merge changes

1 files changed, 113 insertions, 0 deletions

diff --git a/gn2/wqflask/show_trait/export_trait_data.py b/gn2/wqflask/show_trait/export_trait_data.py
new file mode 100644
index 00000000..06c1c502
--- /dev/null
+++ b/gn2/wqflask/show_trait/export_trait_data.py
@@ -0,0 +1,113 @@
+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