Fixed scheme name argument not converting to ID

Added additional error messages to help user with usage.

.devcontainer/Dockerfile

@@ -0,0 +1,16 @@
+FROM mcr.microsoft.com/devcontainers/miniconda:1-3
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment to install a different version of Python than the default
+# RUN conda install -y python=3.6 \
+#     && pip install --no-cache-dir pipx \
+#     && pipx reinstall-all
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -1,9 +1,11 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/python
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
 {
-	"name": "Python 3",
+	"name": "Miniconda (Python 3)",
-	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"build": { 
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	},
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -12,7 +14,9 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt --pre && pip install -e .",
+	"postCreateCommand": "pip install -e .",
+
+	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
 			"extensions": [
@@ -20,8 +24,6 @@
 			]
 		}
 	},
-	// Configure tool-specific properties.
-	// "customizations": {},
 
 	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
 	// "remoteUser": "root"

.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file is copied into the container along with environment.yml* from the
+parent folder. This is done to prevent the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

Jenkinsfile

@@ -9,6 +9,8 @@ pipeline {
     stages {
         stage("install") {
             steps {
+                sh 'conda config --add channels bioconda'
+                sh 'conda config --add channels https://git.reslate.systems/api/packages/ydeng/conda'
                 sh 'conda env update -n base -f environment.yml'
             }
         }

src/autobigs/cli/st.py

@@ -57,17 +57,28 @@ async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         gen_strings = read_multiple_fastas(args.fastas)
         scheme_id_lookup = await bigsdb_index.get_schemes_for_seqdefdb(args.seqdefdb)
-        scheme_id = args.scheme_id or args.scheme_name or (scheme_id_lookup)["MLST"]
         scheme_name_lookup = {value: key for key, value in scheme_id_lookup.items()}
+        known_dbs = await bigsdb_index.get_known_seqdef_dbs()
 
-        async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, scheme_id) as mlst_profiler:
+        if args.seqdefdb not in known_dbs:
+            raise ValueError("\"{0}\" is a known database. See -h for help.")
+        if args.scheme_id and args.scheme_id not in scheme_id_lookup.values():
+            raise ValueError("ID {0} not a known database scheme ID for database \"{1}\". See -h for help.".format(args.scheme_id, args.seqdefdb))
+        if args.scheme_name and args.scheme_name not in scheme_id_lookup:
+            raise ValueError("\"{0}\" not a known database scheme name for database \"{1}\". See -h for help.".format(args.scheme_name, args.seqdefdb))
+        if not (args.scheme_name or args.scheme_id) and "MLST" not in scheme_id_lookup:
+            raise ValueError("\"MLST\" not a known database scheme name for database \"{0}\". See -h for help.".format(args.seqdefdb))
+
+        selected_scheme_id = args.scheme_id or (scheme_id_lookup[args.scheme_name] if args.scheme_name else None) or scheme_id_lookup["MLST"]
+
+        async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, selected_scheme_id) as mlst_profiler:
             if not isinstance(mlst_profiler, BIGSdbMLSTProfiler):
                 raise TypeError("MLST profiler type invalid")
             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)}")
-            print(f"Completed fetching from {args.seqdefdb} for {scheme_name_lookup[scheme_id]}s for {len(args.fastas)} sequences.")
+            print(f"Completed fetching from {args.seqdefdb} for {scheme_name_lookup[selected_scheme_id]}s for {len(args.fastas)} sequences.")
 
 def run_asynchronously(args):
     asyncio.run(run(args))