From 56b7291e53e68ca72c7e4ce82021650ac0175f3b Mon Sep 17 00:00:00 2001 From: j23414 Date: Thu, 29 Dec 2022 17:46:37 -0800 Subject: [PATCH] edit: Use a permalink for each script This would allow us to version the software we use in this workflow without being affected by upstream changes until we want to bump the version. This design adds more maintenance to this workflow, but it also protects users against unexpected issues that are outside of their control. Discussed in https://github.com/nextstrain/ebola/pull/6#discussion_r1048835183 --- .../snakemake_rules/fetch_sequences.smk | 2 +- .../snakemake_rules/slack_notifications.smk | 4 ++-- ingest/workflow/snakemake_rules/transform.smk | 18 +++++++++--------- .../snakemake_rules/trigger_rebuild.smk | 2 +- ingest/workflow/snakemake_rules/upload.smk | 6 +++--- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/workflow/snakemake_rules/fetch_sequences.smk index d1c2173f..fbf9bfe3 100644 --- a/ingest/workflow/snakemake_rules/fetch_sequences.smk +++ b/ingest/workflow/snakemake_rules/fetch_sequences.smk @@ -28,7 +28,7 @@ rule fetch_from_genbank: genbank_ndjson="data/genbank_{serotype}.ndjson", params: serotype_tax_id=download_serotype, - csv_to_ndjson_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/csv-to-ndjson", + csv_to_ndjson_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/csv-to-ndjson", shell: """ if [[ ! -d bin ]]; then diff --git a/ingest/workflow/snakemake_rules/slack_notifications.smk b/ingest/workflow/snakemake_rules/slack_notifications.smk index 638f84af..91d5ffc2 100644 --- a/ingest/workflow/snakemake_rules/slack_notifications.smk +++ b/ingest/workflow/snakemake_rules/slack_notifications.smk @@ -28,7 +28,7 @@ rule notify_on_genbank_record_change: touch("data/notify/genbank-record-change.done"), params: s3_src=S3_SRC, - notify_on_record_change_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/notify-on-record-change", + notify_on_record_change_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/notify-on-record-change", shell: """ if [[ ! -d bin ]]; then @@ -52,7 +52,7 @@ rule notify_on_metadata_diff: touch("data/notify/metadata-diff.done"), params: s3_src=S3_SRC, - notify_on_diff_url = "https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/notify-on-diff", + notify_on_diff_url = "https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/notify-on-diff", shell: """ if [[ ! -d bin ]]; then diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk index c6b29a1d..e48b15aa 100644 --- a/ingest/workflow/snakemake_rules/transform.smk +++ b/ingest/workflow/snakemake_rules/transform.smk @@ -62,15 +62,15 @@ rule transform: metadata_columns=config["transform"]["metadata_columns"], id_field=config["transform"]["id_field"], sequence_field=config["transform"]["sequence_field"], - transform_field_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-field-names", - transform_string_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-string-fields", - transform_strain_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-strain-names", - transform_date_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-date-fields", - transform_genbank_location_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-genbank-location", - transform_authors_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/transform-authors", - apply_geolocation_rules_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/apply-geolocation-rules", - merge_user_metadata_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/merge-user-metadata", - ndjson_to_tsv_and_fasta_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/ndjson-to-tsv-and-fasta", + transform_field_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-field-names", + transform_string_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-string-fields", + transform_strain_names_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-strain-names", + transform_date_fields_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-date-fields", + transform_genbank_location_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-genbank-location", + transform_authors_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/transform-authors", + apply_geolocation_rules_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/apply-geolocation-rules", + merge_user_metadata_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/merge-user-metadata", + ndjson_to_tsv_and_fasta_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/ndjson-to-tsv-and-fasta", shell: """ if [[ ! -d bin ]]; then diff --git a/ingest/workflow/snakemake_rules/trigger_rebuild.smk b/ingest/workflow/snakemake_rules/trigger_rebuild.smk index 6048dd81..aa5e52a1 100644 --- a/ingest/workflow/snakemake_rules/trigger_rebuild.smk +++ b/ingest/workflow/snakemake_rules/trigger_rebuild.smk @@ -14,7 +14,7 @@ rule trigger_build: output: touch("data/trigger/rebuild.done") params: - trigger_on_new_data_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/trigger-on-new-data" + trigger_on_new_data_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/trigger-on-new-data" shell: """ if [[ ! -d bin ]]; then diff --git a/ingest/workflow/snakemake_rules/upload.smk b/ingest/workflow/snakemake_rules/upload.smk index 95ad81e3..db2de41c 100644 --- a/ingest/workflow/snakemake_rules/upload.smk +++ b/ingest/workflow/snakemake_rules/upload.smk @@ -54,9 +54,9 @@ rule upload_to_s3: quiet="" if send_notifications else "--quiet", s3_dst=config["upload"].get("s3", {}).get("dst", ""), cloudfront_domain=config["upload"].get("s3", {}).get("cloudfront_domain", ""), - upload_to_s3_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/upload-to-s3", - sha256sum_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/sha256sum", - cloudfront_invalidate_url="https://raw.githubusercontent.com/nextstrain/monkeypox/master/ingest/bin/cloudfront-invalidate" + upload_to_s3_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/upload-to-s3", + sha256sum_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/sha256sum", + cloudfront_invalidate_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/cloudfront-invalidate" shell: """ if [[ ! -d bin ]]; then