gitattributes
new file mode 100644
index 00000000..c311ac85
--- /dev/null
+++ b/genotype_files/genotypes/.gitattributes
@@ -0,0 +1 @@
+*.geno filter=lfs -crlf
diff --git a/genotype_files/new_genotypes/.gitattributes b/genotype_files/new_genotypes/.gitattributes
new file mode 100644
index 00000000..912ed80c
--- /dev/null
+++ b/genotype_files/new_genotypes/.gitattributes
@@ -0,0 +1 @@
+*.json filter=lfs -crlf
diff --git a/web/images/edit.png b/web/images/edit.png
deleted file mode 100644
index dda50521..00000000
--- a/web/images/edit.png
+++ /dev/null
Binary files differ
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 58bed865..f3648b80 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -549,6 +549,9 @@ class GeneralTrait(object):
if self.alias:
alias = string.replace(self.alias, ";", " ")
alias = string.join(string.split(alias), ", ")
+ else:
+ alias = 'Not available'
+
return alias
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 929f5abb..836a0be5 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -283,13 +283,13 @@ class ShowTrait(object):
# else:
# pass
- g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name)
+ result = g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name)
if this_trait:
addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (self.dataset.group.name, 'dataInput'))
addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
#addSelectionButton.append(addSelectionButton_img)
addSelectionText = "Add"
- elif self.cursor.fetchall():
+ elif result.fetchall():
addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput'))
addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;")
#addSelectionButton.append(addSelectionButton_img)
@@ -368,7 +368,7 @@ class ShowTrait(object):
blatsequence = ''
for seqt in seqs:
if int(seqt[1][-1]) % 2 == 1:
- blatsequence += string.strip(seqt[0])
+ blatsequence += string.strip(seqt[0])## NEEDED FOR UCSC GENOME BROWSER LINK
#--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe
blatsequence = '%3E'+this_trait.name+'%0A'+blatsequence+'%0A'
@@ -469,52 +469,25 @@ class ShowTrait(object):
#XZ: Resource Links:
if this_trait.symbol:
- linkStyle = "background:#dddddd;padding:2"
- tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px")
-
#XZ,12/26/2008: Gene symbol may contain single quotation mark.
#For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948)
#I debug this by using double quotation marks.
if _Species == "rat":
-
- #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
- #symatlas_species = "Rattus norvegicus"
-
- #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % this_trait.symbol)
- self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % this_trait.symbol)
- try:
- kgId, chr, txst, txen = self.cursor.fetchall()[0]
+ result = g.db.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
+ if result != None:
+ kgId, chr, txst, txen = result[0], result[1], result[2], result[3]
if chr and txst and txen and kgId:
txst = int(txst*1000000)
txen = int(txen*1000000)
- #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
- # title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle)
- # , " "*2)
- except:
- pass
if _Species == "mouse":
-
- #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
- #symatlas_species = "Mus musculus"
-
- #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % this_trait.symbol)
- #try:
print("this_trait.symbol:", this_trait.symbol)
result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
if result != None:
this_chr, txst, txen = result[0], result[1], result[2]
- #this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
if this_chr and txst and txen and this_trait.refseq_transcriptid :
txst = int(txst*1000000)
txen = int(txen*1000000)
- #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
- # title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',
- # this_trait.refseq_transcriptid,
- # this_chr,
- # txst,
- # txen),
- # Class="fs14 fwn"), style=linkStyle)
- # , " "*2)
+ ## NEEDED FOR UCSC GENOME BROWSER LINK
#XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
#tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\