Merge branch 'main' into sample_id_mapping_update

Author: jjacobson95

.github/workflows/build.yml

@@ -177,6 +177,30 @@ jobs:
           push: true
           platforms: linux/amd64
 
+  build-pancpdo:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push pancpdo
+        uses: docker/build-push-action@v3
+        with:
+          file: ./build/docker/Dockerfile.pancpdo
+          tags: |
+            sgosline/pancpdo:latest
+            sgosline/pancpdo:${{ github.ref_name }}
+          push: true
+          platforms: linux/amd64
+
   build-upload:
     runs-on: ubuntu-latest
     steps:

.gitignore

@@ -18,3 +18,5 @@ tests/__pycache__
 dist
 build/lib
 build/local
+coderdata/_version.py
+local/

build/broad_sanger/03a-nci60Drugs.py

@@ -16,21 +16,36 @@
 #oct 2024
 smi_strings = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_smiles.csv?version=3&modificationDate=1727924130457&api=v2&download=true'
 
+#jan 2025
+smi_strings ='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_smiles.csv?version=5&modificationDate=1735932227387&api=v2'
+
 pc_ids='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_sid_cid.csv?version=2&modificationDate=1712766341112&api=v2&download=true'
 pc_ids = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_sid_cid.csv?version=4&modificationDate=1727924129121&api=v2&download=true'
 
+#jan 2025
+pc_ids = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_sid_cid.csv?version=5&modificationDate=1735931099618&api=v2'
+
+
+chemnames = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemcal_name.csv?version=1&modificationDate=1710382716000&api=v2&download=true'
 #oct 2024
-chemnames='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemcal_name.csv?version=1&modificationDate=1710382716000&api=v2&download=true'
+chemnames = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemical_name.csv?version=1&modificationDate=1727924127004&api=v2'
+
+#jan 2025
+chemnames = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemical_names.csv?version=1&modificationDate=1735931084378&api=v2'
 
-chemnames='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemical_name.csv?version=1&modificationDate=1727924127004&api=v2'
 #oct 2024
 cas='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_cas.csv?version=1&modificationDate=1710381783000&api=v2&download=true'
 #oct 2024
 cas = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_cas.csv?version=3&modificationDate=1727924126194&api=v2&download=true'
+
+#jan 2025
+cas = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_cas.csv?version=4&modificationDate=1735931080720&api=v2'
+
 conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=11&modificationDate=1712351454136&api=v2'
 ##OCT 2024
 conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=13&modificationDate=1727922354561&api=v2'
-
+#jan 2025
+conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=14&modificationDate=1735932462303&api=v2'
 
 def main():    
     parser = argparse.ArgumentParser()

build/broad_sanger/04b-nci60-updated.py

@@ -14,6 +14,8 @@
 conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=11&modificationDate=1712351454136&api=v2'
 ##OCT 2024
 conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=13&modificationDate=1727922354561&api=v2'
+#jan 2025
+conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=14&modificationDate=1735932462303&api=v2'
 
 cancelled = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP_Cancelled.csv?version=1&modificationDate=1660871847000&api=v2&download=true'
 

build/build_dataset.py

@@ -42,6 +42,7 @@ def process_docker(dataset,validate):
         'beataml': ['beataml'],
         'mpnst': ['mpnst'],
         'mpnstpdx': ['mpnstpdx'],
+        'pancpdo': ['pancpdo'],
         'cptac': ['cptac'],
         'genes': ['genes'],
         'upload': ['upload']
@@ -123,6 +124,7 @@ def process_omics(executor, dataset, should_continue):
         'broad_sanger': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'cptac': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'hcmi': ['mutations', 'transcriptomics'],
+        'pancpdo': ['transcriptomics'],
         'mpnstpdx':['copy_number', 'mutations', 'proteomics', 'transcriptomics']
     }