add dummy dataset

.github/workflows/build-and-deploy.yml

@@ -31,20 +31,54 @@ jobs:
     env:
       VERBOSE: 0
       PYTHONUNBUFFERED: 1
-      DATA_AWS_S3_BUCKET: ${{ secrets.DATA_AWS_S3_BUCKET }}
-      DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID: ${{ secrets.DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID }}
-      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-      AWS_DEFAULT_REGION: us-east-2
       GH_TOKEN: ${{ github.token }}
 
     steps:
+      - name: config
+        id: config
+        run: |
+          echo 'is_fork=${{ (github.event_name == 'pull_request') && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository)) }}' >> $GITHUB_OUTPUT
+
+          echo 'should_deploy=${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/release' }}' >> $GITHUB_OUTPUT
+
+          echo 'is_release=${{ github.ref == 'refs/heads/release' }}' >> $GITHUB_OUTPUT
+
+      - name: "DEBUG"
+        run: |
+          set +x
+
+          echo is_fork=${{ steps.config.outputs.is_fork }}
+          echo should_deploy=${{ steps.config.outputs.should_deploy }}
+          echo is_release=${{ steps.config.outputs.is_release }}
+
+          echo '\n'
+
+          echo 'github.ref =' ${{ github.ref }}
+          echo 'github.event_name =' ${{ github.event_name }}
+          echo 'github.repository =' ${{ github.repository }}
+
+          echo '\n'
+
+          echo 'github.event.pull_request.head.repo.fork =' ${{ github.event.pull_request.head.repo.fork }}
+          echo 'github.event.pull_request.head.repo.full_name =' ${{ github.event.pull_request.head.repo.full_name }}
+
+          echo '\n'
+
+          echo 'github.event.pull_request.base.repo.fork =' ${{ github.event.pull_request.base.repo.fork }}
+          echo 'github.event.pull_request.base.repo.full_name =' ${{ github.event.pull_request.base.repo.full_name }}
+
+          echo '\n'
+
+          echo 'github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name =' ${{ github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name }}
+          echo '(github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository =' ${{ (github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository }}
+          echo 'github.event_name == 'pull_request' && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository)) =' ${{ github.event_name == 'pull_request' && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository)) }}
+
       - name: "Checkout code"
         uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Number of commits to fetch. 0 indicates all history for all branches and tags.
           fetch-tags: true # Whether to fetch tags, even if fetch-depth > 0.
-          ref: ${{ github.event.pull_request.head.ref || github.ref_name }}
+          ref: ${{ github.event.pull_request.head.ref || github.ref }}
 
       - name: "Install system dependencies"
         run: |
@@ -54,33 +88,45 @@ jobs:
         run: |
           pip3 install -r requirements.txt
 
-      - name: "Install awscli"
+      - name: "Rebuild datasets (fork)"
+        if: ${{ steps.config.outputs.is_fork == 'true' }}
         run: |
-          pushd /tmp >/dev/null
-            curl -fsSL "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
-            unzip -oqq awscliv2.zip
-            sudo ./aws/install --update
-          popd >/dev/null
-          aws --version
+          ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --no-pull
 
-      - name: "Rebuild, commit and push datasets"
-        if: github.ref != 'refs/heads/release'
+      - name: "Rebuild, commit and push datasets (non-release branch)"
+        if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.is_release != 'true' }}
         run: |
           git config --global user.email "${{ secrets.BOT_GIT_USER_EMAIL }}"
           git config --global user.name "${{ secrets.BOT_GIT_USER_NAME }}"
 
           ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --push --repo="${GITHUB_REPOSITORY}"
 
-      - name: "Rebuild, commit, push and make a release"
-        if: github.ref == 'refs/heads/release'
+      - name: "Rebuild, commit, push and make a release (release branch)"
+        if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.is_release == 'true' }}
         run: |
           git config --global user.email "${{ secrets.BOT_GIT_USER_EMAIL }}"
           git config --global user.name "${{ secrets.BOT_GIT_USER_NAME }}"
 
           ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --release --repo="${GITHUB_REPOSITORY}"
 
