Merge branch 'main' of https://github.com/PNNL-CompBio/coderdata into documentation-staging

Pulling changes from main so documentation can be updated all at once.

Author: alexandriai168

.github/workflows/build.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Build and push broad sanger omics
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.broad_sanger_omics
+          file: ./coderbuild/docker/Dockerfile.broad_sanger_omics
           tags: |
             sgosline/broad-sanger-omics:latest
             sgosline/broad-sanger-omics:${{ github.ref_name }}
@@ -49,7 +49,7 @@ jobs:
       - name: Build and push broad sanger experiment
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.broad_sanger_exp
+          file: ./coderbuild/docker/Dockerfile.broad_sanger_exp
           tags: |
             sgosline/broad-sanger-exp:latest
             sgosline/broad-sanger-exp:${{ github.ref_name }}
@@ -74,7 +74,7 @@ jobs:
       - name: Build and push genes
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.genes
+          file: ./coderbuild/docker/Dockerfile.genes
           tags: |
             sgosline/genes:latest
             sgosline/genes:${{ github.ref_name }}
@@ -98,14 +98,38 @@ jobs:
       - name: Build and push hcmi
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.hcmi
+          file: ./coderbuild/docker/Dockerfile.hcmi
           tags: |
             sgosline/hcmi:latest
             sgosline/hcmi:${{ github.ref_name }}
           push: true
           platforms: linux/amd64
 
-  build-cptac:
+  # build-cptac:
+  #   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: ${{ secrets.DOCKERHUB_PASSWORD }}
+  #     - name: Build and push cptac
+  #       uses: docker/build-push-action@v3
+  #       with:
+  #         file: ./coderbuild/docker/Dockerfile.cptac
+  #         tags: |
+  #           sgosline/cptac:latest
+  #           sgosline/cptac:${{ github.ref_name }}
+  #         push: true
+  #         platforms: linux/amd64
+
+  build-mpnst:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -119,17 +143,17 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push cptac
+      - name: Build and push mpnst
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.cptac
+          file: ./coderbuild/docker/Dockerfile.mpnst
           tags: |
-            sgosline/cptac:latest
-            sgosline/cptac:${{ github.ref_name }}
+            sgosline/mpnst:latest
+            sgosline/mpnst:${{ github.ref_name }}
           push: true
           platforms: linux/amd64
 
-  build-mpnst:
+  build-beataml:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -143,17 +167,17 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push mpnst
+      - name: Build and push beataml
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.mpnst
+          file: ./coderbuild/docker/Dockerfile.beataml
           tags: |
-            sgosline/mpnst:latest
-            sgosline/mpnst:${{ github.ref_name }}
+            sgosline/beataml:latest
+            sgosline/beataml:${{ github.ref_name }}
           push: true
           platforms: linux/amd64
 
-  build-beataml:
+  build-pancreatic:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -167,17 +191,17 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push beataml
+      - name: Build and push pancreatic
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.beataml
+          file: ./coderbuild/docker/Dockerfile.pancreatic
           tags: |
-            sgosline/beataml:latest
-            sgosline/beataml:${{ github.ref_name }}
+            sgosline/pancreatic:latest
+            sgosline/pancreatic:${{ github.ref_name }}
           push: true
           platforms: linux/amd64
 
-  build-pancpdo:
+  build-upload:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -191,17 +215,17 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push pancpdo
+      - name: Build and push upload
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.pancpdo
+          file: ./coderbuild/docker/Dockerfile.upload
           tags: |
-            sgosline/pancpdo:latest
-            sgosline/pancpdo:${{ github.ref_name }}
+            sgosline/upload:latest
+            sgosline/upload:${{ github.ref_name }}
           push: true
           platforms: linux/amd64
 
