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import datetime
import simplejson as json
from pprint import pformat as pf
from functools import cmp_to_key
from gn2.base.trait import create_trait
from gn2.base import data_set
def export_sample_table(targs):
sample_data = json.loads(targs['export_data'])
trait_name = targs['trait_display_name']
meta_data = get_export_metadata(targs)
final_sample_data = meta_data
column_headers = ["Index", "Name", "Value"]
attr_pos = 2
if any(sample["se"] for sample in sample_data['primary_samples']):
column_headers.append("SE")
attr_pos = 3
if any(sample["num_cases"] for sample in sample_data['primary_samples']):
column_headers.append("N")
attr_pos = 4
for key in sample_data["primary_samples"][0].keys():
if key not in ["name", "value", "se", "num_cases"]:
column_headers.append(key)
final_sample_data.append(column_headers)
for sample_group in ['primary_samples', 'other_samples']:
for i, row in enumerate(sample_data[sample_group]):
sorted_row = [i + 1] + dict_to_sorted_list(row)[:attr_pos]
for attr in sample_data['attributes']:
sorted_row.append(row[attr])
final_sample_data.append(sorted_row)
return trait_name, final_sample_data
def get_export_metadata(trait_metadata):
trait_id, display_name, dataset_name, group_name = trait_metadata['trait_id'], trait_metadata['trait_display_name'], trait_metadata['dataset'], trait_metadata['group']
dataset = data_set.create_dataset(dataset_name, group_name=group_name)
this_trait = create_trait(dataset=dataset,
name=trait_id,
cellid=None,
get_qtl_info=False)
metadata = []
if dataset.type == "Publish":
metadata.append(["Phenotype ID:", display_name])
metadata.append(["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=" + \
trait_id + "&dataset=" + dataset_name])
metadata.append(["Group: ", dataset.group.name])
metadata.append(
["Phenotype: ", this_trait.description_display.replace(",", "\",\"")])
metadata.append(
["Authors: ", (this_trait.authors if this_trait.authors else "N/A")])
metadata.append(
["Title: ", (this_trait.title if this_trait.title else "N/A")])
metadata.append(
["Journal: ", (this_trait.journal if this_trait.journal else "N/A")])
metadata.append(
["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
else:
metadata.append(["Record ID: ", trait_id])
metadata.append(["Trait URL: ", "http://genenetwork.org/show_trait?trait_id=" + \
trait_id + "&dataset=" + dataset_name])
if this_trait.symbol:
metadata.append(["Symbol: ", this_trait.symbol])
metadata.append(["Dataset: ", dataset.name])
metadata.append(["Group: ", dataset.group.name])
metadata.append(
["Export Date: ", datetime.datetime.now().strftime("%B %d, %Y")])
metadata.append(
["Export Time: ", datetime.datetime.now().strftime("%H:%M GMT")])
return metadata
def dict_to_sorted_list(dictionary):
sorted_list = [item for item in list(dictionary.items())]
sorted_list = sorted(sorted_list, key=cmp_to_key(cmp_samples))
sorted_values = [item[1] for item in sorted_list]
return sorted_values
def cmp_samples(a, b):
if b[0] == 'name':
return 1
elif b[0] == 'value':
if a[0] == 'name':
return -1
else:
return 1
elif b[0] == 'se':
if a[0] == 'name' or a[0] == 'value':
return -1
else:
return 1
elif b[0] == 'num_cases':
if a[0] == 'name' or a[0] == 'value' or a[0] == 'se':
return -1
else:
return 1
else:
return -1
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