+      - name: "Install awscli"
+        if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.should_deploy == 'true' }}
+        run: |
+          pushd /tmp >/dev/null
+            curl -fsSL "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+            unzip -oqq awscliv2.zip
+            sudo ./aws/install --update
+          popd >/dev/null
+          aws --version
+
       - name: "Deploy dataset server"
-        if: ${{ endsWith(github.ref, '/master') || endsWith(github.ref, '/staging') || endsWith(github.ref, '/release') }}
+        if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.should_deploy == 'true' }}
+        env:
+          DATA_AWS_S3_BUCKET: ${{ secrets.DATA_AWS_S3_BUCKET }}
+          DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID: ${{ secrets.DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_DEFAULT_REGION: us-east-2
         run: |
           ./scripts/upload 'data_output/'
 

data/community/dummy1/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+First release

data/community/dummy1/README.md

@@ -0,0 +1 @@
+# DUMMY

data/community/dummy1/genome_annotation.gff3

@@ -0,0 +1,3 @@
+#DUMMY
+ref	dummy	region	1	120	.	+	.	ID=ref
+ref	dummy	CDS	1	15	.	+	0	Name=HA1;gene=HA1

data/community/dummy1/pathogen.json

@@ -0,0 +1,24 @@
+{
+  "attributes": {
+    "name": "DUMMY",
+    "reference accession": "D1",
+    "reference name": "DUMMY/1"
+  },
+  "defaultGene": "D",
+  "deprecated": false,
+  "enabled": true,
+  "experimental": true,
+  "geneOrderPreference": [
+    "D", "U", "M"
+  ],
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "schemaVersion": "3.0.0"
+}

data/community/dummy1/reference.fasta

@@ -0,0 +1,2 @@
+>Dummy1/Ref
+AAAAAAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG

data/community/dummy1/sequences.fasta

@@ -0,0 +1,18 @@
+>ref
+AAAAAAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>A
+GGAAAAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>A1
+GAAAAAAGAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>B1
+AACCAACCAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>B2
+AACCAACCAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>C
+AACAGAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>BC1
+AACAAAAAAAGAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>BC2
+AACAAAAAAAGATAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG
+>BC3
+AACAAAAAAAGATCAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG

data/community/dummy1/tree.json

@@ -0,0 +1,109 @@
+{
+  "meta": {
+    "data_provenance": [
+      {
+        "name": "fictional data"
+      }
+    ],
+    "display_defaults": {},
+    "title": "Dummy nextclade reference tree"
+  },
+  "tree": {
+    "branch_attrs": {
+      "mutations": {
+        "nuc": []
+      }
+    },
+    "children": [
+      {
+        "branch_attrs": {
+          "mutations": {
+            "HA1": [
+              "K1G"
+            ],
+            "nuc": [
+              "A1G",
+              "A2G"
+            ]
+          }
+        },
+        "children": [],
+        "name": "A",
+        "node_attrs": {
+          "clade_membership": {
+            "value": "unassigned"
+          },
+          "div": 0.016666666666666666
+        }
+      },
+      {
+        "branch_attrs": {
+          "mutations": {
+            "HA1": [
+              "K1N"
+            ],
+            "nuc": [
+              "A3C"
+            ]
+          }
+        },
+        "children": [
+          {
+            "branch_attrs": {
+              "mutations": {
+                "HA1": [
+                  "K2Q"
+                ],
+                "nuc": [
+                  "A4C"
+                ]
+              }
+            },
+            "children": [],
+            "name": "B",
+            "node_attrs": {
+              "clade_membership": {
+                "value": "unassigned"
+              },
+              "div": 0.016666666666666666
+            }
+          },
+          {
+            "branch_attrs": {
+              "mutations": {
+                "HA1": [
+                  "K2R"
+                ],
+                "nuc": [
+                  "A5G"
+                ]
+              }
+            },
+            "children": [],
+            "name": "C",
+            "node_attrs": {
+              "clade_membership": {
+                "value": "unassigned"
+              },
+              "div": 0.016666666666666666
+            }
+          }
+        ],
+        "name": "NODE_0000001",
+        "node_attrs": {
+          "clade_membership": {
+            "value": "unassigned"
+          },
+          "div": 0.008333333333333333
+        }
+      }
+    ],
+    "name": "NODE_0000000",
+    "node_attrs": {
+      "clade_membership": {
+        "value": "unassigned"
+      },
+      "div": 0
+    }
+  }
+}