diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 10 | ||||
| -rwxr-xr-x | wqflask/base/species.py | 6 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 2 |
3 files changed, 13 insertions, 5 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index a2b13748..843862aa 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -164,6 +164,7 @@ class Markers(object): marker['chr'] = int(marker['chr']) else: marker['chr'] = 19 + print("Mb:", marker['Mb']) marker['Mb'] = float(marker['Mb']) self.markers = markers @@ -670,6 +671,7 @@ class PhenotypeDataSet(DataSet): def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: + if not this_trait.haveinfo: this_trait.retrieve_info(get_qtl_info=True) @@ -679,6 +681,7 @@ class PhenotypeDataSet(DataSet): #phenotype traits, then display the pre-publication description instead #of the post-publication description if this_trait.confidential: + this_trait.description_display = "" continue # for now if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( @@ -688,7 +691,12 @@ class PhenotypeDataSet(DataSet): description = this_trait.pre_publication_description - this_trait.description_display = description.strip() + if len(description) > 0: + this_trait.description_display = description.strip() + else: + this_trait.description_display = "" + + print("this_trait.description_display is:", this_trait.description_display) if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" diff --git a/wqflask/base/species.py b/wqflask/base/species.py index ebc2bfed..52bd8297 100755 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -13,7 +13,7 @@ from pprint import pformat as pf class TheSpecies(object): def __init__(self, dataset): self.dataset = dataset - print("self.dataset is:", pf(self.dataset.__dict__)) + #print("self.dataset is:", pf(self.dataset.__dict__)) self.chromosomes = Chromosomes(self.dataset) self.genome_mb_length = self.chromosomes.get_genome_mb_length() @@ -56,8 +56,8 @@ class Chromosomes(object): InbredSet.Name = %s Order by OrderId """, self.dataset.group.name).fetchall() - print("group: ", self.dataset.group.name) - print("bike:", results) + #print("group: ", self.dataset.group.name) + #print("bike:", results) for item in results: self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 3f80d4a4..2bbd1f2a 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -645,7 +645,7 @@ def get_sample_data(): trait_ob = GeneralTrait(name=trait, dataset_name=dataset) - return json.dumps({key: value.value for key, value in trait_ob.data.iteritems() }) + 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(): |