From e2f19acd5a9a95fc8303769f4b928fdadfa36d85 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Tue, 18 Feb 2025 16:33:08 +0000
Subject: [PATCH] Updated CLI to follow APIs specified by the 0.12.0 engine

---
 .devcontainer/devcontainer.json | 2 +-
 .gitignore                      | 1 +
 pyproject.toml                  | 2 +-
 requirements.txt                | 2 +-
 src/autobigs/cli/info.py        | 4 +++-
 src/autobigs/cli/st.py          | 2 +-
 6 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 0c8c058..3934211 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -12,7 +12,7 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt",
+	"postCreateCommand": "pip3 install --user -r requirements.txt && pip install -e .",
 	"customizations": {
 		"vscode": {
 			"extensions": [
diff --git a/.gitignore b/.gitignore
index a31886c..eda8c45 100644
--- a/.gitignore
+++ b/.gitignore
@@ -212,3 +212,4 @@ pyrightconfig.json
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
+out.csv
diff --git a/pyproject.toml b/pyproject.toml
index 4c50581..aaf389d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ dynamic = ["version"]
 readme = "README.md"
 license = {file = "LICENSE"}
 dependencies = [
-    "autoBIGS-engine==0.11.*"
+    "autoBIGS-engine==0.12.*"
 ]
 requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
diff --git a/requirements.txt b/requirements.txt
index fad55b5..7b54436 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,4 @@ pytest-cov
 build
 twine
 setuptools_scm
-autoBIGS.engine==0.11.*
+autoBIGS.engine
diff --git a/src/autobigs/cli/info.py b/src/autobigs/cli/info.py
index a990a46..c653c89 100644
--- a/src/autobigs/cli/info.py
+++ b/src/autobigs/cli/info.py
@@ -31,15 +31,17 @@ async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         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):")
             print("\n".join(sorted(known_seqdef_dbs.keys())))
 
         for bigsdb_schema_name in args.list_bigsdb_schemas:
             schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
+            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(f"{schema_desc}: {schema_id}")
 
         if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
-            print("Nothing to do. Try specifying \"-l\".")
+            print("Nothing to do. Try specifying \"-l\" for a list of known databases, or \"-h\" for more information.")
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))
diff --git a/src/autobigs/cli/st.py b/src/autobigs/cli/st.py
index c4f2112..9edec5a 100644
--- a/src/autobigs/cli/st.py
+++ b/src/autobigs/cli/st.py
@@ -53,7 +53,7 @@ async def run(args: Namespace):
             mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
             failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
             if len(failed) > 0:
-                print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}")
+                print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")
             print(f"Completed fetching MLSTs for {len(args.fastas)} sequences.")
 
 def run_asynchronously(args):