diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 90 | ||||
| -rw-r--r-- | wqflask/wqflask/parser.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 217 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 34 |
4 files changed, 126 insertions, 225 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index ac6014e7..61bfbaba 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -7,19 +7,18 @@ from pprint import pformat as pf from dbFunction import webqtlDatabaseFunction - class DoSearch(object): """Parent class containing parameters/functions used for all searches""" - + # Used to translate search phrases into classes search_types = dict() - + def __init__(self, search_term, dataset, cursor, db_conn): self.search_term = search_term self.dataset = dataset self.db_conn = db_conn self.cursor = cursor - + #Get group information for dataset and the species id self.dataset.get_group() self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group) @@ -40,7 +39,7 @@ class DoSearch(object): """Strips out newlines/extra spaces and replaces them with just spaces""" step_one = " ".join(stringy.split()) return step_one - + @classmethod def get_search(cls, search_type): return cls.search_types[search_type] @@ -48,9 +47,9 @@ class DoSearch(object): class ProbeSetSearch(DoSearch): """A search within an mRNA expression dataset""" - + DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" - + base_query = """SELECT ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, @@ -63,9 +62,10 @@ class ProbeSetSearch(DoSearch): FROM ProbeSetXRef, ProbeSet """ - def compile_final_query(self, from_clause, where_clause): + def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" + from_clause = '' from_clause = self.normalize_spaces(from_clause) query = (self.base_query + @@ -78,12 +78,12 @@ class ProbeSetSearch(DoSearch): self.escape(self.dataset.id))) print("query is:", pf(query)) - + return query def run(self): """Generates and runs a simple search of an mRNA expression dataset""" - + print("Running ProbeSetSearch") query = (self.base_query + """WHERE (MATCH (ProbeSet.Name, @@ -106,9 +106,9 @@ class ProbeSetSearch(DoSearch): class PhenotypeSearch(DoSearch): """A search within a phenotype dataset""" - + DoSearch.search_types['Publish'] = "PhenotypeSearch" - + base_query = """SELECT PublishXRef.Id, PublishFreeze.createtime as thistable, Publication.PubMed_ID as Publication_PubMed_ID, @@ -125,7 +125,7 @@ class PhenotypeSearch(DoSearch): 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id') - + def get_where_clause(self): """Generate clause for WHERE portion of query""" @@ -140,7 +140,7 @@ class PhenotypeSearch(DoSearch): for field in self.search_fields: where_clause.append('''%s REGEXP "%s"''' % (field, search_term)) where_clause = "(%s)" % ' OR '.join(where_clause) - + return where_clause def run(self): @@ -164,7 +164,7 @@ class PhenotypeSearch(DoSearch): class GenotypeSearch(DoSearch): """A search within a genotype dataset""" - + DoSearch.search_types['Geno'] = "GenotypeSearch" base_query = """SELECT Geno.Name, @@ -185,7 +185,8 @@ class GenotypeSearch(DoSearch): where_clause = [] for field in self.search_fields: where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % (self.dataset.type, field), - self.search_term)) + self.escape(self.search_term))) + print("where_clause is:", pf(where_clause)) where_clause = "(%s)" % ' OR '.join(where_clause) return where_clause @@ -209,7 +210,7 @@ class GenotypeSearch(DoSearch): class RifSearch(ProbeSetSearch): """Searches for traits with a Gene RIF entry including the search term.""" - + DoSearch.search_types['RIF'] = "RifSearch" def run(self): @@ -224,9 +225,9 @@ class RifSearch(ProbeSetSearch): class WikiSearch(ProbeSetSearch): """Searches GeneWiki for traits other people have annotated""" - + DoSearch.search_types['WIKI'] = "WikiSearch" - + def run(self): where_clause = """%s.symbol = GeneRIF.symbol and GeneRIF.versionId=0 and GeneRIF.display>0 @@ -259,43 +260,44 @@ class GoSearch(ProbeSetSearch): from_clause = """ , db_GeneOntology.term as GOterm, db_GeneOntology.association as GOassociation, db_GeneOntology.gene_product as GOgene_product """ - + query = self.compile_final_query(from_clause, where_clause) return self.execute(query) +#ZS: Not sure what the best way to deal with LRS searches is class LrsSearch(ProbeSetSearch): """Searches for genes