Change cancer type IDs to lower case

cBioPortal · Aug 1, 2018 · 054429f · 054429f
1 parent 43f8c38
commit 054429f
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Showing 5 changed files with 6 additions and 5 deletions.
diff --git a/.circleci/portalinfo/cancertypes.json b/.circleci/portalinfo/cancertypes.json
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 .DS_Store
-*.swp
+*.swp
+.idea
diff --git a/seedDB/README.md b/seedDB/README.md
@@ -16,7 +16,7 @@ When using a release version **> 1.14.0**, a migration step to a new database sc
 
 **Schema 2.6.0**: [SQL file with create table statements](https://raw.githubusercontent.com/cBioPortal/cbioportal/v1.13.1/db-scripts/src/main/resources/cgds.sql)<br>
 **Seed database**: [seed-cbioportal_hg19_v2.6.0.sql.gz](https://github.com/cBioPortal/datahub/raw/master/seedDB/seed-cbioportal_hg19_v2.6.0.sql.gz)<br>
-md5sum 4f418394148cb4c0af8a4d739df2dfd7
+md5sum ae7b20340476b0bfcde92ff8379d526c
 
 Contents of seed database:
 - Entrez Gene IDs, HGNC symbols and gene aliases updated in April 2018 from [NCBI](ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz)

diff --git a/seedDB/seed-cbioportal_hg19_v2.6.0.sql.gz b/seedDB/seed-cbioportal_hg19_v2.6.0.sql.gz
diff --git a/seedDB/update_cancer_types.py b/seedDB/update_cancer_types.py
@@ -70,12 +70,12 @@ def parse_cancer_types_json(cancer_types_json):
     def flatten_oncotree(node, node_name):
         """Recursive function to flatten the JSON formatted cancer types"""
 
-        type_of_cancer_id = node_name
+        type_of_cancer_id = node_name.lower()
         name = node['name']
         clinical_trial_keywords = node['name'].lower()
         dedicated_color = node['color']
         short_name = node_name
-        parent = node['parent']
+        parent = node['parent'].lower()
 
         cancer_type = [type_of_cancer_id, name, clinical_trial_keywords, dedicated_color, short_name, parent]
         cancer_types.append(cancer_type)