Revert "ENH: Add three new parameters to run_amrfinderplus_n (bokulic…

…h-lab#97)"

This reverts commit a895429.

q2_amr/amrfinderplus/sample_data.py

@@ -25,8 +25,6 @@ def annotate_sample_data_amrfinderplus(
     curated_ident: bool = False,
     coverage_min: float = 0.5,
     translation_table: str = "11",
-    report_common: bool = False,
-    gpipe_org: bool = False,
     threads: int = None,
 ) -> (
     AMRFinderPlusAnnotationsDirFmt,
@@ -74,9 +72,6 @@ def annotate_sample_data_amrfinderplus(
                 curated_ident=curated_ident,
                 coverage_min=coverage_min,
                 translation_table=translation_table,
-                annotation_format=None,
-                report_common=report_common,
-                gpipe_org=gpipe_org,
                 threads=threads,
             )
 

q2_amr/amrfinderplus/tests/test_sample_data.py

@@ -25,9 +25,6 @@ def mock_run_amrfinderplus_n(
         curated_ident,
         coverage_min,
         translation_table,
-        annotation_format,
-        report_common,
-        gpipe_org,
         threads,
     ):
         with open(os.path.join(working_dir, "amr_annotations.tsv"), "w"):

q2_amr/amrfinderplus/tests/test_utils.py

@@ -23,9 +23,6 @@ def test_run_amrfinderplus_n(self, mock_run_command):
             curated_ident=False,
             coverage_min=1,
             translation_table="11",
-            annotation_format="prodigal",
-            report_common=True,
-            gpipe_org=True,
             threads=4,
         )
         mock_run_command.assert_called_once_with(
@@ -60,10 +57,6 @@ def test_run_amrfinderplus_n(self, mock_run_command):
                 "1",
                 "--translation_table",
                 "11",
-                "--annotation_format",
-                "prodigal",
-                "--report_common",
-                "--gpipe_org",
             ],
             "path_dir",
             verbose=True,
@@ -84,9 +77,6 @@ def test_run_amrfinderplus_n_minimal(self, mock_run_command):
             curated_ident=True,
             coverage_min=None,
             translation_table=None,
-            annotation_format=None,
-            report_common=False,
-            gpipe_org=False,
             threads=None,
         )
         mock_run_command.assert_called_once_with(
@@ -103,49 +93,3 @@ def test_run_amrfinderplus_n_minimal(self, mock_run_command):
             "path_dir",
             verbose=True,
         )
-
-    @patch("q2_amr.amrfinderplus.utils.run_command")
-    def test_run_amrfinderplus_n_value_error_report_common(self, mock_run_command):
-        with self.assertRaisesRegex(
-            ValueError, "--p-report-common requires " "--p-plus and --p-organism"
-        ):
-            run_amrfinderplus_n(
-                working_dir="path_dir",
-                amrfinderplus_db="amrfinderplus_db",
-                dna_sequences=None,
-                protein_sequences=None,
-                gff=None,
-                organism=None,
-                plus=False,
-                report_all_equal=False,
-                ident_min=None,
-                curated_ident=True,
-                coverage_min=None,
-                translation_table=None,
-                annotation_format=None,
-                report_common=True,
-                gpipe_org=False,
-                threads=None,
-            )
-
-    @patch("q2_amr.amrfinderplus.utils.run_command")
-    def test_run_amrfinderplus_n_value_error_gpipe_org(self, mock_run_command):
-        with self.assertRaisesRegex(ValueError, "--p-gpipe_org requires --p-organism"):
-            run_amrfinderplus_n(
-                working_dir="path_dir",
-                amrfinderplus_db="amrfinderplus_db",
-                dna_sequences=None,
-                protein_sequences=None,
-                gff=None,
-                organism=None,
-                plus=False,
-                report_all_equal=False,
-                ident_min=None,
-                curated_ident=True,
-                coverage_min=None,
-                translation_table=None,
-                annotation_format=None,
-                report_common=False,
-                gpipe_org=True,
-                threads=None,
-            )

