diff --git a/.github/workflows/generate_dump.yml b/.github/workflows/generate_dump.yml index 11782fa5d..ac8274c51 100644 --- a/.github/workflows/generate_dump.yml +++ b/.github/workflows/generate_dump.yml @@ -44,7 +44,6 @@ jobs: with: repository: ror-community/curation_ops token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} - ref: v2-crosswalk path: ./curation_ops - name: Set up Python environment uses: actions/setup-python@v2 diff --git a/.github/workflows/staging_manual_index.yml b/.github/workflows/staging_manual_index.yml index c6b422fb2..b2ef5e3c0 100644 --- a/.github/workflows/staging_manual_index.yml +++ b/.github/workflows/staging_manual_index.yml @@ -56,7 +56,6 @@ jobs: uses: actions/checkout@v2 with: repository: ror-community/validation-suite - ref: schema-v2 path: validation-suite - name: Validate files id: validatefiles diff --git a/.github/workflows/staging_pull_request.yml b/.github/workflows/staging_pull_request.yml index 116e1743f..c41958a11 100644 --- a/.github/workflows/staging_pull_request.yml +++ b/.github/workflows/staging_pull_request.yml @@ -49,7 +49,6 @@ jobs: uses: actions/checkout@v2 with: repository: ror-community/validation-suite - ref: schema-v2 path: validation-suite - name: Validate files id: validatefiles diff --git a/.github/workflows/v2_temp/dev_index_dump.yml b/.github/workflows/v2_temp/dev_index_dump.yml new file mode 100644 index 000000000..32966abaf --- /dev/null +++ b/.github/workflows/v2_temp/dev_index_dump.yml @@ -0,0 +1,77 @@ +name: DEV index full data dump +on: + workflow_dispatch: + inputs: + release-dump: + type: string + description: Name of existing release dump file to index, without .zip extension (ex v1.41-2024-02-13-ror-data) + schema-version: + required: true + description: Schema version to index + type: choice + options: + - v1 + - v2 + data-env: + required: true + description: ROR data env (test uses ror-data-test repo, prod uses ror-data) + default: 'test' + type: choice + options: + - test + - prod + + +env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }} + +jobs: + check_permission: + runs-on: ubuntu-latest + if: github.event.ref == 'refs/heads/dev' + steps: + - name: Get Permission + uses: octokit/request-action@v2.x + id: get_permission + with: + route: GET /repos/${{ github.repository }}/collaborators/${{ github.actor }}/permission + env: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + - name: output + run: | + export role_name=${{ fromJson(steps.get_permission.outputs.data).role_name }} + if [[ "$role_name" == "admin" ]]; then + exit 0 + else + exit 1 + fi + index-dump: + runs-on: ubuntu-latest + if: github.event.ref == 'refs/heads/dev' + needs: check_permission + steps: + - name: checkout + uses: actions/checkout@v2 + - name: Index dump file + id: indexdatadump + run: | + cd .github/workflows + python -m pip install --upgrade pip + pip install requests==2.23.0 + if [[ ${{ github.event.inputs.schema-version }} == "v1" ]]; then + python index_dump.py -u ${{ secrets.INDEX_DUMP_DEV_API_URL }} -f ${{ github.event.inputs.release-dump }} -e ${{ github.event.inputs.data-env }} -he ${{ secrets.INDEX_DEV_API_HEADERS }} + else + python index_dump.py -u ${{ secrets.INDEX_DUMP_DEV_API_URL_V2 }} -f ${{ github.event.inputs.release-dump }} -e ${{ github.event.inputs.data-env }} -he ${{ secrets.INDEX_DEV_API_HEADERS }} + fi + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV full index from dump status: ${{ steps.indexdatadump.outcome }}. From file: ${{ github.event.inputs.release-dump }}. Schema version: ${{ github.event.inputs.schema-version }}. Data env: ${{ github.event.inputs.data-env }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + diff --git a/.github/workflows/v2_temp/dev_manual_index.yml b/.github/workflows/v2_temp/dev_manual_index.yml new file mode 100644 index 000000000..b832d1103 --- /dev/null +++ b/.github/workflows/v2_temp/dev_manual_index.yml @@ -0,0 +1,144 @@ +name: DEV manual deploy from dev branch +on: + workflow_dispatch: + inputs: + schema-version: + required: true + description: Schema version + type: choice + options: + - v1 + - v2 + directory-name: + type: string + required: true + description: Name of the directory you would like to deploy to DEV + +env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }} + +jobs: + check_permission: + runs-on: ubuntu-latest + #if: github.event.ref == 'refs/heads/dev' + steps: + - name: Get Permission + uses: octokit/request-action@v2.x + id: get_permission + with: + route: GET /repos/${{ github.repository }}/collaborators/${{ github.actor }}/permission + env: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + - name: output + run: | + export role_name=${{ fromJson(steps.get_permission.outputs.data).role_name }} + if [[ "$role_name" == "maintain" || "$role_name" == "admin" ]]; then + exit 0 + else + exit 1 + fi + check_validation: + runs-on: ubuntu-latest + #if: github.event.ref == 'refs/heads/dev' + needs: check_permission + steps: + - name: checkout + uses: actions/checkout@v2 + with: + ref: ${{ github.event.ref }} + - name: Set up Python environment + uses: actions/setup-python@v2 + with: + python-version: "3.8" + - name: Checkout validation suite + uses: actions/checkout@v2 + with: + repository: ror-community/validation-suite + ref: schema-v2 + path: validation-suite + - name: Validate files + id: validatefiles + run: | + mkdir files + cp ./${{ github.event.inputs.directory-name }}/*.json files/ + cd validation-suite + python -m pip install --upgrade pip + pip install -r requirements.txt + if [[ ${{ github.event.inputs.schema-version }} == 'v1' ]]; then + curl https://raw.githubusercontent.com/ror-community/ror-schema/master/ror_schema.json -o ror_schema.json + if [[ -f "../${{github.event.pull_request.head.ref}}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 1 -s ror_schema.json -f ../${{github.event.pull_request.head.ref}}/relationships.csv -p ../files/ --no-geonames + else + python run_validations.py -i ../files -v 1 -s ror_schema.json --no-geonames + fi + fi + if [[ ${{ github.event.inputs.schema-version }} == 'v2' ]]; then + curl https://raw.githubusercontent.com/ror-community/ror-schema/master/ror_schema_v2_0.json -o ror_schema_v2_0.json + if [[ -f "../${{github.event.pull_request.head.ref}}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json -f ../${{github.event.pull_request.head.ref}}/relationships.csv -p ../files/ --no-geonames + else + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json --no-geonames + fi + fi + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'Validation status during DEV manual index: ${{ steps.validatefiles.outcome }}. In directory: ${{ github.event.inputs.directory-name }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + copy-files: + runs-on: ubuntu-latest + #if: github.event.ref == 'refs/heads/dev' + needs: check_validation + steps: + - name: checkout + uses: actions/checkout@v2 + with: + ref: ${{ github.event.ref }} + - name: Install aws cli + id: install-aws-cli + uses: unfor19/install-aws-cli-action@v1.0.2 + - name: Zip and copy files + id: copyfiles + run: | + cd ./${{ github.event.inputs.directory-name }} + zip files.zip *.json + aws s3 cp files.zip s3://${{ secrets.ROR_DATA_S3_BUCKET_DEV }}/${{ github.event.inputs.directory-name }}-${{ github.event.inputs.schema-version }}/files.zip + aws s3 ls s3://${{ secrets.ROR_DATA_S3_BUCKET_DEV }}/${{ github.event.inputs.directory-name }}-${{ github.event.inputs.schema-version }}/files.zip + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'Copy status to DEV S3 Bucket: ${{ steps.copyfiles.outcome }}. From directory: ${{ github.event.inputs.directory-name }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + - name: Index file + id: indexdata + run: | + cd .github/workflows + python -m pip install --upgrade pip + pip install requests==2.23.0 + if [[ ${{ github.event.inputs.schema-version }} == 'v1' ]]; then + python index_files.py -u ${{ secrets.INDEX_DEV_API_URL_V1 }} -d ${{ github.event.inputs.directory-name }}-v1 -he ${{ secrets.INDEX_DEV_API_HEADERS }} + fi + if [[ ${{ github.event.inputs.schema-version }} == 'v2' ]]; then + python index_files.py -u ${{ secrets.INDEX_DEV_API_URL_V2 }} -d ${{ github.event.inputs.directory-name }}-v2 -he ${{ secrets.INDEX_DEV_API_HEADERS }} + fi + + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV index status: ${{ steps.indexdata.outcome }}. Using version ${{ github.event.inputs.schema-version }}. From directory: ${{ github.event.inputs.directory-name }}-${{ github.event.inputs.schema-version }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + diff --git a/.github/workflows/v2_temp/dev_merge.yml b/.github/workflows/v2_temp/dev_merge.yml new file mode 100644 index 000000000..6de121683 --- /dev/null +++ b/.github/workflows/v2_temp/dev_merge.yml @@ -0,0 +1,69 @@ +name: Deploy to DEV on PR merge to dev branch +on: + push: + branches: + - 'dev' + paths-ignore: + - '**/README.md' + - '**/workflows/**' +env: + MERGE_SHA: ${{ github.event.after }} + REPO_INFO: ${{ github.event.repository.full_name }} + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }} + +jobs: + copy-files: + runs-on: ubuntu-latest + steps: + - name: Get Merge PR + uses: octokit/request-action@v2.x + id: get_merge_pr + with: + route: GET /search/issues + q: 'repo:${{ github.event.repository.full_name }}+is:pr+is:closed+merge_sha_commit:${{ github.event.after }}' + env: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + - name: Get branch name + run: | + export url=${{ fromJson(steps.get_merge_pr.outputs.data).items[0].pull_request.url }} + echo "release_branch=$(curl ${url} | jq -r .head.ref)" >> $GITHUB_ENV + - name: checkout + uses: actions/checkout@v2 + - name: Install aws cli + id: install-aws-cli + uses: unfor19/install-aws-cli-action@v1.0.2 + - name: Zip and copy files + id: copyfiles + run: | + cd ./${{ env.release_branch }} + zip files.zip *.json + aws s3 cp files.zip s3://${{ secrets.ROR_DATA_S3_BUCKET_DEV}}/${{ env.release_branch }}-v2/files.zip + aws s3 ls s3://${{ secrets.ROR_DATA_S3_BUCKET_DEV }}/${{ env.release_branch }}-v2/files.zip + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'Copy status to DEV S3 Bucket: ${{ steps.copyfiles.outcome }}. Using v2. On