diff options
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 25 |
1 files changed, 17 insertions, 8 deletions
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 0e20722e..66d3a448 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -128,7 +128,7 @@ class ShowTrait(object): #Get nearest marker for composite mapping if not self.temp_trait: - if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish": + if check_if_attr_exists(self.this_trait, 'locus_chr') and self.dataset.type != "Geno" and self.dataset.type != "Publish": self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset) #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0] #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1] @@ -243,14 +243,14 @@ class ShowTrait(object): def get_external_links(self): #ZS: There's some weirdness here because some fields don't exist while others are empty strings - self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if hasattr(self.this_trait, 'pubmed_id') else None - self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if hasattr(self.this_trait, 'geneid') else None - self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if hasattr(self.this_trait, 'omim') else None - self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if (hasattr(self.this_trait, 'unigeneid') and self.this_trait.unigeneid != "" and self.this_trait.unigeneid != None) else None - self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if hasattr(self.this_trait, 'homologeneid') else None + self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if check_if_attr_exists(self.this_trait, 'pubmed_id') else None + self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if check_if_attr_exists(self.this_trait, 'geneid') else None + self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if check_if_attr_exists(self.this_trait, 'omim') else None + self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if check_if_attr_exists(self.this_trait, 'unigeneid') else None + self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists(self.this_trait, 'homologeneid') else None self.genbank_link = None - if hasattr(self.this_trait, 'genbankid') and self.this_trait.genbankid != None: + if check_if_attr_exists(self.this_trait, 'genbankid'): genbank_id = '|'.join(self.this_trait.genbankid.split('|')[0:10]) if genbank_id[-1] == '|': genbank_id = genbank_id[0:-1] @@ -516,4 +516,13 @@ def get_trait_units(this_trait): inside_brackets = False if i == "[": inside_brackets = True - return unit_type
\ No newline at end of file + return unit_type + +def check_if_attr_exists(the_trait, id_type): + if hasattr(the_trait, id_type): + if getattr(the_trait, id_type) == None or getattr(the_trait, id_type) == "": + return False + else: + return True + else: + return False
\ No newline at end of file |