added test for pipeline

q2_amr/card/reads.py

@@ -31,35 +31,41 @@ def annotate_reads_card(
     include_other_models=False,
     num_partitions=None,
 ):
+    # Define all actions used by the pipeline
+    if reads.type <= SampleData[SequencesWithQuality]:
+        partition_method = ctx.get_action("demux", "partition_samples_single")
+    elif reads.type <= SampleData[PairedEndSequencesWithQuality]:
+        partition_method = ctx.get_action("demux", "partition_samples_paired")
+
     annotate = ctx.get_action("amr", "_annotate_reads_card")
+
     collate_allele_annotations = ctx.get_action(
         "amr", "collate_reads_allele_annotations"
     )
     collate_gene_annotations = ctx.get_action("amr", "collate_reads_gene_annotations")
     merge_tables = ctx.get_action("feature-table", "merge")
 
-    if reads.type <= SampleData[SequencesWithQuality]:
-        partition_method = ctx.get_action("demux", "partition_samples_single")
-    elif reads.type <= SampleData[PairedEndSequencesWithQuality]:
-        partition_method = ctx.get_action("demux", "partition_samples_paired")
-
+    # Partition the reads
     (partitioned_seqs,) = partition_method(reads, num_partitions)
 
     allele_annotations = []
     gene_annotations = []
     allele_tables = []
     gene_tables = []
 
+    # Run _annotate_reads_card for every partition
     for read in partitioned_seqs.values():
         (allele_annotation, gene_annotation, allele_table, gene_table) = annotate(
             read, card_db, aligner, threads, include_wildcard, include_other_models
         )
 
+        # Append output artifacts to lists
         allele_annotations.append(allele_annotation)
         gene_annotations.append(gene_annotation)
         allele_tables.append(allele_table)
         gene_tables.append(gene_table)
 
+    # Collate annotation and feature table artifacts
     (collated_allele_annotations,) = collate_allele_annotations(allele_annotations)
     (collated_gene_annotations,) = collate_gene_annotations(gene_annotations)
     (collated_allele_tables,) = merge_tables(allele_tables)

q2_amr/card/tests/data/reads_paired/MANIFEST

@@ -0,0 +1,2 @@
+sample-id,filename,direction
+sample1,sample1_00_L001_R1_001.fastq.gz,forward

q2_amr/card/tests/data/reads_paired/metadata.yml

@@ -0,0 +1 @@
+phred-offset: 33

q2_amr/card/tests/data/reads_single/MANIFEST

@@ -0,0 +1,2 @@
+sample-id,filename,direction
+sample1,sample1_00_L001_R1_001.fastq.gz,forward

q2_amr/card/tests/data/reads_single/metadata.yml

@@ -0,0 +1 @@
+phred-offset: 33

q2_amr/card/tests/test_reads.py

@@ -7,9 +7,10 @@
     SingleLanePerSamplePairedEndFastqDirFmt,
     SingleLanePerSampleSingleEndFastqDirFmt,
 )
+from qiime2 import Artifact
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_amr.card.reads import _annotate_reads_card, run_rgi_bwt
+from q2_amr.card.reads import _annotate_reads_card, annotate_reads_card, run_rgi_bwt
 from q2_amr.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDDatabaseDirectoryFormat,
@@ -199,3 +200,50 @@ def test_exception_raised(self):
             mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
             run_rgi_bwt()
             self.assertEqual(str(cm.exception), expected_message)
+
+    def test_kmer_query_reads_card_paired(self):
+        reads_path = self.get_data_path("reads_paired")
+        reads = SingleLanePerSamplePairedEndFastqDirFmt(reads_path, "r")
+        reads_artifact = Artifact.import_data(
+            "SampleData[PairedEndSequencesWithQuality]", reads
+        )
+        self._test_kmer_query_reads_card(reads_artifact)
+
+    def test_kmer_query_reads_card_single(self):
+        reads_path = self.get_data_path("reads_single")
+        reads = SingleLanePerSampleSingleEndFastqDirFmt(reads_path, "r")
+        reads_artifact = Artifact.import_data("SampleData[SequencesWithQuality]", reads)
+        self._test_kmer_query_reads_card(reads_artifact)
+
+    def _test_kmer_query_reads_card(self, reads):
+        # Mock the get_action method to return MagicMock objects
+        mock_ctx = MagicMock()
+        mock_ctx.get_action.side_effect = [
+            MagicMock(
+                return_value=({"1": "artifact_reads_1", "2": "artifact_reads_2"},)
+            ),
+            MagicMock(
+                return_value=(
+                    "artifact_annotation_allele",
+                    "artifact_annotation_gene",
+                    "artifact_feature_table_allele",
+                    "artifact_feature_table_gene",
+                )
+            ),
+            MagicMock(return_value=("artifact_allele_annotation_collated",)),
+            MagicMock(return_value=("artifact_gene_annotation_collated",)),
+            MagicMock(return_value=("artifact_feature_table_merged",)),
+        ]
+
+        # Call function with mocked ctx
+        result = annotate_reads_card(ctx=mock_ctx, reads=reads, card_db=None)
+
+        self.assertEqual(
+            result,
+            (
+                "artifact_allele_annotation_collated",
+                "artifact_gene_annotation_collated",
+                "artifact_feature_table_merged",
+                "artifact_feature_table_merged",
+            ),
+        )