branch: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/tree/${env.GITHUB_REF_NAME}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + - name: Index file + id: indexdata + run: | + cd .github/workflows + python -m pip install --upgrade pip + pip install requests==2.23.0 + python index_files.py -u ${{ secrets.INDEX_DEV_API_URL_V2 }} -d ${{ env.release_branch }}-v2 -he ${{ secrets.INDEX_DEV_API_HEADERS }} + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV index status: ${{ steps.indexdata.outcome }}. Using v2. On branch: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/tree/${env.GITHUB_REF_NAME}. Directory: ${{ env.release_branch }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + diff --git a/.github/workflows/v2_temp/dev_pull_request.yml b/.github/workflows/v2_temp/dev_pull_request.yml new file mode 100644 index 000000000..850f3e508 --- /dev/null +++ b/.github/workflows/v2_temp/dev_pull_request.yml @@ -0,0 +1,77 @@ +name: PR to DEV +on: + pull_request: + types: [opened, reopened, synchronize] + branches: + - '!main' + - '!v**' + - 'dev' + paths-ignore: + - '**/README.md' + - '.github/*' + +env: + USER_INFO: ${{ github.event.pull_request.user.login }} + REPO_INFO: ${{ github.event.pull_request.base.repo.full_name }} + +jobs: + check_permission: + runs-on: ubuntu-latest + steps: + - name: Get Permission + uses: octokit/request-action@v2.x + id: get_permission + with: + route: GET /repos/${{ env.REPO_INFO }}/collaborators/${{ env.USER_INFO }}/permission + env: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + - name: output + run: | + export role_name=${{ fromJson(steps.get_permission.outputs.data).role_name }} + if [[ "$role_name" == "maintain" || "$role_name" == "admin" ]]; then + exit 0 + else + exit 1 + fi + check_validation: + runs-on: ubuntu-latest + needs: check_permission + steps: + - name: checkout + uses: actions/checkout@v2 + with: + ref: ${{ github.event.pull_request.head.sha }} + - name: Set up Python environment + uses: actions/setup-python@v2 + with: + python-version: "3.8" + - name: Checkout validation suite + uses: actions/checkout@v2 + with: + repository: ror-community/validation-suite + ref: schema-v2 + path: validation-suite + - name: Validate files + id: validatefiles + run: | + mkdir files + cp ./${{github.event.pull_request.head.ref}}/*.json files/ + cd validation-suite + python -m pip install --upgrade pip + pip install -r requirements.txt + curl https://raw.githubusercontent.com/ror-community/ror-schema/master/ror_schema_v2_0.json -o ror_schema_v2_0.json + if [[ -f "../${{github.event.pull_request.head.ref}}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json -f ../${{github.event.pull_request.head.ref}}/relationships.csv -p ../files/ --no-geonames + else + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json --no-geonames + fi + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'Validation status during PR to DEV: ${{ steps.validatefiles.outcome }}. Using v2. On branch: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/tree/${env.GITHUB_HEAD_REF}. In directory: ${env.GITHUB_HEAD_REF}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + diff --git a/.github/workflows/v2_temp/generate_dump.yml b/.github/workflows/v2_temp/generate_dump.yml new file mode 100644 index 000000000..9f9daee56 --- /dev/null +++ b/.github/workflows/v2_temp/generate_dump.yml @@ -0,0 +1,99 @@ +name: Create data dump +on: + workflow_dispatch: + inputs: + schema-version: + required: true + description: Release schema version + type: choice + options: + - v1 + - v2 + new-release: + type: string + description: Name of the directory that the new release is located in + prev-release: + type: string + description: Name of the existing release zip file to base this data dump from + +jobs: + generate-dump: + runs-on: ubuntu-latest + steps: + - name: Echo message + id: echo_message + run: echo "Github action triggered with inputs new release ${{github.event.inputs.new-release}} and previous release ${{github.event.inputs.prev-release}}" + - name: checkout ror records repo + uses: actions/checkout@v2 + with: + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + path: ./ror-records-test + - name: checkout ror data repo + uses: actions/checkout@v2 + with: + repository: ror-community/ror-data-test + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + path: ./ror-data-test + - name: copy previous data dump file + id: copyprevdump + run: | + cp -R ./ror-data-test/${{github.event.inputs.prev-release}}.zip ./ror-records-test + - name: checkout ror curation ops repo + uses: actions/checkout@v2 + with: + repository: ror-community/curation_ops + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + ref: v2-crosswalk + path: ./curation_ops + - name: Set up Python environment + uses: actions/setup-python@v2 + with: + python-version: "3.8" + - name: execute script + id: gendumpscript + run: | + cd ./curation_ops/generate_dump/ + if [[ ${{ github.event.inputs.schema-version }} == 'v1' ]]; then + python generate_dump.py -r ${{github.event.inputs.new-release}} -e ${{github.event.inputs.prev-release}} -i '../../ror-records-test' -o '../../ror-records-test' -v 1 + fi + if [[ ${{ github.event.inputs.schema-version }} == 'v2' ]]; then + python generate_dump.py -r ${{github.event.inputs.new-release}} -e ${{github.event.inputs.prev-release}} -i '../../ror-records-test' -o '../../ror-records-test' -v 2 + fi + - name: cat error file + if: ${{ steps.gendumpscript.outcome != 'success'}} + run: | + echo "ERRORS found:" + cat errors.log + - name: copy new data dump file + id: copynewdump + run: | + yes | cp -rf ./ror-records-test/${{github.event.inputs.new-release}}*.zip ./ror-data-test + - name: commit dump file + id: commitdumpfile + if: ${{ steps.copynewdump.outcome == 'success'}} + run: | + cd ./ror-data-test + git config --local user.email "ror-bot@ror.org" + git config --local user.name "ror-bot" + git add *.zip + git commit -m "add new data dump file" + git push origin main + - name: commit changed files + if: ${{ steps.commitdumpfile.outcome == 'success'}} + run: | + pwd + cd ./ror-records-test + git config --local user.email "ror-bot@ror.org" + git config --local user.name "ror-bot" + git add ${{github.event.inputs.new-release}}/v1/ + git commit -m "add generated v1 files" + git push origin main + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV Data dump ${{github.event.inputs.new-release}} generation status: ${{ steps.commitdumpfile.outcome }}. Using base version ${{ github.event.inputs.schema-version }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' diff --git a/.github/workflows/v2_temp/generate_dump_v2_initial_release.yml b/.github/workflows/v2_temp/generate_dump_v2_initial_release.yml new file mode 100644 index 000000000..d7d85a798 --- /dev/null +++ b/.github/workflows/v2_temp/generate_dump_v2_initial_release.yml @@ -0,0 +1,106 @@ +name: Create data dump v2 first release +description: Generates a data dump based on an input file from ror-data-test and uploades the result to ror-data. For use during the first v1 release only. +on: + workflow_dispatch: + inputs: + schema-version: + required: true + description: Release schema version + type: choice + options: + - v1 + - v2 + new-release: + type: string + description: Name of the directory that the new release is located in + prev-release: + type: string + description: Name of the existing release zip file to base this data dump from + +jobs: + generate-dump: + runs-on: ubuntu-latest + steps: + - name: Echo message + id: echo_message + run: echo "Github action triggered with inputs new release ${{github.event.inputs.new-release}} and previous release ${{github.event.inputs.prev-release}}" + - name: checkout ror records repo + uses: actions/checkout@v2 + with: + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + path: ./ror-records-test + - name: checkout ror data test repo + uses: actions/checkout@v2 + with: + repository: ror-community/ror-data-test + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + path: ./ror-data-test + - name: checkout ror data prod repo + uses: actions/checkout@v2 + with: + repository: ror-community/ror-data + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + path: ./ror-data-prod + - name: copy previous data dump file + id: copyprevdump + run: | + cp -R ./ror-data-test/${{github.event.inputs.prev-release}}.zip ./ror-records-test + - name: checkout ror curation ops repo + uses: actions/checkout@v2 + with: + repository: ror-community/curation_ops + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + ref: v2-crosswalk + path: ./curation_ops + - name: Set up Python environment + uses: actions/setup-python@v2 + with: + python-version: "3.8" + - name: execute script + id: gendumpscript + run: | + cd ./curation_ops/generate_dump/ + if [[ ${{ github.event.inputs.schema-version }} == 'v1' ]]; then + python generate_dump.py -r ${{github.event.inputs.new-release}} -e ${{github.event.inputs.prev-release}} -i '../../ror-records-test' -o '../../ror-records-prod' -v 1 + fi + if [[ ${{ github.event.inputs.schema-version }} == 'v2' ]]; then + python generate_dump.py -r ${{github.event.inputs.new-release}} -e ${{github.event.inputs.prev-release}} -i '../../ror-records-test' -o '../../ror-records-prod' -v 2 + fi + - name: cat error file + if: ${{ steps.gendumpscript.outcome != 'success'}} + run: | + echo "ERRORS found:" + cat errors.log + - name: copy new data dump file + id: copynewdump + run: | + yes | cp -rf ./ror-records-prod/${{github.event.inputs.new-release}}*.zip ./ror-data-prod + - name: commit dump file + id: commitdumpfile + if: ${{ steps.copynewdump.outcome == 'success'}} + run: | + cd ./ror-data-prod + git config --local user.email "ror-bot@ror.org" + git config --local user.name "ror-bot" + git add *.zip + git commit -m "add new data dump file" + git push origin main + - name: commit changed files + if: ${{ steps.commitdumpfile.outcome == 'success'}} + run: | + pwd + cd ./ror-records-test + git config --local user.email "ror-bot@ror.org" + git config --local user.name "ror-bot" + git add ${{github.event.inputs.new-release}}/v1/ + git commit -m "add generated v1 files" + git push origin main + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV Data dump ${{github.event.inputs.new-release}} generation status: ${{ steps.commitdumpfile.outcome }}. Using base version ${{ github.event.inputs.schema-version }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' diff --git a/.github/workflows/v2_temp/index_dump.py b/.github/workflows/v2_temp/index_dump.py new file mode 100644 index 000000000..d52967649 --- /dev/null +++ b/.github/workflows/v2_temp/index_dump.py @@ -0,0 +1,43 @@ +import argparse +import os +import requests +import json +import sys + +def set_args(): + parser = argparse.ArgumentParser( + description="Send request to index data dump") + parser.add_argument('-u', '--url', help='URL to index dump file', required=True) + parser.add_argument('-f', '--file', help='name of dump file to be indexed', required=True) + parser.add_argument('-e', '--dataenv', help='data env to retrieve dump file from', required=True) + parser.add_argument('-he', '--headers', help='key:value json string; headers to authenticate request', required=True, type=json.loads) + args = parser.parse_args() + return args + +def send_request(url, headers): + try: + response = requests.get(url,headers=headers) + except requests.exceptions.RequestException as e: + raise e + return response + +def main(): + args = set_args() + url = args.url + filename = args.file + dataenv = args.dataenv + headers = args.headers + full_url = os.path.join(url, filename, dataenv) + print(full_url) + response = send_request(full_url, headers) + if not(response.ok): + print(response.text) + sys.exit(1) + elif response.ok: + print(response.text) + sys.exit(0) + + +if __name__ == "__main__": + main() + diff --git a/.github/workflows/v2_temp/index_files.py b/.github/workflows/v2_temp/index_files.py new file mode 100644 index 000000000..b7281f46f --- /dev/null +++ b/.github/workflows/v2_temp/index_files.py @@ -0,0 +1,39 @@ +import argparse +import os +import requests +import json +import sys + +def set_args(): + parser = argparse.ArgumentParser( + description="Send request to index files") + parser.add_argument('-u', '--url', help='URL to index files', required=True) + parser.add_argument('-d', '--dir', help='directory in S3 bucket that is to be indexed', required=True) + parser.add_argument('-he', '--headers', help='key:value json string; headers to authenticate request', required=True, type=json.loads) + args = parser.parse_args() + return args + +def send_request(url, headers): + try: + response = requests.get(url,headers=headers) + except requests.exceptions.RequestException as e: + raise e + return response + +def main(): + args = set_args() + url = args.url + dir = args.dir + headers = args.headers + full_url = os.path.join(url, dir) + response = send_request(full_url, headers) + if not(response.ok): + print(response.text) + sys.exit(1) + elif response.ok: + sys.exit(0) + + +if __name__ == "__main__": + main() + diff --git a/.github/workflows/v2_temp/main_pull_request.yml b/.github/workflows/v2_temp/main_pull_request.yml new file mode 100644 index 000000000..ec1e20e82 --- /dev/null +++ b/.github/workflows/v2_temp/main_pull_request.yml @@ -0,0 +1,33 @@ +name: PR to Main +on: + pull_request: + types: [opened, reopened, synchronize] + branches: + - '!v**' + - 'main' + - '!staging' + +env: + USER_INFO: ${{ github.event.pull_request.user.login }} + REPO_INFO: ${{ github.event.pull_request.base.repo.full_name }} + +jobs: + check_permission: + runs-on: ubuntu-latest + steps: + - name: Get Permission + uses: octokit/request-action@v2.x + id: get_permission + with: + route: GET /repos/${{ env.REPO_INFO }}/collaborators/${{ env.USER_INFO }}/permission + env: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + - name: output + run: | + export role_name=${{ fromJson(steps.get_permission.outputs.data).role_name }} + if [[ "$role_name" == "maintain" || "$role_name" == "admin" ]]; then + exit 0 + else + exit 1 + fi + diff --git a/.github/workflows/v2_temp/main_release.yml b/.github/workflows/v2_temp/main_release.yml new file mode 100644 index 000000000..386c4d6a2 --- /dev/null +++ b/.github/workflows/v2_temp/main_release.yml @@ -0,0 +1,79 @@ +name: Deploy to Prod +on: + release: + types: [published] + +env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }} + TAG: ${{ github.event.release.tag_name }} + +jobs: + echo_info: + runs-on: ubuntu-latest + steps: + - name: Echo info + id: echo_message + run: echo "Github action Deploy to Prod was triggered with release tag ${{ github.event.release.tag_name }}" + check_permission: + runs-on: ubuntu-latest + steps: + - name: Get Permission + uses: octokit/request-action@v2.x + id: get_permission + with: + route: GET /repos/${{ github.repository }}/collaborators/${{ github.actor }}/permission + env: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + - name: output + run: | + export role_name=${{ fromJson(steps.get_permission.outputs.data).role_name }} + if [[ "$role_name" == "maintain" || "$role_name" == "admin" ]]; then + exit 0 + else + exit 1 + fi + copy_files: + runs-on: ubuntu-latest + needs: check_permission + steps: + - name: checkout + uses: actions/checkout@v2 + with: + ref: ${{ github.event.ref }} + - name: Install aws cli + id: install-aws-cli + uses: unfor19/install-aws-cli-action@v1.0.2 + - name: Zip and copy files + id: copyfiles + run: | + cd ./${{ github.event.release.tag_name }} + zip files.zip *.json + aws s3 cp files.zip s3://${{ secrets.ROR_DATA_S3_BUCKET_DEV }}/${{ github.event.release.tag_name }}-v2/files.zip + aws s3 ls s3://${{ secrets.ROR_DATA_S3_BUCKET_DEV }}/${{ github.event.release.tag_name }}-v2/files.zip + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'Copy status to DEV S3 Bucket: ${{ steps.copyfiles.outcome }}. From directory: ${{ github.event.release.tag_name }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' + - name: Index data + id: indexdata + run: | + cd .github/workflows + python -m pip install --upgrade pip + pip install requests==2.23.0 + python index_files.py -u ${{ secrets.INDEX_DEV_API_URL_V2 }} -d ${{ github.event.release.tag_name }}-v2 -he ${{ secrets.INDEX_DEV_API_HEADERS }} + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV index status: ${{ steps.indexdata.outcome }}. Using v2. From directory: ${{ github.event.release.tag_name }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' diff --git a/.github/workflows/v2_temp/publish_dump_zenodo.yml b/.github/workflows/v2_temp/publish_dump_zenodo.yml new file mode 100644 index 000000000..29b5fbae0 --- /dev/null +++ b/.github/workflows/v2_temp/publish_dump_zenodo.yml @@ -0,0 +1,62 @@ +name: Publish data dump to Zenodo +on: + workflow_dispatch: + inputs: + release: + required: true + type: string + description: Release version (ex v1.17) + zenodo-env: + required: true + description: Zenodo environment + default: 'sandbox' + type: choice + options: + - sandbox + - prod + record-id: + required: true + type: string + description: Parent Zenodo record ID (if different from default) + default: '1098376' +env: + ZENODO_TOKEN_SANDBOX: ${{ secrets.ZENODO_TOKEN_SANDBOX }} + ZENODO_TOKEN_PROD: ${{ secrets.ZENODO_TOKEN_PROD }} + PERSONAL_ACCESS_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + PERSONAL_ACCESS_TOKEN_USER: ${{ secrets.PERSONAL_ACCESS_TOKEN_USER }} + +jobs: + publish-dump: + runs-on: ubuntu-latest + steps: + - name: Echo message + id: echo_message + run: echo "Github action triggered with inputs release ${{github.event.inputs.release}}, Zenodo env ${{github.event.inputs.zenodo-env}}, parent record ID ${{github.event.inputs.record-id}}" + - name: checkout ror data repo + uses: actions/checkout@v2 + with: + repository: ror-community/ror-data + token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + path: ./ror-data-test + - name: Set up Python environment + uses: actions/setup-python@v2 + with: + python-version: "3.8" + - name: execute script + id: publishdumpscript + run: | + cd ./ror-data + python -m pip install --upgrade pip + curl https://raw.githubusercontent.com/ror-community/curation_ops/main/upload_dump_zenodo/requirements.txt -o requirements.txt + pip install -r requirements.txt + curl https://raw.githubusercontent.com/ror-community/curation_ops/main/upload_dump_zenodo/upload_dump_zenodo.py -o upload_dump_zenodo.py + python upload_dump_zenodo.py -r ${{github.event.inputs.release}} -p ${{github.event.inputs.record-id}} -e ${{github.event.inputs.zenodo-env}} + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'DEV Data dump ${{github.event.inputs.release}} Zenodo publication status: ${{ steps.publishdumpscript.outcome }} Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' diff --git a/.github/workflows/v2_temp/validate.yml b/.github/workflows/v2_temp/validate.yml new file mode 100644 index 000000000..a89a80c23 --- /dev/null +++ b/.github/workflows/v2_temp/validate.yml @@ -0,0 +1,116 @@ +name: Validate files +on: + workflow_dispatch: + inputs: + schema-version: + required: true + description: Schema version + type: choice + options: + - v1 + - v2 + with-relationship: + type: boolean + description: Check box to validate with relationships + skip-geonames: + type: boolean + description: Check box to skip Geonames validation + directory-name: + type: string + description: Name of parent directory containing records to validate. Needed only if different from branch name. + +jobs: + validate-files: + runs-on: ubuntu-latest + if: github.event.ref != 'refs/heads/main' + steps: + - name: checkout + uses: actions/checkout@v2 + with: + ref: ${{ github.event.ref }} + - name: Set up Python environment + uses: actions/setup-python@v2 + with: + python-version: "3.8" + - name: Checkout validation suite + uses: actions/checkout@v2 + with: + repository: ror-community/validation-suite + ref: schema-v2 + path: validation-suite + - name: Get directory name + if: "${{ github.event.inputs.directory-name != '' }}" + run: echo "WORKING_DIR=${{ github.event.inputs.directory-name }}" >> $GITHUB_ENV + - name: Get branch name + if: "${{ github.event.inputs.directory-name == '' }}" + run: echo "WORKING_DIR=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV + - name: Validate files + id: validatefiles + run: | + echo ${{ github.event.inputs.schema-version}} + mkdir files + cp ./${{ env.WORKING_DIR }}/*/*.json files/ + cd validation-suite + python -m pip install --upgrade pip + pip install -r requirements.txt + curl