Merge pull request #293 from Sage-Bionetworks/develop

Prepare 1st release of DCA (general template)

.github/workflows/shinyapps_deploy.yml

@@ -8,17 +8,20 @@ name: shiny-deploy
 on:
   push:
     branches:
-      - shiny-server-main
-      - shiny-server-develop # add develop for testing for now
-      - release*
+      - main
+      - develop
+    tags:
+      - v*.*.*
     paths-ignore:
-      - .github/ISSUE_TEMPLATE/**
+      - '.github/ISSUE_TEMPLATE/**'
+      - '**/*.md'
+      - '**/.gitignore'
 
 jobs:
   shiny-deploy:
     runs-on: ubuntu-latest
     # This image seems to be based on rocker/r-ver which in turn is based on debian
-    container: rocker/rstudio
+    container: rocker/rstudio:4.1.2
     env:
       # This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
       GITHUB_PAT: ${{ secrets.REPO_PAT }}
@@ -44,15 +47,10 @@ jobs:
         run: |
           R -f install-pkgs.R
 
-      - name: Install Python Packages Dependencies
-        shell: bash
-        run: |
-          source .venv/bin/activate
-          pip3 install -r requirements.txt
-
       - name: Install Schematic
         shell: bash
         run: |
+          # has to activate each bash step
           source .venv/bin/activate
           # use 'poetry' to install schematic from the develop branch 
           pip3 install poetry
@@ -67,19 +65,17 @@ jobs:
           source .venv/bin/activate
           # download data model to the correct location
           R -e '
-            config <- yaml::yaml.load_file(".github/schematic_config.yml");
+            config <- yaml::yaml.load_file("schematic_config.yml");
             url  <- config$model$input$download_url;
             path <- config$model$input$location;
             system(sprintf("mkdir -p %s", dirname(path)));
             system(sprintf("wget %s -O %s", url, path));
           '
-          # overwrite the config.yml in schematic
-          mv -f .github/schematic_config.yml schematic/config.yml
           # write out configuration files using github secrets
-          echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > schematic/.synapseConfig
-          echo "${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}" > schematic/schematic_service_account_creds.json
-          echo "${{ secrets.SCHEMATIC_CREDS_PATH }}" > schematic/credentials.json
-          echo "${{ secrets.SCHEMATIC_TOKEN_PICKLE }}" | base64 -d > schematic/token.pickle
+          echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > .synapseConfig
+          echo "${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}" > schematic_service_account_creds.json
+          echo "${{ secrets.SCHEMATIC_CREDS_PATH }}" > credentials.json
+          echo "${{ secrets.SCHEMATIC_TOKEN_PICKLE }}" | base64 -d > token.pickle
 
       - name: zip virtual env
         shell: bash
@@ -92,10 +88,12 @@ jobs:
       - name: Authorize and deploy app
         shell: Rscript {0}
         run: |
-          branch <- Sys.getenv("GITHUB_REF_NAME")
+          # if there is a tag, 'refName' will be tag name
+          refName <- Sys.getenv("GITHUB_REF_NAME")
           repo <- Sys.getenv("GITHUB_REPOSITORY")
           appName <- strsplit(repo, "/")[[1]][2]
-          if (!startsWith(branch, "release")) {
+          # if tag is v*.*.*, deploy to prod, otherwise to staging
+          if (!grepl("v[0-9]+.[0-9]+.[0-9]+", refName)) {
             appName <- paste(appName, "staging", sep = "-")
           }
           rsConnectUser <- "${{ secrets.RSCONNECT_USER }}"

.gitignore

@@ -18,7 +18,8 @@ schematic/
 **/token.pickle
 **/__pycache__
 oauth_config.yml
+schematic_config.yml
 .project
 .settings/**
 .venv
-data-models/
+data-models/

README.md

@@ -12,9 +12,9 @@ Follow the steps below to make sure the _Data Curator App_ is fully setup to wor
 
 ### Data Curator App Setup
 
-1.  Clone this repo (front-end) with one single branch (i.e., _shiny-server-main_):
+1.  Clone this repo (front-end) with one single branch (i.e., _main_):
 
-        git clone --single-branch --branch shiny-server-main https://github.com/Sage-Bionetworks/data_curator.git
+        git clone --single-branch --branch main https://github.com/Sage-Bionetworks/data_curator.git
 
 2.  Create and modify the configuration file ([How to obtain OAuth Credential](https://github.com/Sage-Bionetworks/data_curator#Authentication)):
 
@@ -26,11 +26,7 @@ Follow the steps below to make sure the _Data Curator App_ is fully setup to wor
         python -m venv .venv
         source .venv/bin/activate
 
-4.  Install required Python pacakges dependencies:
-
-        pip install -r requirements.txt
-
-5.  Install required R pacakges dependencies:
+4.  Install required R pacakges dependencies:
 
         R -f install-pkgs.R
 
@@ -50,7 +46,7 @@ Follow the steps below to make sure the _Data Curator App_ is fully setup to wor
         poetry build
         pip install dist/schematicpy-1.0.0-py3-none-any.whl
 
