diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 44 |
1 files changed, 22 insertions, 22 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a71d8157..b51b8c72 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -69,11 +69,11 @@ class GeneralTrait(object): self.retrieve_info(get_qtl_info=get_qtl_info) if get_sample_info != False: self.retrieve_sample_data() - - + + def jsonable(self): """Return a dict suitable for using as json - + Actual turning into json doesn't happen here though""" return dict(name=self.name, dataset=self.dataset.name, @@ -258,10 +258,10 @@ class GeneralTrait(object): PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishFreeze.Id = %s """ % (self.name, self.dataset.id) - + trait_info = g.db.execute(query).fetchone() - - + + #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. elif self.dataset.type == 'ProbeSet': @@ -310,27 +310,27 @@ class GeneralTrait(object): if isinstance(trait_info[i], basestring): holder = unicode(trait_info[i], "utf8", "ignore") setattr(self, field, holder) - + if self.dataset.type == 'Publish': self.confidential = 0 if self.pre_publication_description and not self.pubmed_id: self.confidential = 1 - + description = self.post_publication_description - + #If the dataset is confidential and the user has access to confidential #phenotype traits, then display the pre-publication description instead #of the post-publication description if self.confidential: self.description_display = "" - + #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( # privilege=self.dataset.privilege, # userName=self.dataset.userName, # authorized_users=self.authorized_users): - # + # # description = self.pre_publication_description - + if description: self.description_display = description.strip() else: @@ -343,8 +343,8 @@ class GeneralTrait(object): if self.pubmed_id: self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id - - + + self.homologeneid = None if self.dataset.type == 'ProbeSet' and self.dataset.group: if self.geneid: @@ -374,7 +374,7 @@ class GeneralTrait(object): if result: self.homologeneid = result[0] - + description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') @@ -410,7 +410,7 @@ class GeneralTrait(object): #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 @@ -481,7 +481,7 @@ class GeneralTrait(object): self.locus = self.locus_chr = self.locus_mb = self.additive = "" else: self.locus = self.lrs = self.additive = "" - + if (self.dataset.type == 'Publish' or self.dataset.type == "ProbeSet") and self.locus_chr != "" and self.locus_mb != "": #XZ: LRS_location_value is used for sorting try: @@ -493,7 +493,7 @@ class GeneralTrait(object): LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb) self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb)) - if self.lrs != "": + if self.lrs != "": self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs self.LRS_score_value = LRS_score_value = self.lrs else: @@ -712,7 +712,7 @@ def convert_location_to_value(chromosome, mb): else: location_value = (ord(str(chromosome).upper()[0])*1000 + float(mb)) - + return location_value @app.route("/trait/get_sample_data") @@ -720,11 +720,11 @@ def get_sample_data(): params = request.args trait = params['trait'] dataset = params['dataset'] - + trait_ob = GeneralTrait(name=trait, dataset_name=dataset) - + return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }]) - + #jsonable_sample_data = {} #for sample in trait_ob.data.iteritems(): # jsonable_sample_data[sample] = trait_ob.data[sample].value |