diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 7 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 8 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 129 |
5 files changed, 78 insertions, 74 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 68f5e5ed..14e4055e 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -42,12 +42,13 @@ def create_dataset(dataset_name): #cursor = db_conn.cursor() print("dataset_name:", dataset_name) - dataset_type = g.db.execute(""" + query = """ SELECT DBType.Name FROM DBList, DBType - WHERE DBList.Name = %s and + WHERE DBList.Name = '%s' and DBType.Id = DBList.DBTypeId - """, (dataset_name)).fetchone().Name + """ % (escape(dataset_name)) + dataset_type = g.db.execute(query).fetchone().Name #dataset_type = cursor.fetchone()[0] print("[blubber] dataset_type:", pf(dataset_type)) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index d3753fc1..d0158ebd 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -24,7 +24,7 @@ class GeneralTrait: def __init__(self, **kw): print("in GeneralTrait") - self.dataset = kw.get('dataset', None) # database object + self.dataset = kw.get('dataset', None) # database name self.name = kw.get('name', None) # Trait ID, ProbeSet ID, Published ID, etc. self.cellid = kw.get('cellid', None) self.identification = kw.get('identification', 'un-named trait') @@ -230,7 +230,7 @@ class GeneralTrait: if samplelist == None: samplelist = [] - assert self.dataset + #assert self.dataset #if self.cellid: # #Probe Data diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 7c50dfeb..b518ab99 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -112,11 +112,11 @@ class SearchResultPage(templatePage): print("foo locals are:", locals()) trait_id = result[0] - this_trait = GeneralTrait(dataset=self.dataset, name=trait_id) + this_trait = GeneralTrait(dataset=self.dataset.name, name=trait_id) this_trait.retrieve_info(QTL=True) self.trait_list.append(this_trait) - self.dataset.get_trait_info(self.trait_list, species) + self.dataset.get_trait_info(self.trait_list, species) def search(self): diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 25877521..53bb24fb 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -9,7 +9,7 @@ from pprint import pformat as pf class SampleList(object): def __init__(self, cursor, - fd, + dataset, variance_data_page, sample_names, this_trait, @@ -17,7 +17,7 @@ class SampleList(object): header): self.cursor = cursor - self.fd = fd + self.dataset = dataset self.this_trait = this_trait self.sample_group_type = sample_group_type # primary or other self.header = header @@ -42,7 +42,7 @@ class SampleList(object): #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): # sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") sample.extra_info = {} - if self.fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" @@ -124,7 +124,7 @@ class SampleList(object): WHERE Strain.Name = %s and StrainXRef.StrainId = Strain.Id and InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = %s""", (sample_name, self.fd.RISet)) + InbredSet.Name = %s""", (sample_name, self.dataset.group.name)) sample_id = self.cursor.fetchone()[0] diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 2bc4fc9c..73b438d0 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -7,6 +7,8 @@ import cPickle from collections import OrderedDict +from flask import Flask, g + from htmlgen import HTMLgen2 as HT from base import webqtlConfig @@ -140,10 +142,10 @@ class ShowTrait(templatePage): #else: # hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named - self.dispTraitInformation(fd, "", hddn, this_trait) #Display trait information + function buttons + self.dispTraitInformation(args, "", hddn, this_trait) #Display trait information + function buttons if this_trait == None: - this_trait = webqtlTrait(data=fd.allTraitData, dataset=None) + this_trait = webqtlTrait(data=args['allTraitData'], dataset=None) ## Variance submit page only #if fd.enablevariance and not variance_data_page: @@ -156,15 +158,14 @@ class ShowTrait(templatePage): # print("Calling dispBasicStatistics") # self.dispBasicStatistics(fd, this_trait) - self.build_correlation_tools(fd, this_trait) - + self.build_correlation_tools(args, this_trait) - self.make_sample_lists(fd, variance_data_page, this_trait) + self.make_sample_lists(args, variance_data_page, this_trait) - if fd.allsamplelist: - hddn['allsamplelist'] = string.join(fd.allsamplelist, ' ') + if args['allsamplelist']: + hddn['allsamplelist'] = string.join(args['allsamplelist'], ' ') - if fd.varianceDispName != 'Variance': + if args['varianceDispName'] != 'Variance': hddn['isSE'] = "yes" # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self @@ -172,8 +173,8 @@ class ShowTrait(templatePage): self.hddn = hddn self.sample_group_types = OrderedDict() - self.sample_group_types['samples_primary'] = fd.group + " Only" - self.sample_group_types['samples_other'] = "Non-" + fd.group + self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only" + self.sample_group_types['samples_other'] = "Non-" + self.dataset.group.name self.sample_group_types['samples_all'] = "All Cases" sample_lists = [group.sample_list for group in self.sample_groups] print("sample_lists is:", pf(sample_lists)) @@ -221,7 +222,7 @@ class ShowTrait(templatePage): incf1 = [] if not self.genotype: - self.readGenotype() + self.dataset.read_genotype_file() if not samplelist: if incf1: samplelist = self.f1list + self.samplelist @@ -296,9 +297,9 @@ class ShowTrait(templatePage): print("allTraitData is:", pf(self.allTraitData)) - def dispTraitInformation(self, fd, title1Body, hddn, this_trait): + def