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authorzsloan2022-08-01 16:00:25 +0000
committerzsloan2022-08-01 17:01:54 +0000
commit00baf5bab27fd034a53add29111e9aa0d9e45d6b (patch)
tree38bff0fb1bfe4b8f35c18ce26a56c59d0ac56195 /wqflask
parent82922e5a052abf22b9d458ddebaf8ee523bd6f55 (diff)
downloadgenenetwork2-00baf5bab27fd034a53add29111e9aa0d9e45d6b.tar.gz
Add index column and phenotype group code to trait export
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/show_trait/export_trait_data.py39
1 files changed, 21 insertions, 18 deletions
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 4b328a4a..ae83907e 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -11,11 +11,11 @@ def export_sample_table(targs):
sample_data = json.loads(targs['export_data'])
trait_name = targs['trait_display_name']
- meta_data = get_export_metadata(targs['trait_id'], targs['dataset'])
+ meta_data = get_export_metadata(targs)
final_sample_data = meta_data
- column_headers = ["Name", "Value"]
+ column_headers = ["Index", "Name", "Value"]
attr_pos = 2
if any(sample["se"] for sample in sample_data['primary_samples']):
column_headers.append("SE")
@@ -30,8 +30,8 @@ def export_sample_table(targs):
final_sample_data.append(column_headers)
for sample_group in ['primary_samples', 'other_samples']:
- for row in sample_data[sample_group]:
- sorted_row = dict_to_sorted_list(row)[:attr_pos]
+ 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)
@@ -39,7 +39,10 @@ def export_sample_table(targs):
return trait_name, final_sample_data
-def get_export_metadata(trait_id, dataset_name):
+def get_export_metadata(trait_metadata):
+
+ trait_id, display_name, dataset_name = trait_metadata['trait_id'], trait_metadata['trait_display_name'], trait_metadata['dataset']
+
dataset = data_set.create_dataset(dataset_name)
this_trait = create_trait(dataset=dataset,
name=trait_id,
@@ -48,28 +51,28 @@ def get_export_metadata(trait_id, dataset_name):
metadata = []
if dataset.type == "Publish":
- metadata.append(["Phenotype ID: " + trait_id])
- metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
+ 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(["Group: ", dataset.group.name])
metadata.append(
- ["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
+ ["Phenotype: ", this_trait.description_display.replace(",", "\",\"")])
metadata.append(
- ["Authors: " + (this_trait.authors if this_trait.authors else "N/A")])
+ ["Authors: ", (this_trait.authors if this_trait.authors else "N/A")])
metadata.append(
- ["Title: " + (this_trait.title if this_trait.title else "N/A")])
+ ["Title: ", (this_trait.title if this_trait.title else "N/A")])
metadata.append(
- ["Journal: " + (this_trait.journal if this_trait.journal else "N/A")])
+ ["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])
+ ["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=" + \
+ 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(["Symbol: ", this_trait.symbol])
+ metadata.append(["Dataset: ", dataset.name])
+ metadata.append(["Group: ", dataset.group.name])
metadata.append([])