diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/trait.py | 102 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/parser.py | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 23 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 50 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 22 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 12 |
7 files changed, 72 insertions, 172 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index d0158ebd..8c9e3b10 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -258,113 +258,15 @@ class GeneralTrait: #else: results = self.dataset.retrieve_sample_data(self) - #if self.dataset.type == 'Temp': - # query = ''' - # SELECT - # Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - # FROM - # TempData, Temp, Strain - # WHERE - # TempData.StrainId = Strain.Id AND - # TempData.Id = Temp.DataId AND - # Temp.name = '%s' - # Order BY - # Strain.Name - # ''' % self.name - ##XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE - #elif self.dataset.type == 'Publish': - # query = ''' - # SELECT - # Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id - # FROM - # (PublishData, Strain, PublishXRef, PublishFreeze) - # left join PublishSE on - # (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) - # left join NStrain on - # (NStrain.DataId = PublishData.Id AND - # NStrain.StrainId = PublishData.StrainId) - # WHERE - # PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - # PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND - # PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id - # Order BY - # Strain.Name - # ''' % (self.name, self.dataset.id) - - #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE - #elif self.cellid: - - #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE - #elif self.dataset.type == 'ProbeSet': - # #ProbeSet Data - # query = ''' - # SELECT - # Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id - # FROM - # (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) - # left join ProbeSetSE on - # (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) - # WHERE - # ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - # ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - # ProbeSetFreeze.Name = '%s' AND - # ProbeSetXRef.DataId = ProbeSetData.Id AND - # ProbeSetData.StrainId = Strain.Id - # Order BY - # Strain.Name - # ''' % (self.name, self.dataset.name) - ##XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE - #else: - # #Geno Data - # #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search. - # query = ''' - # SELECT - # Strain.Name, GenoData.value, GenoSE.error, GenoData.Id - # FROM - # (GenoData, GenoFreeze, Strain, Geno, GenoXRef) - # left join GenoSE on - # (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) - # WHERE - # Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND - # GenoXRef.GenoFreezeId = GenoFreeze.Id AND - # GenoFreeze.Name = '%s' AND - # GenoXRef.DataId = GenoData.Id AND - # GenoData.StrainId = Strain.Id - # Order BY - # Strain.Name - # ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group), self.name, self.dataset.name) - - - #self.cursor.execute(query) - #results = self.cursor.fetchall() - # Todo: is this necessary? If not remove self.data.clear() if results: - #self.mysqlid = results[0][-1] - #if samplelist: for item in results: #name, value, variance, num_cases = item if not samplelist or (samplelist and name in samplelist): - #if value != None: - # num_cases = None - # if self.dataset.type in ('Publish', 'Temp'): - # ndata = item[3] name = item[0] self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) - #end for - # else: - # for item in results: - # val = item[1] - # if val != None: - # var = item[2] - # ndata = None - # if self.dataset.type in ('Publish', 'Temp'): - # ndata = item[3] - # self.data[item[0]] = webqtlCaseData(val, var, ndata) - # #end for - # #end if #def keys(self): # return self.__dict__.keys() @@ -429,7 +331,9 @@ class GeneralTrait: GenoXRef.GenoId = Geno.Id AND GenoFreeze.Name = '%s' AND Geno.Name = '%s' - """ % (escape(display_fields_string), escape(self.dataset.name), escape(self.name)) + """ % (escape(display_fields_string), + escape(self.dataset.name), + escape(self.name)) traitInfo = g.db.execute(query).fetchone() print("traitInfo is: ", pf(traitInfo)) else: #Temp type diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 3ce613e9..fc45395c 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -60,7 +60,7 @@ class DoSearch(object): return cls.search_types[search_type] -class ProbeSetSearch(DoSearch): +class MrnaAssaySearch(DoSearch): """A search within an mRNA expression dataset""" DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" @@ -265,7 +265,7 @@ class GenotypeSearch(DoSearch): return self.execute(self.query) -class RifSearch(ProbeSetSearch): +class RifSearch(MrnaAssaySearch): """Searches for traits with a Gene RIF entry including the search term.""" DoSearch.search_types['RIF'] = "RifSearch" @@ -280,7 +280,7 @@ class RifSearch(ProbeSetSearch): return self.execute(query) -class WikiSearch(ProbeSetSearch): +class WikiSearch(MrnaAssaySearch): """Searches GeneWiki for traits other people have annotated""" DoSearch.search_types['WIKI'] = "WikiSearch" @@ -298,7 +298,7 @@ class WikiSearch(ProbeSetSearch): return self.execute(query) -class GoSearch(ProbeSetSearch): +class GoSearch(MrnaAssaySearch): """Searches for synapse-associated genes listed in the Gene Ontology.""" DoSearch.search_types['GO'] = "GoSearch" @@ -323,7 +323,7 @@ class GoSearch(ProbeSetSearch): return self.execute(query) #ZS: Not sure what the best way to deal with LRS searches is -class LrsSearch(ProbeSetSearch): +class LrsSearch(MrnaAssaySearch): """Searches for genes with a QTL within the given LRS values LRS searches can take 3 different forms: @@ -484,7 +484,7 @@ class TransLrsSearch(CisTransLrsSearch): return self.real_run(">") -class MeanSearch(ProbeSetSearch): +class MeanSearch(MrnaAssaySearch): """Searches for genes expressed within an interval (log2 units) determined by the user""" DoSearch.search_types['MEAN'] = "MeanSearch" @@ -514,7 +514,7 @@ class MeanSearch(ProbeSetSearch): return self.execute(self.query) -class RangeSearch(ProbeSetSearch): +class RangeSearch(MrnaAssaySearch): """Searches for genes with a range of expression varying between two values""" DoSearch.search_types['RANGE'] = "RangeSearch" @@ -571,7 +571,7 @@ class PositionSearch(DoSearch): return self.execute(self.query) -class MrnaPositionSearch(ProbeSetSearch, PositionSearch): +class MrnaPositionSearch(MrnaAssaySearch, PositionSearch): """Searches for genes located within a specified range on a specified chromosome""" def run(self): @@ -591,7 +591,7 @@ class GenotypePositionSearch(GenotypeSearch, PositionSearch): return self.execute(self.query) -class PvalueSearch(ProbeSetSearch): +class PvalueSearch(MrnaAssaySearch): """Searches for traits with a permutationed p-value between low and high""" def run(self): diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index f991d8c7..be92014d 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -73,6 +73,23 @@ def parse(pstring): print("* items are:", pf(items) + "\n") return(items) + #def encregexp(self,str): + # if not str: + # return [] + # else: + # wildcardkeyword = str.strip() + # wildcardkeyword = string.replace(wildcardkeyword,',',' ') + # wildcardkeyword = string.replace(wildcardkeyword,';',' ') + # wildcardkeyword = wildcardkeyword.split() + # NNN = len(wildcardkeyword) + # for i in range(NNN): + # keyword = wildcardkeyword[i] + # keyword = string.replace(keyword,"*",".*") + # keyword = string.replace(keyword,"?",".") + # wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]' + # return wildcardkeyword + + if __name__ == '__main__': parse("foo=[3 2 1]") parse("WIKI=ho*") diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 5cb8e314..d986a2e0 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -54,11 +54,6 @@ class SearchResultPage(templatePage): # change back to self.dataset #if not self.dataset or self.dataset == 'spacer': # #Error, No dataset selected - # heading = "Search Result" - # detail = ['''No dataset was selected for this search, please - # go back and SELECT at least one dataset.'''] - # self.error(heading=heading,detail=detail,error="No dataset Selected") - # return ########################################### # Names and IDs of group / F2 set @@ -144,21 +139,3 @@ class SearchResultPage(templatePage): print("in the search results are:", self.results) self.header_fields = the_search.header_fields - - - #ZS: This should be handled in the parser - def encregexp(self,str): - if not str: - return [] - else: - wildcardkeyword = str.strip() - wildcardkeyword = string.replace(wildcardkeyword,',',' ') - wildcardkeyword = string.replace(wildcardkeyword,';',' ') - wildcardkeyword = wildcardkeyword.split() - NNN = len(wildcardkeyword) - for i in range(NNN): - keyword = wildcardkeyword[i] - keyword = string.replace(keyword,"*",".*") - keyword = string.replace(keyword,"?",".") - wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]' - return wildcardkeyword diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 0f593216..836d37ea 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -828,35 +828,34 @@ class ShowTrait(object): elif this_trait and this_trait.dataset and this_trait.dataset.type == 'Geno': #Check if trait is genotype - GenoInfo = HT.Paragraph() if this_trait.chr and this_trait.mb: location = ' Chr %s @ %s Mb' % (this_trait.chr,this_trait.mb) else: location = "not available" - if this_trait.sequence and len(this_trait.sequence) > 100: - if _Species == "rat": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', this_trait.sequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', this_trait.sequence) - elif _Species == "mouse": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', this_trait.sequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', this_trait.sequence) - elif _Species == "human": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', this_trait.sequence) - else: - UCSC_BLAT_URL = "" - UTHSC_BLAT_URL = "" - if UCSC_BLAT_URL: - #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) - verifyButton = HT.Href(url="#") - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") - verifyButton.append(verifyButtonImg) - verifyText = "Verify" - rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - rnaseqButton.append(rnaseqButtonImg) - rnaseqText = "RNA-seq" + #if this_trait.sequence and len(this_trait.sequence) > 100: + # if _Species == "rat": + # UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', this_trait.sequence) + # UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', this_trait.sequence) + # elif _Species == "mouse": + # UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', this_trait.sequence) + # UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', this_trait.sequence) + # elif _Species == "human": + # UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) + # UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', this_trait.sequence) + # else: + # UCSC_BLAT_URL = "" + # UTHSC_BLAT_URL = "" + # if UCSC_BLAT_URL: + # #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) + # verifyButton = HT.Href(url="#") + # verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") + # verifyButton.append(verifyButtonImg) + # verifyText = "Verify" + # rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) + # rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + # rnaseqButton.append(rnaseqButtonImg) + # rnaseqText = "RNA-seq" #tbl.append(HT.TR( # HT.TD('Location: ', Class="fs13 fwb", @@ -872,7 +871,7 @@ class ShowTrait(object): # valign="top", width=740) # )) - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1") + #menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1") #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) @@ -1629,7 +1628,6 @@ class ShowTrait(object): header="%s Only" % (self.dataset.group.name)) print("primary_samples is: ", pf(primary_samples)) - other_sample_names = [] for sample in this_trait.data.keys(): if sample not in all_samples_ordered: diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 278a134b..04d55be7 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -110,6 +110,7 @@ $ -> change_stats_value(sample_sets, category, row.vn, row.digits) edit_data_change = -> + already_seen = {} sample_sets = samples_primary: new Stats([]) samples_other: new Stats([]) @@ -117,21 +118,14 @@ $ -> console.log("at beginning:", sample_sets) - # ########## - # Bug here #value_table doesn't exist and why is it a class? - # ########## - - #values = $('.value_table').find(".edit_sample_value") - - tables = ['samples_primary', 'samples_other'] for table in tables rows = $("#" + table).find('tr') console.log("[fuji3] rows:", rows) for row in rows + name = $(row).find('.edit_sample_sample_name').html() + name = $.trim(name) real_value = $(row).find('.edit_sample_value').val() - #row = $(value).closest("tr") - #category = row[0].id console.log("real_value:", real_value) checkbox = $(row).find(".edit_sample_checkbox") checked = $(checkbox).attr('checked') @@ -139,11 +133,13 @@ $ -> if checked and is_number(real_value) and real_value != "" console.log("in the iffy if") real_value = parseFloat(real_value) - #if _(category).startsWith("Primary") + sample_sets[table].add_value(real_value) - #else if _(category).startsWith("Other") - # sample_sets.other_only.add_value(real_value) - sample_sets['samples_all'].add_value(real_value) + console.log("checking name of:", name) + if not (name of already_seen) + console.log("haven't seen") + sample_sets['samples_all'].add_value(real_value) + already_seen[name] = true console.log("towards end:", sample_sets) update_stat_values(sample_sets) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 3a7bc387..1037c890 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -115,7 +115,8 @@ return _results; }; edit_data_change = function() { - var checkbox, checked, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1; + var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1; + already_seen = {}; sample_sets = { samples_primary: new Stats([]), samples_other: new Stats([]), @@ -129,6 +130,8 @@ console.log("[fuji3] rows:", rows); for (_j = 0, _len1 = rows.length; _j < _len1; _j++) { row = rows[_j]; + name = $(row).find('.edit_sample_sample_name').html(); + name = $.trim(name); real_value = $(row).find('.edit_sample_value').val(); console.log("real_value:", real_value); checkbox = $(row).find(".edit_sample_checkbox"); @@ -137,7 +140,12 @@ console.log("in the iffy if"); real_value = parseFloat(real_value); sample_sets[table].add_value(real_value); - sample_sets['samples_all'].add_value(real_value); + console.log("checking name of:", name); + if (!(name in already_seen)) { + console.log("haven't seen"); + sample_sets['samples_all'].add_value(real_value); + already_seen[name] = true; + } } } } |