https://raw.githubusercontent.com/ror-community/ror-schema/master/ror_schema.json -o ror_schema.json + curl https://raw.githubusercontent.com/ror-community/ror-schema/master/ror_schema_v2_0.json -o ror_schema_v2_0.json + ls ../files/ + if [[ ${{ github.event.inputs.schema-version }} == 'v1' ]]; then + echo "validating v1" + if [[ ${{ github.event.inputs.skip-geonames }} == true ]]; then + if [[ ${{ github.event.inputs.with-relationship }} == true ]]; then + if [[ -f "../${{ env.WORKING_DIR }}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 1 -s ror_schema.json -f ../${{ env.WORKING_DIR }}/relationships.csv -p ../files/ --no-geonames + else + python run_validations.py -i ../files -v 1 -s ror_schema.json -p ../files/ --no-geonames + fi + elif [[ ${{ github.event.inputs.with-relationship }} == false ]]; then + python run_validations.py -i ../files -v 1 -s ror_schema.json --no-geonames + fi + else + if [[ ${{ github.event.inputs.with-relationship }} == true ]]; then + if [[ -f "../${{ env.WORKING_DIR }}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 1 -s ror_schema.json -f ../${{ env.WORKING_DIR }}/relationships.csv -p ../files/ + else + python run_validations.py -i ../files -v 1 -s ror_schema.json -p ../files/ + fi + elif [[ ${{ github.event.inputs.with-relationship }} == false ]]; then + python run_validations.py -i ../files -v 1 -s ror_schema.json + fi + fi + fi + if [[ ${{ github.event.inputs.schema-version }} == 'v2' ]]; then + echo "validating v2" + if [[ ${{ github.event.inputs.skip-geonames }} == true ]]; then + if [[ ${{ github.event.inputs.with-relationship }} == true ]]; then + if [[ -f "../${{ env.WORKING_DIR }}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json -f ../${{ env.WORKING_DIR }}/relationships.csv -p ../files/ --no-geonames + else + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json -p ../files/ --no-geonames + fi + elif [[ ${{ github.event.inputs.with-relationship }} == false ]]; then + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json --no-geonames + fi + else + if [[ ${{ github.event.inputs.with-relationship }} == true ]]; then + if [[ -f "../${{ env.WORKING_DIR }}/relationships.csv" ]]; then + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json -f ../${{ env.WORKING_DIR }}/relationships.csv -p ../files/ + else + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json -p ../files/ + fi + elif [[ ${{ github.event.inputs.with-relationship }} == false ]]; then + python run_validations.py -i ../files -v 2 -s ror_schema_v2_0.json + fi + fi + fi + + - name: Notify Slack + if: always() + uses: edge/simple-slack-notify@master + env: + SLACK_WEBHOOK_URL: ${{ secrets.CURATOR_SLACK_WEBHOOK_URL }} + with: + channel: '#ror-curation-releases' + color: 'good' + text: 'Validation status ${{ steps.validatefiles.outcome }} in ${env.GITHUB_REPOSITORY}. Using version ${{ github.event.inputs.schema-version }}. On branch: ${{ env.WORKING_DIR }}. Please check: ${env.GITHUB_SERVER_URL}/${env.GITHUB_REPOSITORY}/actions/runs/${env.GITHUB_RUN_ID}' diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml index c0adc3897..d5df7da30 100644 --- a/.github/workflows/validate.yml +++ b/.github/workflows/validate.yml @@ -36,7 +36,6 @@ jobs: uses: actions/checkout@v2 with: repository: ror-community/validation-suite - ref: schema-v2 path: validation-suite - name: Get directory name if: "${{ github.event.inputs.directory-name != '' }}" diff --git a/README.md b/README.md index ced1fdfca..08c1cde63 100644 --- a/README.md +++ b/README.md @@ -102,7 +102,7 @@ JSON files for new and updated ROR records should be validated before generating 4. If this workflow fails, there's an issue with the data in one of more ROR record JSON files that needs to be corrected. In that case, check the error details, make the needed corrections, commit and push the files to your working branch and repeat steps 1-3 to re-run the Validate files workflow. ## Generate relationships -Relationships are not included in the intitial ROR record JSON files. Relationships are generated using a script [generaterelationships.py](https://github.com/ror-community/curation_ops/blob/v2-crosswalk/generate_relationships/generate_relationships.py) triggered by a Github action [Create relationships](https://github.com/ror-community/ror-updates/actions/workflows/generate_relationships.yml), which should be run AFTER all new and updated JSON records to be included in the release are uploaded to ror-updates. +Relationships are not included in the intitial ROR record JSON files. Relationships are generated using a script [generaterelationships.py](https://github.com/ror-community/curation_ops/blob/main/generate_relationships/generate_relationships.py) triggered by a Github action [Create relationships](https://github.com/ror-community/ror-updates/actions/workflows/generate_relationships.yml), which should be run AFTER all new and updated JSON records to be included in the release are uploaded to ror-updates. 