fix build context.

.github/workflows/deploy_release_software.yml

@@ -28,5 +28,6 @@ jobs:
       uses: docker/build-push-action@v4
       with:
         file: deployment/dockerhub/Dockerfile
+        context: seqcolapi
         push: true
         tags: databio/seqcolapi:latest

README_seqcolapi.md

@@ -3,7 +3,7 @@
 This repository contains:
 
 1. Sequence collections API software (the `seqcolapi` package). This package is based on the `refget` package. It simply provides an wrapper to implement the Sequence Collections API.
-2. Configuration and GitHub Actions for demo server instance ([servers subfolder](/servers)).
+2. Configuration and GitHub Actions for demo server instance ([deployment subfolder](/deployment)).
 
 ## Instructions
 

load_demo_data.py

@@ -4,7 +4,10 @@
 from refget.models import *
 from refget.agents import *
 
+
+
 dbc = RefgetDBAgent()
+print(f"SQL Engine: {dbc.engine}")
 
 fa_root="test_fasta"
 
@@ -20,36 +23,33 @@
 
 
 
+# import json
+# from refget import SeqColClient
 
-import json
-from refget import SeqColClient
-
-template = """
-Filepath: {f}
-Digest: {digest}
-Object:
-{pretty_str}
-"""
-
-scc = SeqColClient("http://127.0.0.1:8100")
-scc.get_collection(digest)
-
-for demo_file in DEMO_FILES:
-    f = os.path.join(fa_root, demo_file)
-    print("Fasta file to be loaded: {}".format(f))
-    digest = refget.fasta_file_to_digest(f, dbc.inherent_attrs)
-    seqcol = scc.get_collection(digest)
-    pretty_str = json.dumps(
-        seqcol,
-        separators=(",", ":"),
-        ensure_ascii=False,
-        allow_nan=False,
-        sort_keys=True,
-        indent=2,
-    )
-    print(template.format(f=f, digest=digest, pretty_str=pretty_str))
+# template = """
+# Filepath: {f}
+# Digest: {digest}
+# Object:
+# {pretty_str}
+# """
 
+# scc = SeqColClient("http://127.0.0.1:8100")
+# scc.get_collection(digest)
 
+# for demo_file in DEMO_FILES:
+#     f = os.path.join(fa_root, demo_file)
+#     print("Fasta file to be loaded: {}".format(f))
+#     digest = refget.fasta_file_to_digest(f, dbc.inherent_attrs)
+#     seqcol = scc.get_collection(digest)
+#     pretty_str = json.dumps(
+#         seqcol,
+#         separators=(",", ":"),
+#         ensure_ascii=False,
+#         allow_nan=False,
+#         sort_keys=True,
+#         indent=2,
+#     )
+#     print(template.format(f=f, digest=digest, pretty_str=pretty_str))
 
 
 # demo_results = {}

tests/conftest.py

@@ -40,7 +40,7 @@ def schema_path():
 def fa_root():
     return os.path.join(
         os.path.join(os.path.dirname(os.path.abspath(__file__)), os.pardir),
-        "demo_fasta",
+        "test_fasta",
     )