with a QTL within the given LRS values - + LRS searches can take 2 different forms: - LRS=(min_LRS max_LRS) - LRS=(min_LRS max_LRS chromosome start_Mb end_Mb) where min/max_LRS represent the range of LRS scores and start/end_Mb represent the range in megabases on the given chromosome - + """ - + DoSearch.search_types['LRS'] = 'LrsSearch' class CisLrsSearch(LrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values - + A cisLRS search can take 2 forms: - cisLRS=(min_LRS max_LRS) - cisLRS=(min_LRS max_LRS mb_buffer) where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around a particular QTL where its eQTL would be considered "cis". If there is no third parameter, mb_buffer will default to 5 megabases. - + A QTL is a cis-eQTL if a gene's expression is regulated by a QTL in roughly the same area (where the area is determined by the mb_buffer that the user can choose). - + """ - + # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps # between this and the LrsSearch code. In the original code, commands are divided by # the number of inputs they take, so these commands are completely separate - + DoSearch.search_types['CISLRS'] = "CisLrsSearch" def run(self): @@ -318,27 +320,28 @@ class CisLrsSearch(LrsSearch): self.dataset.type, min_threshold ) - else: - NeedSomeErrorHere + NeedSomeErrorHere - return None + query = self.compile_final_query(where_clause) + + return self.execute(query) class TransLrsSearch(LrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values - + A transLRS search can take 2 forms: - transLRS=(min_LRS max_LRS) - transLRS=(min_LRS max_LRS mb_buffer) where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around a particular QTL where its eQTL would be considered "cis". If there is no third parameter, mb_buffer will default to 5 megabases. - + A QTL is a trans-eQTL if a gene's expression is regulated by a QTL in a different location/area (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL. - + """ - + # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps # between this and the LrsSearch code. In the original code, commands are divided by # the number of inputs they take, so these commands are completely separate @@ -370,8 +373,8 @@ class TransLrsSearch(LrsSearch): NeedSomeErrorHere return None - - + + #itemCmd = item[0] #lowerLimit = float(item[1]) #upperLimit = float(item[2]) @@ -402,15 +405,15 @@ class TransLrsSearch(LrsSearch): # query.append(" (%s) " % clauseItem) # self.orderByDefalut = itemCmd # DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)))) - - + + class MeanSearch(ProbeSetSearch): """Searches for genes expressed within an interval (log2 units) determined by the user""" - + DoSearch.search_types['MEAN'] = "MeanSearch" - + def run(self): - + return None @@ -443,8 +446,9 @@ if __name__ == "__main__": #results = RifSearch("diabetes", dataset, cursor, db_conn).run() #results = WikiSearch("nicotine", dataset, cursor, db_conn).run() results = CisLrsSearch(['9','99','10'], dataset, cursor, db_conn).run() + #results = TransLrsSearch(['9', '999', '10'], dataset, cursor, db_conn).run() #results = PhenotypeSearch("brain", dataset, cursor, db_conn).run() #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() #results = GoSearch("0045202", dataset, cursor, db_conn).run() - + print("results are:", pf(results)) \ No newline at end of file diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index b220f837..74343b8a 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -9,9 +9,9 @@ def parse(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) - + items = [] - + for item in pstring: if ":" in item: key, seperator, value = item.partition(':') @@ -19,7 +19,7 @@ def parse(pstring): key, seperator, value = item.partition('=') else: seperator = None - + if seperator: if '(' in value: assert value.startswith("("), "Invalid token" @@ -41,11 +41,11 @@ def parse(pstring): term = dict(key=None, seperator=None, search_term = item) - + items.append(term) print(pf(items)) return(items) - + if __name__ == '__main__': parse("foo=(3 2 1)") parse("shh") diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 4aa1f2bc..dc3c72fc 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -45,7 +45,6 @@ from utility import formatting class SearchResultPage(templatePage): maxReturn = 3000 - #NPerPage = 100 nkeywords = 0 def __init__(self, fd): @@ -155,6 +154,13 @@ class SearchResultPage(templatePage): 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id'] + self.header_fields = ['', + 'ID', + 'Description', + 'Authors', + 'Year', + 'Max LRS', + 'Max LRS Location'] elif self.dataset.type == "ProbeSet": self.search_fields = ['Name', @@ -175,13 +181,19 @@ class SearchResultPage(templatePage): 'Max LRS Location'] elif self.dataset.type == "Geno": self.search_fields = ['Name','Chr'] + self.header_fields = ['', + 'ID', + 'Location'] self.search() self.gen_search_result() def gen_search_result(self): - + """Get the info displayed in the search result table from the set of results computed in + the "search" function + + """ self.trait_list = [] # result_set represents the results for each search term; a search of # "shh grin2b" would have two sets of results, one for each term @@ -192,52 +204,27 @@ class SearchResultPage(templatePage): seq = 1 group = self.dataset.group - self.form_name = form_name = 'show_dataset_'+group - tblobj = {} species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=group) - #### Excel file - - # Todo: Replace this with official Python temp file naming functions? - filename= webqtlUtil.genRandStr("Search_") - #xlsUrl = HT.Input(type='button', value = 'Download Table', onClick= "location.href='/tmp/%s.xls'" % filename, Class='button') - # Create a new Excel workbook - #workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+filename)) - #headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white") - - #XZ, 3/18/2010: pay attention to the line number of header in this file. As of today, there are 7 lines. - #worksheet = self.createExcelFileWithTitleAndFooter(workbook=workbook, db=this_trait.db, returnNumber=len(self.trait_list)) - newrow = 7 - - #### Excel file stuff stops - - if self.dataset.type == "ProbeSet": - print("foo locals are:", locals()) - probe_set_id = result[0] - this_trait = webqtlTrait(db=self.dataset, name=probe_set_id, cursor=self.cursor) - this_trait.retrieveInfo(QTL=True) - print("this_trait is:", pf(this_trait)) - self.trait_list.append(this_trait) - #elif self.dataset.type == "Publish": - # tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, species=species) - #elif self.dataset.type == "Geno": - # tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet) - - #traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden')) - hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group} - hddn['incparentsf1']='ON' + #### Excel file needs to be generated #### + + print("foo locals are:", locals()) + trait_id = result[0] + this_trait = webqtlTrait(db=self.dataset, name=trait_id, cursor=self.cursor) + this_trait.retrieveInfo(QTL=True) + print("this_trait is:", pf(this_trait)) + self.trait_list.append(this_trait) if self.dataset.type == "ProbeSet": - tblobj['body'] = self.getTableBodyForProbeSet(trait_list=self.trait_list, formName=self.form_name, species=species) + self.getTraitInfoForProbeSet(trait_list=self.trait_list, species=species) elif self.dataset.type == "Publish": - tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=self.form_name, species=species) + self.getTraitInfoForPublish(trait_list=self.trait_list, species=species) elif self.dataset.type == "Geno": - tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=self.form_name) + self.getTraitInfoForGeno(trait_list=self.trait_list) def search(self): - print("fd.search_terms:", self.fd['search_terms']) self.search_terms = parser.parse(self.fd['search_terms']) print("After parsing:", self.search_terms) @@ -267,6 +254,7 @@ class SearchResultPage(templatePage): print("in the search results are:", self.results) + #ZS: This should be handled in the parser def encregexp(self,str): if not str: return [] @@ -284,24 +272,12 @@ class SearchResultPage(templatePage): return wildcardkeyword - def getTableBodyForGeno(self, trait_list, formName=None): - - tblobj_body = [] - - className = "fs12 fwn ffl b1 c222" + def getTraitInfoForGeno(self, trait_list): for this_trait in trait_list: - tr = [] - if not this_trait.haveinfo: this_trait.retrieveInfo() - trId = str(this_trait) - - tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId)) - - tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name,url="javascript:showDatabase3('%s','%s','%s','')" % (formName, this_trait.db.name, this_trait.name), Class="fs12 fwn