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authorzsloan2019-11-21 14:55:50 -0600
committerzsloan2019-11-21 14:55:50 -0600
commit8427ddfd7b60d74f4be3a453dd0b21ce7bfdb6f3 (patch)
tree4a036c0613cce54b067476e4f1c6a881c6ff4bb2 /wqflask/base/trait.py
parent74e81163fb3c2418b88f6d4fbb99760c63a3fea6 (diff)
downloadgenenetwork2-8427ddfd7b60d74f4be3a453dd0b21ce7bfdb6f3.tar.gz
Added 3-letter codes to unpublished phenotype traits and fixed issue with ordering phenotype results from searches
Diffstat (limited to 'wqflask/base/trait.py')
-rw-r--r--wqflask/base/trait.py9
1 files changed, 7 insertions, 2 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 322fb252..5fae34cf 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -352,7 +352,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if dataset.type == 'Publish':
query = """
SELECT
- PublishXRef.Id, Publication.PubMed_ID,
+ PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
@@ -361,12 +361,13 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
Publication.Month, Publication.Year, PublishXRef.Sequence,
Phenotype.Units, PublishXRef.comments
FROM
- PublishXRef, Publication, Phenotype, PublishFreeze
+ PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
WHERE
PublishXRef.Id = %s AND
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishXRef.InbredSetId = InbredSet.Id AND
PublishFreeze.Id = %s
""" % (trait.name, dataset.id)
@@ -428,6 +429,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
# holder = unicode(trait_info[i], "utf-8", "ignore")
setattr(trait, field, holder)
+ trait.display_name = trait.name
if dataset.type == 'Publish':
trait.confidential = 0
if trait.pre_publication_description and not trait.pubmed_id:
@@ -462,6 +464,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if trait.pubmed_id:
trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
+ else:
+ if trait.group_code:
+ trait.display_name = trait.group_code + "_" + str(trait.name)
if dataset.type == 'ProbeSet' and dataset.group:
description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')