diff options
| -rw-r--r-- | wqflask/wqflask/parser.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 210 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 4 |
5 files changed, 143 insertions, 107 deletions
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 53df2001..67325b56 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -5,7 +5,7 @@ import re from pprint import pformat as pf def parse(pstring): - pstring = re.split(r"""(?:(\w+\s*=\s*\([^)]*\))|(\w+\s*[=:]\w+))""", pstring) + pstring = re.split(r"""(?:(\w+\s*=\s*\([^)]*\))|(\w+\s*[=:]\w+)|(\w+))""", pstring) pstring = [item.strip() for item in pstring if item and item.strip()] print(pstring) @@ -33,7 +33,7 @@ def parse(pstring): term = dict(search_term = item) items.append(term) - #print(pf(items)) + print(pf(items)) return(items) parse("foo=(3 2 1)") diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 6847c369..5d8c7221 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -72,20 +72,13 @@ class SearchResultPage(templatePage): go back and SELECT at least one database.'''] self.error(heading=heading,detail=detail,error="No Database Selected") return - elif type(self.database) == type(""): - #convert database into a database list - #was used for multiple databases search, this - #feature has been abandoned, - self.database = string.split(self.database,',') - else: - pass - ########################################### # Names and IDs of RISet / F2 set ########################################### if self.database == ['_allPublish']: - self.cursor.execute("""select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze, + self.cursor.execute(""" + select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze, InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id = PublishFreeze.InbredSetId""") results = self.cursor.fetchall() @@ -95,7 +88,7 @@ class SearchResultPage(templatePage): self.singleCross = False else: self.database = map(lambda x: webqtlDataset(x, self.cursor), self.database) - #currently, webqtl wouldn't allow multiple crosses + #currently, webqtl won't allow multiple crosses #for other than multiple publish db search #so we can use the first database as example if self.database[0].type=="Publish": @@ -105,10 +98,16 @@ class SearchResultPage(templatePage): #userExist = None for individualDB in self.database: - self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %sFreeze WHERE Name = "%s"' % (self.database[0].type, individualDB)) - indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0] - - if confidential == 1: + self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, + AuthorisedUsers FROM %sFreeze WHERE Name = %s''', ( + self.database[0].type, individualDB)) + (indId, + indName, + indFullName, + confidential, + AuthorisedUsers) = self.cursor.fetchall()[0] + + if confidential: access_to_confidential_dataset = 0 #for the dataset that confidentiality is 1 @@ -144,7 +143,8 @@ class SearchResultPage(templatePage): ########################################### # make sure search from same type of databases ########################################### - dbTypes = map(lambda X: X.type, self.database) + #dbTypes = map(lambda X: X.type, self.database) + dbTypes = [table.type for table in self.database] self.dbType = dbTypes[0] for item in dbTypes: if item != self.dbType: @@ -153,89 +153,107 @@ class SearchResultPage(templatePage): self.error(heading=heading,detail=detail,error="Error") return if self.dbType == "Publish": - self.searchField = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', 'Phenotype.Post_publication_abbreviation', 'Phenotype.Lab_code', 'Publication.PubMed_ID', 'Publication.Abstract', 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id'] + self.searchField = ['Phenotype.Post_publication_description', + 'Phenotype.Pre_publication_description', + 'Phenotype.Pre_publication_abbreviation', + 'Phenotype.Post_publication_abbreviation', + 'Phenotype.Lab_code', + 'Publication.PubMed_ID', + 'Publication.Abstract', + 'Publication.Title', + 'Publication.Authors', + 'PublishXRef.Id'] elif self.dbType == "ProbeSet": - self.searchField = ['Name','Description','Probe_Target_Description','Symbol','Alias','GenbankId', 'UniGeneId','RefSeq_TranscriptId'] + self.searchField = ['Name', + 'Description', + 'Probe_Target_Description', + 'Symbol', + 'Alias', + 'GenbankId', + 'UniGeneId', + 'RefSeq_TranscriptId'] elif self.dbType == "Geno": self.searchField = ['Name','Chr'] ########################################### # Search Options ########################################### - self.matchwhole = fd['matchwhole'] + #self.matchwhole = fd['matchwhole'] #split result into pages - self.pageNumber = fd.get('pageno', 0) - - try: - self.pageNumber = int(self.pageNumber) - except Exception as why: - print(why) - self.pageNumber = 0 + #self.pageNumber = fd.get('pageno', 0) + # + #try: + # self.pageNumber = int(self.pageNumber) + #except Exception as why: + # print(why) + # self.pageNumber = 0 ########################################### # Generate Mysql Query ########################################### - geneIdListQuery = fd.get('geneId', '') - if geneIdListQuery: - geneIdListQuery = string.replace(geneIdListQuery, ",", " ") - geneIdListQuery = " geneId=%s" % string.join(string.split(geneIdListQuery), "-") + + # Sam: We presume lines below aren't used... + #geneIdListQuery = fd.get('geneId', '') + #if geneIdListQuery: + # geneIdListQuery = string.replace(geneIdListQuery, ",", " ") + # geneIdListQuery = " geneId=%s" % string.join(string.split(geneIdListQuery), "-") - self.ANDkeyword = fd.get('ANDkeyword', "") - self.ORkeyword = fd.get('ORkeyword', "") + #self.ANDkeyword = fd.get('ANDkeyword', "") + #self.ORkeyword = fd.get('ORkeyword', "") - self.ORkeyword += geneIdListQuery + #self.ORkeyword += geneIdListQuery - self.ANDkeyword = self.ANDkeyword.replace("\\", "").strip() - self.ORkeyword = self.ORkeyword.replace("\\", "").strip() + #self.ANDkeyword = self.ANDkeyword.replace("\\", "").strip() + #self.ORkeyword = self.ORkeyword.replace("\\", "").strip() #user defined sort option - self.orderByUserInput = fd.get('orderByUserInput', "").strip() + #self.orderByUserInput = fd.get('orderByUserInput', "").strip() #default sort option if user have not defined - self.orderByDefalut = "" + #self.orderByDefalut = "" #XZ, Dec/16/2010: I add examples to help understand this block of code. See details in function pattersearch. - - #XZ: self._1mPattern examples: WIKI=xxx, RIF=xxx, GO:0045202 - self._1mPattern = re.compile('\s*(\S+)\s*[:=]\s*([a-zA-Z-\+\d\.]+)\s*') - - #XZ: self._2mPattern examples: Mean=(15.0 16.0), Range=(10 100), LRS=(Low_LRS_limit, High_LRS_limit), pvalue=(Low_limit, High_limit), Range=(10 100) - self._2mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*([-\d\.]+)[, \t]+([-\d\.]+)[, \t]*([-\d\.]*)\s*\)') - - #XZ: self._3mPattern examples: Position=(Chr1 98 104), Pos=(Chr1 98 104), Mb=(Chr1 98 104), CisLRS=(Low_LRS_limit, High_LRS_limit, Mb_buffer), TransLRS=(Low_LRS_limit, High_LRS_limit, Mb_buffer) - self._3mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*[Cc][Hh][Rr]([^, \t]+)[, \t]+([-\d\.]+)[, \t]+([-\d\.]+)\s*\)') - - #XZ: self._5mPattern examples: LRS=(Low_LRS_limit, High_LRS_limit, ChrNN, Mb_Low_Limit, Mb_High_Limit) - self._5mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*([-\d\.]+)[, \t]+([-\d\.]+)[, \t]+[Cc][Hh][Rr]([^, \t]+)[, \t]+([-\d\.]+)[, \t]+([-\d\.]