1. Create relationships list as a CSV file using the template [[TEMPLATE] relationships.csv](https://docs.google.com/spreadsheets/d/17rA549Q6Vc-YyH8WUtXUOvsAROwCDmt1vy4Rjce-ELs) and name the file relationships.csv. **IMPORTANT! File must be named relationships.csv and fields used by the script must be formatted correctly**. Template fields used by the script are: @@ -136,7 +136,7 @@ Relationships are not included in the intitial ROR record JSON files. Relationsh ## Remove relationships to inactive records Active records cannot contain relationships to inactive or withdrawn records. On each release, all release records must be checked for status changes and, for any where status changed from active to inactive or withdrawn, relationships to those records must be removed from active records (both in the release and in production). -Relationships to inactive records are removed using a script [remove_relationships.py](https://github.com/ror-community/curation_ops/blob/v2-crosswalk/remove_relationships/remove_relationships.py) triggered by a Github action [Remove relationships to inactive records](https://github.com/ror-community/ror-updates/actions/workflows/remove_relationships.yml), which must be run AFTER the Generate relationships action. +Relationships to inactive records are removed using a script [remove_relationships.py](https://github.com/ror-community/curation_ops/blob/main/remove_relationships/remove_relationships.py) triggered by a Github action [Remove relationships to inactive records](https://github.com/ror-community/ror-updates/actions/workflows/remove_relationships.yml), which must be run AFTER the Generate relationships action. 1. Go to https://github.com/ror-community/ror-updates/actions/workflows/remove_relationships.yml (Actions > Remove relationships to inactive records in the ror-updates repository) @@ -168,7 +168,7 @@ All release records must have their locations.geonames_details checked against t ## Update last modified dates All release records must have their last modified date updated to match the (planned) date of the release. Ideally, this date should match the data dump file date. Release file generation is often completed 1 or more days before the release is actually deployed. In that case, the planned release date should be used (not the current date). -Last modified dates are updated using a script [update_last_mod.py](https://github.com/ror-community/curation_ops/blob/v2-crosswalk/utilities/update_last_mod/update_last_mod.py) triggered by a Github action [Update last modified date](https://github.com/ror-community/ror-updates/actions/workflows/update_last_mod.yml). This action should be run after all other changes to release files are complete. +Last modified dates are updated using a script [update_last_mod.py](https://github.com/ror-community/curation_ops/blob/main/utilities/update_last_mod/update_last_mod.py) triggered by a Github action [Update last modified date](https://github.com/ror-community/ror-updates/actions/workflows/update_last_mod.yml). This action should be run after all other changes to release files are complete. 1. Go to https://github.com/ror-community/ror-updates/actions/workflows/update_last_mod.yml(Actions > Update last modified date in the ror-updates repository) 2. Click Run workflow at right and set the following options: diff --git a/v1.45/v1/004j8pp46.json b/v1.45/v1/004j8pp46.json new file mode 100644 index 000000000..5655f151f --- /dev/null +++ b/v1.45/v1/004j8pp46.json @@ -0,0 +1,71 @@ +{ + "id": "https://ror.org/004j8pp46", + "name": "Salim Habib University", + "email_address": null, + "ip_addresses": [], + "established": 2017, + "types": [ + "Education" + ], + "relationships": [], + "addresses": [ + { + "lat": 24.8608, + "lng": 67.0104, + "state": null, + "state_code": null, + "city": "Karachi", + "geonames_city": { + "id": 1174872, + "city": "Karachi", + "geonames_admin1": { + "ascii_name": null, + "code": null, + "id": null, + "name": null + }, + "geonames_admin2": { + "ascii_name": null, + "code": null, + "id": null, + "name": null + }, + "license": { + "attribution": "Data from geonames.org under a CC-BY 3.0 license", + "license": "http://creativecommons.org/licenses/by/3.0/" + }, + "nuts_level1": { + "code": null, + "name": null + }, + "nuts_level2": { + "code": null, + "name": null + }, + "nuts_level3": { + "code": null, + "name": null + } + }, + "postcode": null, + "primary": false, + "line": null, + "country_geonames_id": null + } + ], + "links": [ + "https://www.shu.edu.pk" + ], + "aliases": [], + "acronyms": [ + "SHU" + ], + "status": "active", + "wikipedia_url": null, + "labels": [], + "country": { + "country_name": "Pakistan", + "country_code": "PK" + }, + "external_ids": {} +} \ No newline at end of file diff --git a/v1.45/v1/0065v9d27.json b/v1.45/v1/0065v9d27.json new file mode 100644 index 000000000..93003f0f4 --- /dev/null +++ b/v1.45/v1/0065v9d27.json @@ -0,0 +1,88 @@ +{ + "id": "https://ror.org/0065v9d27", + "name": "International Clinical Epidemiology Network", + "email_address": null, + "ip_addresses": [], + "established": 1980, + "types": [ + "Healthcare" + ], + "relationships": [], + "addresses": [ + { + "lat": 28.62137, + "lng": 77.2148, + "state": null, + "state_code": null, + "city": "New 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