diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 17 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 103 |
2 files changed, 107 insertions, 13 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fddfce58..04436a2e 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -271,7 +271,8 @@ class DatasetGroup(object): self.f1list = None self.parlist = None self.get_f1_parent_strains() - #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list)) + + self.accession_id = self.get_accession_id() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -279,6 +280,20 @@ class DatasetGroup(object): self.allsamples = None self._datasets = None + def get_accession_id(self): + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by + PublishFreeze.CreateTime desc""", (self.name)).fetchone() + + if results != None: + return str(results[0]) + else: + return "None" + def get_specified_markers(self, markers = []): self.markers = HumanMarkers(self.name, markers) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 276c624a..8788d983 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -91,16 +91,27 @@ class GeneralTrait(object): additive=self.additive ) elif self.dataset.type == "Publish": - return dict(name=self.name, - dataset=self.dataset.name, - description=self.description_display, - authors=self.authors, - pubmed_text=self.pubmed_text, - pubmed_link=self.pubmed_link, - lrs_score=self.LRS_score_repr, - lrs_location=self.LRS_location_repr, - additive=self.additive - ) + if self.pubmed_id: + return dict(name=self.name, + dataset=self.dataset.name, + description=self.description_display, + authors=self.authors, + pubmed_text=self.pubmed_text, + pubmed_link=self.pubmed_link, + lrs_score=self.LRS_score_repr, + lrs_location=self.LRS_location_repr, + additive=self.additive + ) + else: + return dict(name=self.name, + dataset=self.dataset.name, + description=self.description_display, + authors=self.authors, + pubmed_text=self.pubmed_text, + lrs_score=self.LRS_score_repr, + lrs_location=self.LRS_location_repr, + additive=self.additive + ) elif self.dataset.type == "Geno": return dict(name=self.name, dataset=self.dataset.name, @@ -109,6 +120,62 @@ class GeneralTrait(object): else: return dict() + def jsonable_table_row(self, index, search_type): + """Return a list suitable for json and intended to be displayed in a table + + Actual turning into json doesn't happen here though""" + + if self.dataset.type == "ProbeSet": + if self.mean == "": + mean = "N/A" + else: + mean = "%.3f" % round(float(self.additive), 2) + if self.additive == "": + additive = "N/A" + else: + additive = "%.3f" % round(float(self.additive), 2) + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">', + index, + '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>', + self.symbol, + self.description_display, + self.location_repr, + mean, + self.LRS_score_repr, + self.LRS_location_repr, + additive] + elif self.dataset.type == "Publish": + if self.additive == "": + additive = "N/A" + else: + additive = "%.2f" % round(float(self.additive), 2) + if self.pubmed_id: + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">', + index, + '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>', + self.description_display, + self.authors, + '<a href="' + self.pubmed_link + '">' + self.pubmed_text + '</href>', + self.LRS_score_repr, + self.LRS_location_repr, + additive] + else: + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">', + index, + '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>', + self.description_display, + self.authors, + self.pubmed_text, + self.LRS_score_repr, + self.LRS_location_repr, + additive] + elif self.dataset.type == "Geno": + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">', + index, + '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>', + self.location_repr] + else: + return dict() def get_name(self): stringy = "" @@ -418,7 +485,7 @@ class GeneralTrait(object): self.description_display = description_display #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' + self.location_repr = 'N/A' trait_location_value = 1000000 if self.chr and self.mb: @@ -438,6 +505,18 @@ class GeneralTrait(object): self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) self.location_value = trait_location_value + elif self.dataset.type == "Geno": + self.location_repr = 'N/A' + trait_location_value = 1000000 + + if self.chr and self.mb: + #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") + #This is so we can convert the location to a number used for sorting + trait_location_value = convert_location_to_value(self.chr, self.mb) + + #ZS: Put this in function currently called "convert_location_to_value" + self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) + self.location_value = trait_location_value if get_qtl_info: #LRS and its location @@ -459,7 +538,7 @@ class GeneralTrait(object): logger.sql(query) trait_qtl = g.db.execute(query).fetchone() if trait_qtl: - self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl + self.locus, self.lrs, self.pvalue, self.mean, self.additive = trait_qtl if self.locus: query = """ select Geno.Chr, Geno.Mb from Geno, Species |