Change monkeypox to mpox wherever possible

nextstrain · Sep 23, 2023 · e5e79ab · e5e79ab
1 parent 28a4d71
commit e5e79ab
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/ingest/workflow/snakemake_rules/trigger_rebuild.smk b/ingest/workflow/snakemake_rules/trigger_rebuild.smk
@@ -1,5 +1,5 @@
 """
-This part of the workflow handles triggering new monkeypox builds after the
+This part of the workflow handles triggering new mpox builds after the
 latest metadata TSV and sequence FASTA files have been uploaded to S3.
 
 Designed to be used internally by the Nextstrain team with hard-coded paths

diff --git a/scripts/deploy.py b/scripts/deploy.py
@@ -51,14 +51,14 @@ def add_branch_id_recursive(node):
 
             # Upload basic builds to staging
             for auspice_file in ['', '_root-sequence']:
-                os.system(f"aws s3 cp s3://nextstrain-staging/monkeypox_{build_name}{auspice_file}.json s3://nextstrain-data/monkeypox_{build_name}{auspice_file}.json")
-            print(f">> Uploaded {build_name} to production: https://nextstrain.org/staging/monkeypox/{build_name.replace('_', '/')}/")
+                os.system(f"aws s3 cp s3://nextstrain-staging/mpox_{build_name}{auspice_file}.json s3://nextstrain-data/mpox_{build_name}{auspice_file}.json")
+            print(f">> Uploaded {build_name} to production: https://nextstrain.org/staging/mpox/{build_name.replace('_', '/')}/")
 
 
             if not args.no_dated:
                 # Check how many today dated builds exist
                 today = datetime.date.today().strftime("%Y-%m-%d")
-                os.system(f"aws s3 ls nextstrain-data/monkeypox_{build_name}_{today}.json > dated_builds.txt")
+                os.system(f"aws s3 ls nextstrain-data/mpox_{build_name}_{today}.json > dated_builds.txt")
 
                 with open('dated_builds.txt') as fh:
                     today_dated_builds_count = len(fh.readlines())
@@ -68,28 +68,28 @@ def add_branch_id_recursive(node):
                         print(f">> Overwriting existing dated build due to --force flag being present")
 
                     for auspice_file in ['', '_root-sequence']:
-                        os.system(f"aws s3 cp s3://nextstrain-staging/monkeypox_{build_name}{auspice_file}.json staging/")
+                        os.system(f"aws s3 cp s3://nextstrain-staging/mpox_{build_name}{auspice_file}.json staging/")
 
                     # Load auspice json
-                    with gzip.open(f"staging/monkeypox_{build_name}.json") as fh:
+                    with gzip.open(f"staging/mpox_{build_name}.json") as fh:
                         auspice_json = json.load(fh)
 
                     add_branch_id_recursive(auspice_json['tree'])
 
-                    with open(f"staging/monkeypox_{build_name}_{today}.json", 'wt') as fh:
+                    with open(f"staging/mpox_{build_name}_{today}.json", 'wt') as fh:
                         json.dump(auspice_json, fh)
 
-                    os.system(f"aws s3 cp staging/monkeypox_{build_name}_{today}.json s3://nextstrain-data")
-                    os.system(f"aws s3 cp s3://nextstrain-staging/monkeypox_{build_name}_root-sequence.json s3://nextstrain-data/monkeypox_{build_name}_{today}_root-sequence.json")
-                    print(f">> Uploaded dated {build_name} to production: https://nextstrain.org/monkeypox/{build_name.replace('_', '/')}/{today}/")
+                    os.system(f"aws s3 cp staging/mpox_{build_name}_{today}.json s3://nextstrain-data")
+                    os.system(f"aws s3 cp s3://nextstrain-staging/mpox_{build_name}_root-sequence.json s3://nextstrain-data/mpox_{build_name}_{today}_root-sequence.json")
+                    print(f">> Uploaded dated {build_name} to production: https://nextstrain.org/mpox/{build_name.replace('_', '/')}/{today}/")
 
                 else:
-                    print(f">> Warning: Dated {build_name} with date today already exists, skipping upload: https://nextstrain.org/monkeypox/{build_name.replace('_', '/')}/{today}/")
+                    print(f">> Warning: Dated {build_name} with date today already exists, skipping upload: https://nextstrain.org/mpox/{build_name.replace('_', '/')}/{today}/")
                     print(f">> Hint: Use the --f/--force flag to overwrite existing dated builds")
         if args.staging:
             print(f">> Deploying build {build_name} to staging")
             for auspice_file in ['', '_root-sequence']:
-                os.system(f"aws s3 cp auspice/monkeypox_{build_name}{auspice_file}.json s3://nextstrain-staging/monkeypox_{build_name}{auspice_file}.json")
-            print(f">> Uploaded {build_name} to staging: https://nextstrain.org/staging/monkeypox/{build_name.replace('_', '/')}/")
+                os.system(f"aws s3 cp auspice/mpox_{build_name}{auspice_file}.json s3://nextstrain-staging/mpox_{build_name}{auspice_file}.json")
+            print(f">> Uploaded {build_name} to staging: https://nextstrain.org/staging/mpox/{build_name.replace('_', '/')}/")
 
         print("----------------------------------------")
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
@@ -6,7 +6,7 @@ This part of the workflow expects input files
 
 and will produce output files as
 
-        auspice_json = auspice_dir + "/monkeypox_{build_name}.json"
+        auspice_json = auspice_dir + "/mpox_{build_name}.json"
 
 Parameter are expected to sit in the `config` data structure.
 In addition, `build_dir` and `auspice_dir` need to be defined upstream.