q2_amr/amrfinderplus/utils.py

@@ -16,17 +16,8 @@ def run_amrfinderplus_n(
     curated_ident,
     coverage_min,
     translation_table,
-    annotation_format,
-    report_common,
-    gpipe_org,
     threads,
 ):
-    # Check for unallowed parameter combinations
-    if report_common and (not plus or not organism):
-        raise ValueError("--p-report-common requires --p-plus and --p-organism")
-    if gpipe_org and not organism:
-        raise ValueError("--p-gpipe_org requires --p-organism")
-
     cmd = [
         "amrfinder",
         "--database",
@@ -82,13 +73,6 @@ def run_amrfinderplus_n(
         cmd.extend(["--coverage_min", str(coverage_min)])
     if translation_table:
         cmd.extend(["--translation_table", str(translation_table)])
-    if annotation_format:
-        cmd.extend(["--annotation_format", str(annotation_format)])
-    if report_common:
-        cmd.append("--report_common")
-    if gpipe_org:
-        cmd.append("--gpipe_org")
-
     try:
         run_command(cmd, working_dir, verbose=True)
     except subprocess.CalledProcessError as e:

q2_amr/plugin_setup.py

@@ -1127,35 +1127,6 @@
     "Vibrio_vulnificus",
 ]
 
-organisms_gpipe = [
-    "Acinetobacter",
-    "Burkholderia_cepacia_complex",
-    "Burkholderia_pseudomallei",
-    "Campylobacter",
-    "Citrobacter_freundii",
-    "Clostridioides_difficile",
-    "Enterobacter_asburiae",
-    "Enterobacter_cloacae",
-    "Enterococcus_faecalis",
-    "Enterococcus_faecium",
-    "Escherichia_coli_Shigella",
-    "Klebsiella_oxytoca",
-    "Klebsiella",
-    "Neisseria_gonorrhoeae",
-    "Neisseria_meningitidis",
-    "Pseudomonas_aeruginosa",
-    "Salmonella",
-    "Serratia",
-    "Staphylococcus_aureus",
-    "Staphylococcus_pseudintermedius",
-    "Streptococcus_agalactiae",
-    "Streptococcus_pneumoniae",
-    "Streptococcus_pyogenes",
-    "Vibrio_cholerae",
-    "Vibrio_parahaemolyticus",
-    "Vibrio_vulnificus",
-]
-
 translation_tables = [
     "1",
     "2",
@@ -1185,29 +1156,20 @@
     "33",
 ]
 
-P_gpipe_org, P_organism, _ = TypeMap(
-    {
-        (Bool % Choices(True), Str % Choices(organisms_gpipe)): Int,
-        (Bool % Choices(False), Str % Choices(organisms)): Int,
-    }
-)
-
 plugin.methods.register_function(
     function=annotate_sample_data_amrfinderplus,
     inputs={
         "sequences": SampleData[MAGs | Contigs],
         "amrfinderplus_db": AMRFinderPlusDatabase,
     },
     parameters={
-        "organism": P_organism,
+        "organism": Str % Choices(organisms),
         "plus": Bool,
         "report_all_equal": Bool,
         "ident_min": Float % Range(0, 1, inclusive_start=True, inclusive_end=True),
         "curated_ident": Bool,
         "coverage_min": Float % Range(0, 1, inclusive_start=True, inclusive_end=True),
         "translation_table": Str % Choices(translation_tables),
-        "report_common": Bool,
-        "gpipe_org": P_gpipe_org,
         "threads": Int % Range(0, None, inclusive_start=False),
     },
     outputs=[
@@ -1242,9 +1204,6 @@
         "coverage_min": "Minimum proportion of reference gene covered for a "
         "BLAST-based hit (Methods BLAST or PARTIAL).",
         "translation_table": "Translation table used for BLASTX.",
-        "report_common": "Report proteins common to a taxonomy group.",
-        "gpipe_org": "Use Pathogen Detection taxgroup names as arguments to the "
-        "organism option.",
         "threads": "The number of threads to use for processing. AMRFinderPlus "
         "defaults to 4 on hosts with >= 4 cores. Setting this number higher"
         " than the number of cores on the running host may cause blastp to "