Changing CSV argument to --csv or -o

Jenkinsfile

@@ -32,6 +32,11 @@ pipeline {
         stage("publish") {
             parallel {
                 stage ("git.reslate.systems") {
+                    when {
+                        not {
+                            tag '*.*.*'
+                        }
+                    }
                     environment {
                         CREDS = credentials('username-password-rs-git')
                     }
@@ -41,7 +46,7 @@ pipeline {
                 }
                 stage ("pypi.org") {
                     when {
-                        tag '*.*'
+                        tag '*.*.*'
                     }
                     environment {
                         TOKEN = credentials('pypi.org')

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "autoBIGS.cli"
 dynamic = ["version"]
 readme = "README.md"
-license = {file = "LICENSE"}
+license = {text = "GPL-3.0-or-later"}
 dependencies = [
     "autoBIGS-engine==0.12.*"
 ]
@@ -14,8 +14,8 @@ requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
 [project.urls]
-Repository = "https://github.com/RealYHD/autoBIGS.cli"
+Repository = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli"
-Issues = "https://github.com/RealYHD/autoBIGS.cli/issues"
+Issues = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli/issues"
 
 
 [project.scripts]

src/autobigs/cli/info.py

@@ -1,5 +1,7 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
+import csv
+from os import path
 from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
@@ -24,24 +26,50 @@ def setup_parser(parser: ArgumentParser):
         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(
+        "--csv", "-o",
+        dest="csv_output",
+        required=False,
+        default=None,
+        help="Output list as CSV at a given path. A suffix is added depending on the action taken."
+    )
+
     parser.set_defaults(run=run_asynchronously)
     return parser
 
 async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
+        if args.list_dbs and len(args.list_bigsdb_schemas) > 0:
+            print("Cannot specify both database listing and schema listing, please choose one!")
+            exit(1)
+
         if args.list_dbs:
             known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
-            print("The following are all known BIGS database names (sorted alphabetically):")
+            sorted_seqdef_dbs = [(name, source) for name, source in sorted(known_seqdef_dbs.items())]
-            print("\n".join(sorted(known_seqdef_dbs.keys())))
+            print("The following are all known BIGS database names, and their source (sorted alphabetically):")
+            print("\n".join(["{0}: {1}".format(name, source) for name, source in sorted_seqdef_dbs]))
+            if args.csv_output:
+                with open(args.csv_output, "w") as csv_out_handle:
+                    writer = csv.writer(csv_out_handle)
+                    writer.writerow(("BIGSdb Names", "Source"))
+                    writer.writerows(sorted_seqdef_dbs)
+                    print("\nDatabase output written to {0}".format(args.csv_output))
 
         for bigsdb_schema_name in args.list_bigsdb_schemas:
             schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
+            sorted_schemas = [(name, id) for name, id in sorted(schemas.items())]
             print("The following are the known schemas for \"{0}\", and their associated IDs:".format(bigsdb_schema_name))
-            for schema_desc, schema_id in schemas.items():
+            print("\n".join(["{0}: {1}".format(name, id) for name, id in sorted_schemas]))
-                print(f"{schema_desc}: {schema_id}")
+            if args.csv_output:
+                with open(args.csv_output, "w") as csv_out_handle:
+                    writer = csv.writer(csv_out_handle)
+                    writer.writerow(("Name", "ID"))
+                    writer.writerows(sorted_schemas)
+                    print("\nSchema list output written to {0}".format(args.csv_output))
 
         if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
             print("Nothing to do. Try specifying \"-l\" for a list of known databases, or \"-h\" for more information.")
+            exit(1)
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))

src/autobigs/cli/st.py

@@ -50,7 +50,7 @@ async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         gen_strings = read_multiple_fastas(args.fastas)
         async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler:
-            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, args.stop_on_fail)
             failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
             if len(failed) > 0:
                 print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")