-3.  Set up the `schematic` configuration. To do so, follow the instructions on the [schematic's documentation](https://sage-schematic.readthedocs.io/en/develop/index.html#package-installation-and-setup)
+3.  Modify the `schematic_config.yml` to set up schematic configuration. To do so, follow the instructions on the [schematic's documentation](https://sage-schematic.readthedocs.io/en/develop/index.html#package-installation-and-setup)
 
 ### Data Model Configuration
 
@@ -60,8 +56,9 @@ Use the app configuration file `www/config.json` to adapt this app to your DCC.
   - `display_name` : The display name for the dropdown. (e.g. _scRNA-seq Level 1_)
   - `schema_name`: The name of the manifest in the JSON-LD schema (e.g. _ScRNA-seqLevel1_)
   - `type`: The type of manifest. As currently configured in `app.R`, will only display manifests of type _assay_.
-- `main_fileview` : The Synapse ID of a fileview that is scoped to all files, folders, & projects in your community. (e.g. _syn20446927_)
-- `community` : the abbreviated name of the community or project. (e.g. _HTAN_)
+- `community` (optional): The abbreviated name of the community or project. (e.g. _HTAN_)
+- `schema` (optional): The version of data model 
+- `schematic_service` (optional): The version of schematic service
 
 ---
 
@@ -74,16 +71,21 @@ This utilizes a Synapse Authentication (OAuth) client (code motivated by [ShinyO
 
 ---
 
+## Deployment
+To deploy the app to shinyapps.io, please follow the instructions in the [shinyapps_deploy.md](./shinyapps_deploy.md).
+
 ## Contributors
 
 Main contributors and developers:
 
 - [Rongrong Chai](https://github.com/rrchai)
-- [Xengie Doan](https://github.com/xdoan)
+- [Anthony Williams](https://github.com/afwillia)
 - [Milen Nikolov](https://github.com/milen-sage)
-- [Sujay Patil](https://github.com/sujaypatil96)
+- [Lauren Wolfe](https://github.com/lakikowolfe)
 - [Robert Allaway](https://github.com/allaway)
 - [Bruno Grande](https://github.com/BrunoGrandePhD)
+- [Xengie Doan](https://github.com/xdoan)
+- [Sujay Patil](https://github.com/sujaypatil96)
 
 <!-- Links -->
 

functions/metadata_model.py

@@ -2,12 +2,12 @@
 from schematic import CONFIG
 
 
-config = CONFIG.load_config("schematic/config.yml")
+config = CONFIG.load_config("schematic_config.yml")
 
 inputMModelLocation = CONFIG["model"]["input"]["location"]
 inputMModelLocationType = CONFIG["model"]["input"]["file_type"]
 
 manifest_title = CONFIG["manifest"]["title"]
-manifest_data_type = CONFIG["manifest"]["data_type"]
+manifest_data_type = CONFIG["manifest"]["data_type"][0]
 
 metadata_model = MetadataModel(inputMModelLocation, inputMModelLocationType)

global.R

@@ -26,7 +26,7 @@ system("chmod -R +x .venv")
 # Activate virtual env
 # Don't necessarily have to set `RETICULATE_PYTHON` env variable
 Sys.unsetenv("RETICULATE_PYTHON")
-reticulate::use_virtualenv(file.path(getwd(), ".venv"))
+reticulate::use_virtualenv(file.path(getwd(), ".venv"), required = TRUE)
 
 suppressPackageStartupMessages({
   library(shiny)

schematic_config.yml

@@ -0,0 +1,40 @@
+# Do not change the 'definitions' section unless you know what you're doing
+definitions:
+  synapse_config: ".synapseConfig"
+  creds_path: "credentials.json"
+  token_pickle: "token.pickle"
+  service_acct_creds: "schematic_service_account_creds.json"
+
+synapse:
+  master_fileview: 'syn23643253'
+  manifest_folder: 'manifests'
+  manifest_filename: 'synapse_storage_manifest.csv'
+  token_creds: 'syn23643259'
+  service_acct_creds: 'syn25171627'
+
+manifest:
+  # if making many manifests, just include name prefix
+  title: 'example'
+  # to make all manifests enter only 'all manifests'
+  data_type: 
+    - 'Biospecimen'
+    - 'Patient'
+
+model:
+  input:
+    download_url: 'https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld' # url to download JSON-LD data model
+    location: 'schematic/tests/data/example.model.jsonld' # path to JSON-LD data mode
+    file_type: 'local'
+
+style:
+  google_manifest:
+    req_bg_color:
+      red: 0.9215
+      green: 0.9725
+      blue: 0.9803
+    opt_bg_color:
+      red: 1.0
+      green: 1.0
+      blue: 0.9019
+    master_template_id: '1LYS5qE4nV9jzcYw5sXwCza25slDfRA1CIg3cs-hCdpU'
+    strict_validation: true