Merge pull request #22 from nextstrain/fix-ingest-automation

ingest/automation: Update S3 URLs to uppercase
nextstrain · Oct 10, 2024 · b047081 · b047081
2 parents 7e3e75b + 13bcd8a
commit b047081
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Showing 5 changed files with 11 additions and 11 deletions.
diff --git a/.github/workflows/ingest-to-phylogenetic.yaml b/.github/workflows/ingest-to-phylogenetic.yaml
@@ -65,8 +65,8 @@ jobs:
           AWS_DEFAULT_REGION: ${{ vars.AWS_DEFAULT_REGION }}
         run: |
           s3_urls=(
-            "s3://nextstrain-data/files/workflows/wnv/all/metadata.tsv.zst"
-            "s3://nextstrain-data/files/workflows/wnv/all/sequences.fasta.zst"
+            "s3://nextstrain-data/files/workflows/WNV/all/metadata.tsv.zst"
+            "s3://nextstrain-data/files/workflows/WNV/all/sequences.fasta.zst"
           )
 
           # Code below is modified from ingest/upload-to-s3

diff --git a/.github/workflows/ingest.yaml b/.github/workflows/ingest.yaml
@@ -26,8 +26,8 @@ on:
       trial_name:
         description: |
           Trial name for outputs.
-          If not set, outputs will overwrite files at s3://nextstrain-data/files/workflows/wnv/
-          If set, outputs will be uploaded to s3://nextstrain-data/files/workflows/wnv/trials/<trial_name>/
+          If not set, outputs will overwrite files at s3://nextstrain-data/files/workflows/WNV/
+          If set, outputs will be uploaded to s3://nextstrain-data/files/workflows/WNV/trials/<trial_name>/
         required: false
         type: string
 
@@ -43,7 +43,7 @@ jobs:
           config=""
           if [[ "$TRIAL_NAME" ]]; then
             config+="--config"
-            config+=" s3_dst='s3://nextstrain-data/files/workflows/wnv/trials/"$TRIAL_NAME"'"
+            config+=" s3_dst='s3://nextstrain-data/files/workflows/WNV/trials/"$TRIAL_NAME"'"
           fi
 
           echo "config=$config" >> "$GITHUB_OUTPUT"

diff --git a/.github/workflows/phylogenetic.yaml b/.github/workflows/phylogenetic.yaml
@@ -26,8 +26,8 @@ on:
       trial_name:
         description: |
           Trial name for deploying builds.
-          If not set, builds will overwrite existing builds at s3://nextstrain-data/wnv*
-          If set, builds will be deployed to s3://nextstrain-staging/wnv_trials_<trial_name>_*
+          If not set, builds will overwrite existing builds at s3://nextstrain-data/WNV*
+          If set, builds will be deployed to s3://nextstrain-staging/WNV_trials_<trial_name>_*
         required: false
         type: string
       sequences_url:
@@ -57,7 +57,7 @@ jobs:
           config=""
 
           if [[ "$TRIAL_NAME" ]]; then
-            config+=" deploy_url='s3://nextstrain-staging/wnv_trials_"$TRIAL_NAME"_'"
+            config+=" deploy_url='s3://nextstrain-staging/WNV_trials_"$TRIAL_NAME"_'"
           fi
 
           if [[ "$SEQUENCES_URL" ]]; then

diff --git a/ingest/build-configs/nextstrain-automation/config.yaml b/ingest/build-configs/nextstrain-automation/config.yaml
@@ -12,7 +12,7 @@ cloudfront_domain: "data.nextstrain.org"
 
 # Nextstrain AWS S3 Bucket with pathogen prefix
 # Replace <pathogen> with the pathogen repo name.
-s3_dst: "s3://nextstrain-data/files/workflows/wnv"
+s3_dst: "s3://nextstrain-data/files/workflows/WNV"
 
 # Mapping of files to upload
 files_to_upload:

diff --git a/phylogenetic/defaults/config.yaml b/phylogenetic/defaults/config.yaml
@@ -7,8 +7,8 @@ root: "AF481864"
 
 # Sequences must be FASTA and metadata must be TSV
 # Both files must be zstd compressed
-sequences_url: "https://data.nextstrain.org/files/workflows/wnv/sequences.fasta.zst"
-metadata_url: "https://data.nextstrain.org/files/workflows/wnv/metadata.tsv.zst"
+sequences_url: "https://data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst"
+metadata_url: "https://data.nextstrain.org/files/workflows/WNV/metadata.tsv.zst"
 
 # Pull in metadata and sequences from the ingest workflow
 input_metadata: "data/metadata.tsv"