ffl"),align="left", Class=className), text=this_trait.name, val=this_trait.name.upper())) - #XZ: trait_location_value is used for sorting trait_location_repr = 'N/A' trait_location_value = 1000000 @@ -315,70 +291,37 @@ class SearchResultPage(templatePage): else: trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb - trait_location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) + this_trait.location_repr = 'Chr%s: %.4f' % (this_trait.chr, float(this_trait.mb) ) + this_trait.location_value = trait_location_value - tr.append(TDCell(HT.TD(trait_location_repr, Class="fs12 fwn b1 c222", nowrap="on"), trait_location_repr, trait_location_value)) - tblobj_body.append(tr) - - #for ncol, item in enumerate([this_trait.name, trait_location_repr]): - # worksheet.write([newrow, ncol], item) - - return tblobj_body - - - def getTableBodyForPublish(self, trait_list, formName=None, species=''): - - tblobj_body = [] - - className = "fs12 fwn b1 c222" + def getTraitInfoForPublish(self, trait_list, species=''): for this_trait in trait_list: - tr = [] - if not this_trait.haveinfo: this_trait.retrieveInfo(QTL=1) - trId = str(this_trait) - - tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId)) - - tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name,url="javascript:showDatabase3('%s','%s','%s','')" % (formName, this_trait.db.name, this_trait.name), Class="fs12 fwn"), nowrap="yes",align="center", Class=className),str(this_trait.name), this_trait.name)) - - PhenotypeString = this_trait.post_publication_description + description = this_trait.post_publication_description if this_trait.confidential: if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): - PhenotypeString = this_trait.pre_publication_description - tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper())) - - tr.append(TDCell(HT.TD(this_trait.authors, Class="fs12 fwn b1 c222 fsI"),this_trait.authors, this_trait.authors.strip().upper())) + description = this_trait.pre_publication_description + this_trait.description_display = description try: - PubMedLinkText = myear = repr = int(this_trait.year) + this_trait.pubmed_text = int(this_trait.year) except: - PubMedLinkText = repr = "N/A" - myear = 0 + this_trait.pubmed_text = "N/A" if this_trait.pubmed_id: - PubMedLink = HT.Href(text= repr,url= webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id,target='_blank', Class="fs12 fwn") - else: - PubMedLink = repr - - tr.append(TDCell(HT.TD(PubMedLink, Class=className, align='center'), repr, myear)) + this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id #LRS and its location - LRS_score_repr = 'N/A' - LRS_score_value = 0 - LRS_location_repr = 'N/A' - LRS_location_value = 1000000 - LRS_flag = 1 - + this_trait.LRS_score_repr = 'N/A' + this_trait.LRS_score_value = 0 + this_trait.LRS_location_repr = 'N/A' + this_trait.LRS_location_value = 1000000 if this_trait.lrs: - LRS_score_repr = '%3.1f' % this_trait.lrs - LRS_score_value = this_trait.lrs - tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value)) - self.cursor.execute(""" select Geno.Chr, Geno.Mb from Geno, Species where Species.Name = '%s' and @@ -401,27 +344,14 @@ class SearchResultPage(templatePage): else: LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb) - LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) ) - LRS_flag = 0 - - tr.append(TDCell(HT.TD(LRS_location_repr, Class=className, nowrap="on"), LRS_location_repr, LRS_location_value)) - - else: - tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A")) - tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A")) - - tblobj_body.append(tr) - - #for ncol, item in enumerate([this_trait.name, PhenotypeString, this_trait.authors, this_trait.year, this_trait.pubmed_id, LRS_score_repr, LRS_location_repr]): - # worksheet.write([newrow, ncol], item) + this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs + this_trait.LRS_score_value = LRS_score_value = this_trait.lrs + this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) ) - return tblobj_body + def getTraitInfoForProbeSet(self, trait_list=None, species=''): - def getTableBodyForProbeSet(self, trait_list=None, primaryTrait=None, formName=None, species=''): # Note: setting trait_list to [] is probably not a great idea. - tblobj_body = [] - if not trait_list: trait_list = [] @@ -435,27 +365,6 @@ class SearchResultPage(templatePage): else: this_trait.symbol = "N/A" - tr = [] - - trId = str(this_trait) - - #XZ, 12/08/2008: checkbox - #tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId)) - - #XZ, 12/08/2008: probeset name - #if this_trait.cellid: - # tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name, url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, this_trait.db.name,this_trait.name,this_trait.cellid), Class="fs12 fwn"), Class=className), this_trait.name, this_trait.name.upper())) - #else: - # tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name, url="javascript:showDatabase3('%s','%s','%s','')" % (formName, this_trait.db.name,this_trait.name), Class="fs12 fwn"), Class=className), this_trait.name, this_trait.name.upper())) - # - #if this_trait.geneid: - # symbolurl = HT.Href(text=this_trait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % this_trait.geneid, Class="font_black fs12 fwn") - #else: - # symbolurl = HT.Href(text=this_trait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % this_trait.symbol, Class="font_black fs12 fwn") - # - ##XZ, 12/08/2008: gene symbol - #tr.append(TDCell(HT.TD(symbolurl, Class="fs12 fwn b1 c222 fsI"),this_trait.symbol, this_trait.symbol.upper())) - #XZ, 12/08/2008: description #XZ, 06/05/2009: Rob asked to add probe target description description_string = str(this_trait.description).strip() @@ -487,8 +396,8 @@ class SearchResultPage(templatePage): else: trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb - trait_location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) ) - this_trait.trait_location_repr = trait_location_repr + this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) ) + this_trait.location_value = trait_location_value #this_trait.trait_location_value = trait_location_value #XZ, 01/12/08: This SQL query is much faster. @@ -517,11 +426,10 @@ class SearchResultPage(templatePage): this_trait.mean = repr = "%2.3f" % mean #LRS and its location - LRS_score_repr = 'N/A' - LRS_score_value = 0 - LRS_location_repr = 'N/A' - LRS_location_value = 1000000 - LRS_flag = 1 + this_trait.LRS_score_repr = 'N/A' + this_trait.LRS_score_value = 0 + this_trait.LRS_location_repr = 'N/A' + this_trait.LRS_location_value = 1000000 #Max LRS and its Locus location if this_trait.lrs and this_trait.locus: @@ -550,28 +458,3 @@ class SearchResultPage(templatePage): this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) ) - LRS_flag = 0 - - #if LRS_flag: - #tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value)) - #tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value)) - - #else: - #tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A")) - #tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A")) - - tblobj_body.append(tr) - - return tblobj_body - - - def getSortByValue(self, datasetType=''): - - if datasetType == 'Geno': - sortby = ("location", "up") - elif datasetType == 'ProbeSet': - sortby = ("symbol", "up") - else: #Phenotype - sortby = ("record_id", "down") - - return sortby diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 65182e1f..e393ced6 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -50,18 +50,32 @@ </TD> <TD> <a href="{{ url_for('show_trait_page', - database=this_trait.db.name, - ProbeSetID=this_trait.name, incparentsf1='ON', - RISet='BXD')}}"> - {{ this_trait.name.upper() }} + dataset = dataset.name, + trait_id = this_trait.name, + group = dataset.group)}}"> + {{ this_trait.name }} </a> </TD> - <TD>{{ this_trait.symbol }}</TD> - <TD>{{ this_trait.description_display }}</TD> - <TD>{{ this_trait.trait_location_repr }}</TD> - <TD>{{ this_trait.mean }}</TD> - <TD>{{ this_trait.LRS_score_repr }}</TD> - <TD>{{ this_trait.LRS_location_repr }}</TD> + {% if dataset.type == 'ProbeSet' %} + <TD>{{ this_trait.symbol }}</TD> + <TD>{{ this_trait.description_display }}</TD> + <TD>{{ this_trait.location_repr }}</TD> + <TD>{{ this_trait.mean }}</TD> + <TD>{{ this_trait.LRS_score_repr }}</TD> + <TD>{{ this_trait.LRS_location_repr }}</TD> + {% elif dataset.type == 'Publish' %} + <TD>{{ this_trait.description_display }}</TD> + <TD>{{ this_trait.authors }}</TD> + <TD> + <a href="{{ this_trait.pubmed_link }}"> + {{ this_trait.pubmed_text }} + </a> + </TD> + <TD>{{ this_trait.LRS_score_repr }}</TD> + <TD>{{ this_trait.LRS_location_repr }}</TD> + {% elif dataset.type == 'Geno' %} + <TD>{{ this_trait.location_repr }}</TD> + {% endif %} </TR> {% endfor %} </tbody> |