-  build-upload:
+  build-sarcoma:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -215,12 +239,108 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push upload
+      - name: Build and push sarcoma
         uses: docker/build-push-action@v3
         with:
-          file: ./build/docker/Dockerfile.upload
+          file: ./coderbuild/docker/Dockerfile.sarcoma
           tags: |
-            sgosline/upload:latest
-            sgosline/upload:${{ github.ref_name }}
+            sgosline/sarcoma:latest
+            sgosline/sarcoma:${{ github.ref_name }}
+          push: true
+          platforms: linux/amd64
+
+  build-liver:
+    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: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push liver
+        uses: docker/build-push-action@v3
+        with:
+          file: ./coderbuild/docker/Dockerfile.liver
+          tags: |
+            sgosline/liver:latest
+            sgosline/liver:${{ github.ref_name }}
+          push: true
+          platforms: linux/amd64
+
+  build-bladder:
+    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: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push bladder
+        uses: docker/build-push-action@v3
+        with:
+          file: ./coderbuild/docker/Dockerfile.bladder
+          tags: |
+            sgosline/bladder:latest
+            sgosline/bladder:${{ github.ref_name }}
+          push: true
+          platforms: linux/amd64
+
+  build-colorectal:
+    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: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push colorectal
+        uses: docker/build-push-action@v3
+        with:
+          file: ./coderbuild/docker/Dockerfile.colorectal
+          tags: |
+            sgosline/colorectal:latest
+            sgosline/colorectal:${{ github.ref_name }}
           push: true
           platforms: linux/amd64
+
+  build-novartis:
+    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: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push novartis
+        uses: docker/build-push-action@v3
+        with:
+          file: ./coderbuild/docker/Dockerfile.novartis
+          tags: |
+            sgosline/novartis:latest
+            sgosline/novartis:${{ github.ref_name }}
+          push: true
+          platforms: linux/amd64

.github/workflows/main.yml

@@ -36,22 +36,22 @@ please see the [schema description](schema/README.md).
 
 ## Building a local version
 
-The build process can be found in our [build
-directory](build/README.md). Here you can follow the instructions to
+The build process can be found in our [coderbuild
+directory](coderbuild/README.md). Here you can follow the instructions to
 build your own local copy of the data on your machine. 
 
 ## Adding a new dataset
 
-We have standardized the build process so an additional dataset can be
+We have standardized the build (coderbuild) process so an additional dataset can be
 built locally or as part of the next version of coder. Here are the
 steps to follow:
 
-1. First visit the [build
-directory](build/README.md) and ensure you can build a local copy of
+1. First visit the [coderbuild
+directory](coderbuild/README.md) and ensure you can build a local copy of
 CoderData. 
 
 2. Checkout this repository and  create a subdirectory of the
-[build directory](build) with your own build files. 
+[coderbuild directory](coderbuild) with your own build files. 
 
 3. Develop your scripts to build the data files according to our
 [LinkML Schema](schema/coderdata.yaml]). This will require collecting
@@ -66,10 +66,10 @@ validator](https://linkml.io/linkml/data/validating-data) together
 with our schema file. 
 
 You can use the following scripts as part of your build process:
-- [build/utils/fit_curve.py](build/utils/fit_curve.py): This script
+- [coderbuild/utils/fit_curve.py](coderbuild/utils/fit_curve.py): This script
   takes dose-response data and generates the dose-response statistics
   required by CoderData/
-- [build/utils/pubchem_retrieval.py](build/utils/pubchem_retreival.py):
+- [coderbuild/utils/pubchem_retrieval.py](coderbuild/utils/pubchem_retreival.py):
   This script retreives structure and drug synonym information
   required to populate the `Drug` table. 
 
@@ -78,13 +78,13 @@ and arguments:
 
 | shell script     | arguments                | description         |
 |------------------|--------------------------|---------------------|
-| `build_samples.sh` | [latest_samples] | Latest version of samples generated by coderdata build |
+| `build_samples.sh` | [latest_samples] | Latest version of samples generated by coderbuild |
 | `build_omics.sh` | [gene file] [samplefile] | This includes the `genes.csv` that was generated in the original build as well as the sample file generated above. |
 | `build_drugs.sh` | [drugfile1,drugfile2,...]       | This includes a comma-delimited list of all drugs files generated from previous build  |
 | `build_exp.sh`| [samplfile ] [drugfile] | sample file and drug file generated by previous scripts |
 
 5. Put the Docker container file inside the [Docker
-directory](./build/docker) with the name
+directory](./coderbuild/docker) with the name
 `Dockerfile.[datasetname]`. 
 
 6. Run `build_all.py` from the root directory, which should now add in