dispTraitInformation(self, args, title1Body, hddn, this_trait): - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, group=fd.group) + _Species = webqtlDatabaseFunction.retrieve_species(group=self.dataset.group.name) #tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1") @@ -323,31 +324,31 @@ class ShowTrait(templatePage): snpBrowserText = "" updateText = "" - if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: - - if this_trait==None or this_trait.dataset.type=='Temp': - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - elif this_trait.dataset.type != 'Temp': - if this_trait.dataset.type == 'Publish' and this_trait.confidential: #XZ: confidential phenotype trait - if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - else: - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - else: - pass + #if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: + # + # if this_trait==None or this_trait.dataset.type=='Temp': + # updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") + # updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") + # updateButton.append(updateButton_img) + # updateText = "Edit" + # elif this_trait.dataset.type != 'Temp': + # if this_trait.dataset.type == 'Publish' and this_trait.confidential: #XZ: confidential phenotype trait + # if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): + # updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") + # updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") + # updateButton.append(updateButton_img) + # updateText = "Edit" + # else: + # updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") + # updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") + # updateButton.append(updateButton_img) + # updateText = "Edit" + # else: + # pass - self.cursor.execute('SELECT Name FROM InbredSet WHERE Name="%s"' % fd.group) + 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');" % (fd.group, 'dataInput')) + 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" @@ -373,8 +374,7 @@ class ShowTrait(templatePage): if this_trait.symbol: #XZ: Show SNP Browser only for mouse if _Species == 'mouse': - self.cursor.execute("select geneSymbol from GeneList where geneSymbol = %s", this_trait.symbol) - geneName = self.cursor.fetchone() + geneName = g.db.execute("SELECT geneSymbol FROM GeneList WHERE geneSymbol = %s", this_trait.symbol).fetchone() if geneName: snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0] else: @@ -496,15 +496,14 @@ class ShowTrait(templatePage): if this_trait.dataset.name.find('Liver') >= 0 and this_trait.dataset.name.find('F2') < 0: pass else: + query = """SELECT count(*) + FROM Probe, ProbeSet + WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (this_trait.name) #query database for number of probes associated with trait; if count > 0, set probe tool button and text - self.cursor.execute("""SELECT count(*) - FROM Probe, ProbeSet - WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (this_trait.name)) - - probeResult = self.cursor.fetchone() + probeResult = g.db.execute(query).fetchone() if probeResult[0] > 0: probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&group=%s&incparentsf1=ON" \ - % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.dataset, this_trait.name, this_trait.cellid, fd.group) + % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.dataset, this_trait.name, this_trait.cellid, self.dataset.group.name) probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") #probeButton.append(probeButton_img) @@ -632,18 +631,21 @@ class ShowTrait(templatePage): #symatlas_species = "Mus musculus" #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % this_trait.symbol) - self.cursor.execute('SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = "%s"' % this_trait.symbol) - try: - chr, txst, txen = self.cursor.fetchall()[0] - if 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,chr,txst,txen), - Class="fs14 fwn"), style=linkStyle) - , " "*2) - except: - pass + #try: + 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) + #except: + # pass #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",\ @@ -1147,11 +1149,11 @@ class ShowTrait(templatePage): #title2Body.append(submitTable) - def build_correlation_tools(self, fd, this_trait): + def build_correlation_tools(self, this_trait): #species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, group=fd.group) - this_group = fd.group + this_group = self.dataset.group.name # We're checking a string here! assert isinstance(this_group, basestring), "We need a string type thing here" @@ -1172,6 +1174,7 @@ class ShowTrait(templatePage): dataset_menu = [] print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) + query = self.cursor.execute('''SELECT PublishFreeze.FullName,PublishFreeze.Name FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = %s and PublishFreeze.public > %s''', @@ -1610,10 +1613,10 @@ class ShowTrait(templatePage): def make_sample_lists(self, fd, variance_data_page, this_trait): - if fd.parlist: - all_samples_ordered = fd.parlist + fd.f1list + fd.samplelist + if args['parlist']: + all_samples_ordered = args['parlist'] + args['f1list'] + args['samplelist'] else: - all_samples_ordered = fd.f1list + fd.samplelist + all_samples_ordered = args['f1list'] + args['samplelist'] this_trait_samples = set(this_trait.data.keys()) @@ -1622,12 +1625,12 @@ class ShowTrait(templatePage): print("-*- primary_samplelist is:", pf(primary_sample_names)) primary_samples = SampleList(self.cursor, - fd=fd, + args=args, variance_data_page=variance_data_page, sample_names=primary_sample_names, this_trait=this_trait, sample_group_type='primary', - header="%s Only" % (fd.group)) + header="%s Only" % (self.dataset.group.name)) other_sample_names = [] for sample in this_trait.data.keys(): |