Completed updating CLI to be more organized with bettert error messages

src/automlst/cli/exactmatch.py

@@ -0,0 +1,48 @@
+
+from argparse import ArgumentParser
+import asyncio
+import datetime
+from automlst.engine.local.csv import write_mlst_profiles_as_csv
+from automlst.engine.local.fasta import read_multiple_fastas
+from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+
+
+def setup_parser(parser: ArgumentParser):
+    parser.description = "Returns MLST exact profile matches."
+    parser.add_argument(
+        "fastas",
+        nargs="+",
+        action='extend',
+        default=[],
+        type=str,
+        help="The FASTA files to process. Multiple can be listed."
+    )
+
+    parser.add_argument(
+        "seqdefdb",
+        help="The BIGSdb seqdef database to use for typing."
+    )
+
+    parser.add_argument(
+        "schema",
+        type=int,
+        help="The BIGSdb seqdef database schema ID (integer) to use for typing."
+    )
+
+    parser.add_argument(
+        "out",
+        default=f'./{datetime.datetime.now().strftime(r"%Y%m%d%H%M%S")}',
+        help="The output CSV name (.csv will be appended)."
+    )
+    parser.set_defaults(func=run_asynchronously)
+
+async def run(args):
+    async with BIGSdbIndex() as bigsdb_index:
+        gen_strings = read_multiple_fastas(args.fastas)
+        async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler:
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
+            await write_mlst_profiles_as_csv(mlst_profiles, args.out)
+
+def run_asynchronously(args):
+    asyncio.run(run(args))
+

src/automlst/cli/info.py

@@ -1,36 +1,38 @@
+from argparse import ArgumentParser
 import asyncio
-from automlst.cli import program
 from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
 
 
-parser = program.subparsers.add_parser(__name__)
+def setup_parser(parser: ArgumentParser):
+    parser.description = "Fetches the latest BIGSdb MLST database definitions."
+    parser.usage = "test"
+    parser.add_argument(
+        "--retrieve-bigsdbs", "-l",
+        action="store_true",
+        dest="list_dbs",
+        required=False,
+        default=False,
+        help="Lists all known BIGSdb MLST databases (fetched from known APIs and cached)."
+    )
 
-parser.add_argument(
-    "--retrieve-bigsdbs", "-l",
-    action="store_true",
-    dest="list_dbs",
-    required=False,
-    default=False,
-    type=bool,
-    help="Lists all known BIGSdb MLST databases (fetched from known APIs and cached)."
-)
+    parser.add_argument(
+        "--retrieve-bigsdb-schemas", "-lschemas",
+        nargs="+",
+        action="extend",
+        dest="list_bigsdb_schemas",
+        required=False,
+        default=[],
+        type=str,
+        help="Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given."
+    )
 
-parser.add_argument(
-    "--retrieve-bigsdb-schemas", "-lschemas",
-    nargs="+",
-    action="extend",
-    dest="list_bigsdb_schemas",
-    required=False,
-    default=[],
-    type=str,
-    help="Lists the known schema IDs for a given BIGSdb sequence definition database name"
-)
+    parser.set_defaults(func=run_asynchronously)
 
 async def run(args):
     async with BIGSdbIndex() as bigsdb_index:
         if args.list_dbs:
             known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
-            print(", ".join(known_seqdef_dbs.keys()))
+            print("\n".join(known_seqdef_dbs.keys()))
 
         for bigsdb_schema_name in args.list_bigsdb_schemas:
             schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
@@ -40,4 +42,3 @@ async def run(args):
 def run_asynchronously(args):
     asyncio.run(run(args))
 
-parser.set_defaults(func=run_asynchronously)

src/automlst/cli/meta.py

@@ -0,0 +1,2 @@
+def get_module_base_name(name):
+    return name.split(".")[-1]

src/automlst/cli/profile.py

@@ -1,55 +0,0 @@
-
-import asyncio
-import datetime
-from typing import Any, AsyncGenerator, AsyncIterable, Iterable, Sequence, Union
-from automlst.cli import program
-from automlst.engine.data.genomics import NamedString
-from automlst.engine.data.mlst import MLSTProfile
-from automlst.engine.local.abif import read_abif, reference_consensus_assembly
-from automlst.engine.local.csv import write_mlst_profiles_as_csv
-from automlst.engine.local.fasta import read_fasta, read_multiple_fastas
-from automlst.engine.remote.databases.bigsdb import BIGSdbIndex, BigSDBMLSTProfiler
-
-
-parser = program.subparsers.add_parser(__name__)
-
-parser.add_argument(
-    "--fasta", "-fa", "-fst",
-    nargs="+",
-    action='extend',
-    dest="fastas",
-    required=False,
-    default=[],
-    type=str,
-    help="The FASTA files to process. Multiple can be listed."
-)
-
-parser.add_argument(
-    "seqdefdb",
-    help="The BIGSdb seqdef database to use for typing."
-)
-
-parser.add_argument(
-    "schema",
-    type=int,
-    help="The BIGSdb seqdef database schema ID (integer) to use for typing."
-)
-
-parser.add_argument(
-    "out",
-    default=f'./{datetime.datetime.now().strftime(r"%Y%m%d%H%M%S")}',
-    help="The output CSV name (.csv will be appended)."
-)
-
-
-async def run(args):
-    async with BIGSdbIndex() as bigsdb_index:
-        gen_strings = read_multiple_fastas(args.fastas)
-        async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler:
-            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
-            await write_mlst_profiles_as_csv(mlst_profiles, args.out)
-
-def run_asynchronously(args):
-    asyncio.run(run(args))
-
-parser.set_defaults(func=run_asynchronously)

src/automlst/cli/program.py

@@ -4,6 +4,8 @@ import datetime
 from os import path
 import os
 
+from automlst.cli import exactmatch, info
+from automlst.cli.meta import get_module_base_name
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.local.abif import read_abif
 from automlst.engine.local.csv import write_mlst_profiles_as_csv
@@ -13,10 +15,13 @@ from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
 root_parser = argparse.ArgumentParser()
 subparsers = root_parser.add_subparsers(required=True)
 
+info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
+exactmatch.setup_parser(subparsers.add_parser(get_module_base_name(exactmatch.__name__)))
+
+
 def run():
     args = root_parser.parse_args()
     args.func(args)
 
-
 if __name__ == "__main__":
     run()