+)\s*\)') + # + ##XZ: self._1mPattern examples: WIKI=xxx, RIF=xxx, GO:0045202 + #self._1mPattern = re.compile('\s*(\S+)\s*[:=]\s*([a-zA-Z-\+\d\.]+)\s*') + # + ##XZ: self._2mPattern examples: Mean=(15.0 16.0), Range=(10 100), LRS=(Low_LRS_limit, High_LRS_limit), pvalue=(Low_limit, High_limit), Range=(10 100) + #self._2mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*([-\d\.]+)[, \t]+([-\d\.]+)[, \t]*([-\d\.]*)\s*\)') + # + ##XZ: self._3mPattern examples: Position=(Chr1 98 104), Pos=(Chr1 98 104), Mb=(Chr1 98 104), CisLRS=(Low_LRS_limit, High_LRS_limit, Mb_buffer), TransLRS=(Low_LRS_limit, High_LRS_limit, Mb_buffer) + #self._3mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*[Cc][Hh][Rr]([^, \t]+)[, \t]+([-\d\.]+)[, \t]+([-\d\.]+)\s*\)') + # + ##XZ: self._5mPattern examples: LRS=(Low_LRS_limit, High_LRS_limit, ChrNN, Mb_Low_Limit, Mb_High_Limit) + #self._5mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*([-\d\.]+)[, \t]+([-\d\.]+)[, \t]+[Cc][Hh][Rr]([^, \t]+)[, \t]+([-\d\.]+)[, \t]+([-\d\.]+)\s*\)') #Error, No keyword input - if not (self.ORkeyword or self.ANDkeyword): - heading = "Search Result" - detail = ["Please make sure to enter either your search terms (genes, traits, markers), or advanced search commands."] - self.error(heading=heading,detail=detail,error="No search terms were entered") - return + #if not (self.ORkeyword or self.ANDkeyword): + # heading = "Search Result" + # detail = ["Please make sure to enter either your search terms (genes, traits, markers), or advanced search commands."] + # self.error(heading=heading,detail=detail,error="No search terms were entered") + # return #query clauses - self.ANDQuery = [] - self.ORQuery = [] - #descriptions, one for OR search, one for AND search - self.ANDDescriptionText = [] - self.ORDescriptionText = [] - - if not self.normalSearch(): - return - if not self.patternSearch(): - return - if not self.assembleQuery(): - return - self.nresults = self.executeQuery() + #self.ANDQuery = [] + #self.ORQuery = [] + ##descriptions, one for OR search, one for AND search + #self.ANDDescriptionText = [] + #self.ORDescriptionText = [] - if len(self.database) > 1: - dbUrl = "Multiple phenotype databases" - dbUrlLink = " were" - else: - dbUrl = self.database[0].genHTML() - dbUrlLink = " was" + #if not self.normalSearch(): + # return + #if not self.patternSearch(): + # return + #if not self.assembleQuery(): + # return + #self.nresults = self.executeQuery() + # + #if len(self.database) > 1: + # dbUrl = "Multiple phenotype databases" + # dbUrlLink = " were" + #else: + # dbUrl = self.database[0].genHTML() + # dbUrlLink = " was" #SearchText = HT.Blockquote('GeneNetwork searched the ', dbUrl, ' for all records ') #if self.ORkeyword2: @@ -313,11 +331,15 @@ class SearchResultPage(templatePage): #TD_LR.append(HT.Paragraph('Search Results', Class="title"), SearchText) + self.start_search() self.genSearchResultTable() #self.dict['body'] = str(TD_LR) #self.dict['js1'] = '' #self.dict['js2'] = 'onLoad="pageOffset()"' #self.dict['layer'] = self.generateWarningLayer() + + def start_search(self): + def genSearchResultTable(self): @@ -556,12 +578,23 @@ class SearchResultPage(templatePage): incGenoTbl = "" else: incGenoTbl = " Geno, " - newclause.append("SELECT %d, PublishXRef.Id, PublishFreeze.createtime as thistable, Publication.PubMed_ID as Publication_PubMed_ID, Phenotype.Post_publication_description as Phenotype_Name FROM %s PublishFreeze, Publication, PublishXRef, Phenotype WHERE PublishXRef.InbredSetId = %d and %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %d" % (j, incGenoTbl, self.databaseCrossIds[j], item, database.id)) + newclause.append("""SELECT %d, PublishXRef.Id, + PublishFreeze.createtime as