Adding more missed name changes

Author: jjacobson95

coderbuild/build_dataset.py

@@ -41,15 +41,15 @@ def process_docker(dataset,validate):
         'hcmi': ['hcmi'],
         'beataml': ['beataml'],
         'mpnst': ['mpnst'],
-        'pancpdo': ['pancpdo'],
+        'pancreatic': ['pancreatic'],
         'cptac': ['cptac'],
-        'sarcpdo': ['sarcpdo'],
+        'sarcoma': ['sarcoma'],
         'genes': ['genes'],
         'upload': ['upload'],
         'colorectal': ['colorectal'], 
-        'bladderpdo': ['bladderpdo'],
-        'liverpdo': ['liverpdo'],
-        'novartispdx': ['novartispdx']
+        'bladder': ['bladder'],
+        'liver': ['liver'],
+        'novartis': ['novartis']
     }
 
     # Collect container names to build based on the dataset provided. Always build 'genes'.
@@ -128,12 +128,12 @@ def process_omics(executor, dataset, should_continue):
         'broad_sanger': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'cptac': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'hcmi': ['mutations', 'transcriptomics'],
-        'sarcpdo': ['mutations', 'transcriptomics'],
-        'pancpdo': ['transcriptomics'],
-        'bladderpdo': ['copy_number', 'mutations', 'transcriptomics'],
+        'sarcoma': ['mutations', 'transcriptomics'],
+        'pancreatic': ['transcriptomics'],
+        'bladder': ['copy_number', 'mutations', 'transcriptomics'],
         'colorectal':['copy_number', 'mutations', 'transcriptomics'],
-        'novartispdx':['copy_number', 'mutations', 'transcriptomics'],
-        'liverpdo':['copy_number', 'mutations', 'transcriptomics']
+        'novartis':['copy_number', 'mutations', 'transcriptomics'],
+        'liver':['copy_number', 'mutations', 'transcriptomics']
     }
 
     expected_omics = dataset_omics_files.get(dataset, [])

coderbuild/docker/docker-compose.yml

@@ -26,14 +26,14 @@ services:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
     image: hcmi:latest
-  pancpdo:
+  pancreatic:
     build:
       context: ../../
-      dockerfile: coderbuild/docker/Dockerfile.pancpdo
+      dockerfile: coderbuild/docker/Dockerfile.pancreatic
       args:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
-    image: pancpdo:latest
+    image: pancreatic:latest
 
   beataml:
     build:
@@ -70,22 +70,22 @@ services:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
     image: cptac:latest
-  sarcpdo:
+  sarcoma:
     build:
       context: ../../
-      dockerfile: coderbuild/docker/Dockerfile.sarcpdo
+      dockerfile: coderbuild/docker/Dockerfile.sarcoma
       args:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
-    image: sarcpdo:latest
-  bladderpdo:
+    image: sarcoma:latest
+  bladder:
     build:
       context: ../../
-      dockerfile: coderbuild/docker/Dockerfile.bladderpdo
+      dockerfile: coderbuild/docker/Dockerfile.bladder
       args:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
-    image: bladderpdo:latest
+    image: bladder:latest
 
   genes:
     build:
@@ -105,29 +105,29 @@ services:
     platform: linux/amd64
     image: upload:latest
 
-  crcpdo:
+  colorectal:
     build:
       context: ../../
-      dockerfile: coderbuild/docker/Dockerfile.crcpdo
+      dockerfile: coderbuild/docker/Dockerfile.colorectal
       args:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
-    image: crcpdo:latest
+    image: colorectal:latest
 
-  liverpdo:
+  liver:
     build:
       context: ../../
-      dockerfile: coderbuild/docker/Dockerfile.liverpdo
+      dockerfile: coderbuild/docker/Dockerfile.liver
       args:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
-    image: liverpdo:latest
+    image: liver:latest
 
-  novartispdx:
+  novartis:
     build:
       context: ../../
-      dockerfile: coderbuild/docker/Dockerfile.novartispdx
+      dockerfile: coderbuild/docker/Dockerfile.novartis
       args:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
-    image: novartispdx:latest
+    image: novartis:latest