Add index column and phenotype group code to trait export

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([])