thistable, + Publication.PubMed_ID as Publication_PubMed_ID, + Phenotype.Post_publication_description as Phenotype_Name + FROM %s PublishFreeze, Publication, PublishXRef, + Phenotype WHERE PublishXRef.InbredSetId = %d and %s and + PublishXRef.PhenotypeId = Phenotype.Id and + PublishXRef.PublicationId = Publication.Id and + PublishFreeze.Id = %d""" % (j, incGenoTbl, + self.databaseCrossIds[j], item, database.id)) elif self.dbType == "ProbeSet": if item.find("GOgene") < 0: incGoTbl = "" else: - incGoTbl = " ,db_GeneOntology.term as GOterm, db_GeneOntology.association as GOassociation, db_GeneOntology.gene_product as GOgene_product " + incGoTbl = """ ,db_GeneOntology.term as GOterm, + db_GeneOntology.association as GOassociation, + db_GeneOntology.gene_product as GOgene_product """ if item.find("Geno.name") < 0: incGenoTbl = "" else: @@ -581,7 +614,13 @@ class SearchResultPage(templatePage): WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %d """ % (j, incGeneRIFTbl, incGenoTbl, incGoTbl, item, database.id)) elif self.dbType == "Geno": - newclause.append("SELECT %d, Geno.Name, GenoFreeze.createtime as thistable, Geno.Name as Geno_Name, Geno.Source2 as Geno_Source2, Geno.chr_num as Geno_chr_num, Geno.Mb as Geno_Mb FROM GenoXRef, GenoFreeze, Geno WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %d"% (j, item, database.id)) + newclause.append("""SELECT %d, Geno.Name, GenoFreeze.createtime as thistable, + Geno.Name as Geno_Name, Geno.Source2 as Geno_Source2, + Geno.chr_num as Geno_chr_num, Geno.Mb as Geno_Mb FROM + GenoXRef, GenoFreeze, Geno WHERE %s and Geno.Id + = GenoXRef.GenoId and GenoXRef.GenoFreezeId = + GenoFreeze.Id and GenoFreeze.Id = %d""" % ( + j, item, database.id)) else: pass @@ -651,10 +690,14 @@ class SearchResultPage(templatePage): clauseItem = "(%s)" % string.join(clause2, clausejoin) query.append(" (%s) " % clauseItem) if ANDFulltext: - clauseItem = " MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('+%s' IN BOOLEAN MODE) " % string.join(ANDFulltext, " +") + clauseItem = """ MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId, UniGeneId, Probe_Target_Description) + AGAINST ('+%s' IN BOOLEAN MODE) """ % string.join(ANDFulltext, " +") self.ANDQuery.append(" (%s) " % clauseItem) if ORFulltext: - clauseItem = " MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) " % string.join(ORFulltext, " ") + clauseItem = """ MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias, + GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) + """ % string.join(ORFulltext, " ") self.ORQuery.append(" (%s) " % clauseItem) else: pass @@ -711,16 +754,21 @@ class SearchResultPage(templatePage): detail = ["Pattern search is not available for phenotype databases at this time."] self.error(heading=heading,detail=detail,error="Error") return 0 - elif self.dbType == "ProbeSet" and \ - ((_2Cmds and reduce(lambda x, y: (y not in ["MEAN", "LRS", "PVALUE", "TRANSLRS", "CISLRS", "RANGE", "H2"]) or x, _2Cmds, False))\ + elif (self.dbType == "ProbeSet" and + ((_2Cmds and reduce(lambda x, y: (y not in [ + "MEAN", "LRS", "PVALUE", "TRANSLRS", "CISLRS", "RANGE", "H2" + ]) or x, _2Cmds, False))\ or (_3Cmds and reduce(lambda x, y: (y not in ["POS", "POSITION", "MB"]) or x, _3Cmds, False))\ or (_5Cmds and reduce(lambda x, y: (y not in ["LRS"]) or x, _5Cmds, False))\ - or (_1Cmds and reduce(lambda x, y: (y not in ["FLAG", "STRAND_PROBE", "STRAND_GENE", "GO", "WIKI", "RIF", "GENEID"]) or x, _1Cmds, False))): + or (_1Cmds and reduce(lambda x, y: ( + y not in ["FLAG", "STRAND_PROBE", "STRAND_GENE", "GO", "WIKI", "RIF", "GENEID"] + ) or x, _1Cmds, False)))): heading = "Search Result" detail = ["You entered at least one incorrect search