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-rw-r--r--wqflask/base/trait.py114
1 files changed, 31 insertions, 83 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 41e2603c..96a09302 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -27,11 +27,13 @@ def create_trait(**kw):
assert bool(kw.get('name')), "Needs trait name"
- if kw.get('dataset_name'):
+ if bool(kw.get('dataset')):
+ dataset = kw.get('dataset')
+ else:
if kw.get('dataset_name') != "Temp":
dataset = create_dataset(kw.get('dataset_name'))
- else:
- dataset = kw.get('dataset')
+ else:
+ dataset = create_dataset("Temp", group_name=kw.get('group_name'))
if dataset.type == 'Publish':
permissions = check_resource_availability(
@@ -51,7 +53,7 @@ def create_trait(**kw):
return None
-class GeneralTrait(object):
+class GeneralTrait:
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
@@ -284,17 +286,19 @@ def get_sample_data():
return None
-def jsonable(trait):
+def jsonable(trait, dataset=None):
"""Return a dict suitable for using as json
Actual turning into json doesn't happen here though"""
- dataset = create_dataset(dataset_name=trait.dataset.name,
- dataset_type=trait.dataset.type,
- group_name=trait.dataset.group.name)
+ if not dataset:
+ dataset = create_dataset(dataset_name=trait.dataset.name,
+ dataset_type=trait.dataset.type,
+ group_name=trait.dataset.group.name)
if dataset.type == "ProbeSet":
return dict(name=trait.name,
+ view=trait.view,
symbol=trait.symbol,
dataset=dataset.name,
dataset_name=dataset.shortname,
@@ -308,103 +312,46 @@ def jsonable(trait):
elif dataset.type == "Publish":
if trait.pubmed_id:
return dict(name=trait.name,
+ view=trait.view,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
+ pubmed_id=trait.pubmed_id,
pubmed_text=trait.pubmed_text,
pubmed_link=trait.pubmed_link,
+ mean=trait.mean,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
else:
return dict(name=trait.name,
+ view=trait.view,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
+ mean=trait.mean,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
elif dataset.type == "Geno":
return dict(name=trait.name,
+ view=trait.view,
dataset=dataset.name,
dataset_name=dataset.shortname,
location=trait.location_repr
)
- else:
- return dict()
-
-
-def jsonable_table_row(trait, dataset_name, index):
- """Return a list suitable for json and intended to be displayed in a table
-
- Actual turning into json doesn't happen here though"""
-
- dataset = create_dataset(dataset_name)
-
- if dataset.type == "ProbeSet":
- if trait.mean == "":
- mean = "N/A"
- else:
- mean = "%.3f" % round(float(trait.mean), 2)
- if trait.additive == "":
- additive = "N/A"
- else:
- additive = "%.3f" % round(float(trait.additive), 2)
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
- index,
- '<a href="/show_trait?trait_id=' +
- str(trait.name)+'&dataset='+dataset.name +
- '">'+str(trait.name)+'</a>',
- trait.symbol,
- trait.description_display,
- trait.location_repr,
- mean,
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- elif dataset.type == "Publish":
- if trait.additive == "":
- additive = "N/A"
- else:
- additive = "%.2f" % round(float(trait.additive), 2)
- if trait.pubmed_id:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
- index,
- '<a href="/show_trait?trait_id=' +
- str(trait.name)+'&dataset='+dataset.name +
- '">'+str(trait.name)+'</a>',
- trait.description_display,
- trait.authors,
- '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- else:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
- index,
- '<a href="/show_trait?trait_id=' +
- str(trait.name)+'&dataset='+dataset.name +
- '">'+str(trait.name)+'</a>',
- trait.description_display,
- trait.authors,
- trait.pubmed_text,
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- elif dataset.type == "Geno":
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
- index,
- '<a href="/show_trait?trait_id=' +
- str(trait.name)+'&dataset='+dataset.name +
- '">'+str(trait.name)+'</a>',
- trait.location_repr]
+ elif dataset.name == "Temp":
+ return dict(name=trait.name,
+ view=trait.view,
+ dataset="Temp",
+ dataset_name="Temp")
else:
return dict()
@@ -516,10 +463,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
# 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
- trait.description_display = ""
+ trait.description_display = "N/A"
if not trait.pubmed_id:
trait.abbreviation = trait.pre_publication_abbreviation
- trait.description_display = trait.pre_publication_description
+ if trait.pre_publication_description:
+ trait.description_display = trait.pre_publication_description
else:
trait.abbreviation = trait.post_publication_abbreviation
if description:
@@ -542,9 +490,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
else:
description_display = trait.symbol
- if (str(description_display or "") != "" and
- description_display != 'N/A' and
- str(target_string or "") != "" and target_string != 'None'):
+ if (str(description_display or "") != ""
+ and description_display != 'N/A'
+ and str(target_string or "") != "" and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
@@ -638,6 +586,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if str(trait.lrs or "") != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
else:
- raise KeyError(repr(trait.name) +
- ' information is not found in the database.')
+ raise KeyError(repr(trait.name)
+ + ' information is not found in the database.')
return trait
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 09:31:01 +0000