ingest/ci: Use custom rules to manage example data

Keeps the default rules simpler by hiding the use of example data
in the custom rules for CI.

This matches how we manage example data in the phylogenetic workflow.

ingest/build-configs/ci/config.yaml

@@ -1,5 +1,5 @@
-# Use cached ncbi datasets package to speed up tests and isolate from ncbi servers
-mock_fetch: true
+custom_rules:
+  - "build-configs/ci/copy_example_data.smk"
 
 # Snakemake requires at least one top level key in a config file, so including
 # a bogus key here that should not be used anywhere in the Snakemake workflow

ingest/build-configs/ci/copy_example_data.smk

@@ -0,0 +1,14 @@
+rule copy_example_data:
+    input:
+        ncbi_dataset="example_data/ncbi_dataset.zip"
+    output:
+        ncbi_dataset=temp("data/ncbi_dataset.zip")
+    shell:
+        """
+        cp -f {input.ncbi_dataset} {output.ncbi_dataset}
+        """
+
+# Add a Snakemake ruleorder directive here if you need to resolve ambiguous rules
+# that have the same output as the copy_example_data rule.
+
+ruleorder: copy_example_data > fetch_ncbi_dataset_package

ingest/rules/fetch_from_ncbi.smk

@@ -45,18 +45,9 @@ rule fetch_ncbi_dataset_package:
         """
 
 
-def get_ncbi_dataset_package_path():
-    """
-    Use cached data package in ci to isolate from ncbi server
-    """
-    if config.get("mock_fetch", False):
-        return "test_data/ncbi_dataset.zip"
-    return "data/ncbi_dataset.zip"
-
-
 rule extract_ncbi_dataset_sequences:
     input:
-        dataset_package=get_ncbi_dataset_package_path(),
+        dataset_package="data/ncbi_dataset.zip",
     output:
         ncbi_dataset_sequences=temp("data/ncbi_dataset_sequences.fasta"),
     benchmark:
@@ -70,7 +61,7 @@ rule extract_ncbi_dataset_sequences:
 
 rule format_ncbi_dataset_report:
     input:
-        dataset_package=get_ncbi_dataset_package_path(),
+        dataset_package="data/ncbi_dataset.zip",
     output:
         ncbi_dataset_tsv=temp("data/ncbi_dataset_report.tsv"),
     params:
@@ -116,4 +107,3 @@ rule format_ncbi_datasets_ndjson:
             --duplicate-reporting warn \
             2> {log} > {output.ndjson}
         """
-