command."] self.error(heading=heading,detail=detail,error="Error") return 0 - elif self.dbType == "Geno" and (_1Cmds or _2Cmds or _5Cmds or (_3Cmds and reduce(lambda x, y: (y not in ["POS", "POSITION", "MB"]) or x, _3Cmds, False)) ): + elif self.dbType == "Geno" and (_1Cmds or _2Cmds or _5Cmds or (_3Cmds and reduce( + lambda x, y: (y not in ["POS", "POSITION", "MB"]) or x, _3Cmds, False)) ): heading = "Search Result" detail = ["You entered at least one incorrect search command."] self.error(heading=heading,detail=detail,error="Error") diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 285d5ef4..5e47dedc 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -206,6 +206,7 @@ $ -> ##End Block Samples By Attribute Value Code ##Block Samples By Index Code + block_by_index = -> index_string = $('#remove_samples_field').val() console.log("index_string is:", index_string) @@ -253,13 +254,8 @@ $ -> $('.value_se').each (index, element) => if $(element).find('.trait_value_input').val() == 'x' $(element).hide() - - show_no_value = -> - $('.value_se').each (index, element) => - if $(element).find('.trait_value_input').val() == 'x' - $(element).show() - $('#show_hide_no_value').click(hide_no_value) + $('#hide_no_value').click(hide_no_value) ##End Hide Sample Rows With No Value Code @@ -284,9 +280,9 @@ $ -> ##End Reset Table Values Code - console.log("before registering show_hide_outliers") - $('#show_hide_outliers').click(show_hide_outliers) - console.log("after registering show_hide_outliers") + console.log("before registering block_outliers") + $('#block_outliers').click(block_outliers) + console.log("after registering block_outliers") _.mixin(_.str.exports()); # Add string fuctions directly to underscore $('#value_table').change(edit_data_change) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index d52b2756..7af60fae 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -11,7 +11,7 @@ }; $(function() { - var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, show_hide_outliers, show_no_value, stats_mdp_change, update_stat_values; + var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, show_hide_outliers, stats_mdp_change, update_stat_values; hide_tabs = function(start) { var x, _i, _results; _results = []; @@ -297,15 +297,7 @@ } }); }; - show_no_value = function() { - var _this = this; - return $('.value_se').each(function(index, element) { - if ($(element).find('.trait_value_input').val() === 'x') { - return $(element).show(); - } - }); - }; - $('#show_hide_no_value').click(hide_no_value); + $('#hide_no_value').click(hide_no_value); block_outliers = function() { var _this = this; return $('.outlier').each(function(index, element) { @@ -323,9 +315,9 @@ }); }; $('#reset').click(reset_samples_table); - console.log("before registering show_hide_outliers"); - $('#show_hide_outliers').click(show_hide_outliers); - console.log("after registering show_hide_outliers"); + console.log("before registering block_outliers"); + $('#block_outliers').click(block_outliers); + console.log("after registering block_outliers"); _.mixin(_.str.exports()); $('#value_table').change(edit_data_change); console.log("loaded"); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index e2ee210c..61d6275b 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1245,9 +1245,9 @@ <strong> Options:</strong> - <input type="button" id="show_hide_no_value" class="button" value="Hide No Value"> + <input type="button" id="hide_no_value" class="button" value="Hide No Value"> - <input type="button" id="show_hide_outliers" class="button" value="Hide Outliers"> + <input type="button" id="block_outliers" class="button" value="Block Outliers"> <input type="button" id="reset" class="button" value="Reset"> |