From a6e33c7ee6952ca332a7fb20607c991c9b21fe1a Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Thu, 20 Feb 2020 19:48:43 -0800
Subject: [PATCH] -> Re-enable seed-pull

---
 idc/metadata_utils.py         |  1 -
 idc/views.py                  |  3 ++-
 scripts/database_bootstrap.py | 22 +++++++++++-----------
 shell/database-refresh.sh     |  2 +-
 shell/python-su.sh            |  2 +-
 5 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/idc/metadata_utils.py b/idc/metadata_utils.py
index dbdbbf044..a31aa8737 100644
--- a/idc/metadata_utils.py
+++ b/idc/metadata_utils.py
@@ -72,7 +72,6 @@ def get_collex_metadata(filters, fields, with_docs=True, record_limit=10, counts
             'query_string': "*:*",
             'facets': solr_facets,
             'limit': record_limit if with_docs else 0,
-            # what is with_docs supposed to do?? 'limit': 10 if with_docs else 0,
             'collapse_on': 'SeriesInstanceUID',
             'counts_only': counts_only
         })
diff --git a/idc/views.py b/idc/views.py
index fc258ef36..0003facec 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -124,7 +124,7 @@ def explore_data(request):
     context = {}
     try:
         # These are example filters; typically they will be reconstituted from the request
-        filters = {"vital_status": ["Alive", "Dead"], "age_at_diagnosis_btw": [15,40], "bmi": "underweight"}
+        filters = {"vital_status": ["Alive", "Dead"], "age_at_diagnosis_btw": [15,40], "bmi": "underweight", "race": "BLACK OR AFRICAN AMERICAN"}
         # These are the actual data fields to display in the expanding table; again this is just an example
         # set that should be properly supplied in the reuqest
         fields = ["BodyPartExamined", "Modality", "StudyDescription", "StudyInstanceUID", "SeriesInstanceUID"]
@@ -139,6 +139,7 @@ def explore_data(request):
                 'cross_collex_attr_counts': facets_and_lists['facets']['cross_collex'],
                 'listings': facets_and_lists['docs']
             }
+
     except Exception as e:
         logger.error("[ERROR] In explore_data:")
         logger.exception(e)
diff --git a/scripts/database_bootstrap.py b/scripts/database_bootstrap.py
index 25320cf3d..66f4322ab 100644
--- a/scripts/database_bootstrap.py
+++ b/scripts/database_bootstrap.py
@@ -38,7 +38,7 @@
 import django
 django.setup()
 
-from idc_collections.models import Program, Collection, Attribute, Attribute_Display_Values, SolrCollection, BigQueryTable, DataVersion
+from idc_collections.models import Program, Collection, Attribute, Attribute_Ranges, Attribute_Display_Values, SolrCollection, BigQueryTable, DataVersion
 
 from django.contrib.auth.models import User
 idc_superuser = User.objects.get(username="idc")
@@ -165,6 +165,10 @@ def add_attributes(attr_set):
                 preformatted_values=True if 'preformatted_values' in attr else False,
                 is_cross_collex=True if 'cross_collex' in attr else False
             )
+            if 'range' in attr:
+                Attribute_Ranges.objects.update_or_create(
+                    attribute=obj
+                )
             if 'display_vals' in attr:
                 for dv in attr['display_vals']:
                     Attribute_Display_Values.objects.update_or_create(
@@ -288,6 +292,9 @@ def main():
                 else:
                     attr['display_vals'] = display_vals[attr['name']]['vals']
 
+            if attr['name'] == "age_at_diagnosis":
+                attr['range'] = True
+
             attr_set.append(attr)
 
         attr_file.close()
@@ -299,23 +306,16 @@ def main():
             line = line.strip()
             line_split = line.split(",")
 
-            attr_set.append({
+            attr = {
                 'name': line_split[0],
                 "display_name": line_split[0].replace("_", " ").title() if re.search(r'_', line_split[1]) else line_split[1],
                 "type": Attribute.CATEGORICAL if line_split[2] == 'CATEGORICAL STRING' else Attribute.STRING if line_split[2] == "STRING" else Attribute.CONTINUOUS_NUMERIC,
                 'cross_collex': True,
                 'solr_collex': ['tcia_images'],
                 'bq_tables': ["idc-dev-etl.tcia.dicom_metadata"]
-            })
+            }
 
-        attr_set.append({
-            'name': 'collection_id',
-            'display_name': "Collection",
-            "type": Attribute.CATEGORICAL,
-            "cross_collex": True,
-            'solr_collex': ['tcia_images'],
-            'bq_tables': ["idc-dev-etl.tcia.dicom_metadata"]
-        })
+            attr_set.append(attr)
 
         add_attributes(attr_set)
 
diff --git a/shell/database-refresh.sh b/shell/database-refresh.sh
index 9ee5c0ecf..7e9f49663 100755
--- a/shell/database-refresh.sh
+++ b/shell/database-refresh.sh
@@ -8,7 +8,7 @@ else
         exit 1
     fi
     # Doublecheck where we're running this...
-    if [ $DATABASE_HOST != "localhost" ]; then
+    if [ "${DATABASE_HOST}" != "localhost" ]; then
         echo "[ERROR] Possible remote database detected! This script IS ONLY intended for use on local developer builds!"
         echo "[ERROR] Host seen: ${DATABASE_HOST}"
         exit 1
diff --git a/shell/python-su.sh b/shell/python-su.sh
index 9042ac8f1..79022a76e 100755
--- a/shell/python-su.sh
+++ b/shell/python-su.sh
@@ -1,2 +1,2 @@
 #!/bin/bash
-sudo PYTHONPATH="$PYTHONPATH" SECURE_LOCAL_PATH="$SECURE_LOCAL_PATH" /usr/bin/python3 "$@"
\ No newline at end of file
+sudo PYTHONPATH="$VM_PYTHONPATH" SECURE_LOCAL_PATH="$SECURE_LOCAL_PATH" /usr/bin/python3 "$@"
\ No newline at end of file