Updated docs & deleted untracked files

.docker/.env

-# Example values to override for non-test deployments
-
-#BASE_URL=https://example.com
-#ADMIN_EMAIL=noreply@example.com
-#LOG_LEVEL=info
-#IDENTITY_SERVICE_ADMIN_PASSWORD=admin
-#AUTH_SERVICE_ADMIN_PASSWORD=admin
-#METADATA_DB_PASSWORD=dbrepo
-#DATA_DB_PASSWORD=dbrepo
-#AUTH_DB_PASSWORD=dbrepo
-#S3_ACCESS_KEY_ID=seaweedfsadmin
-#S3_SECRET_ACCESS_KEY=seaweedfsadmin
-#SYSTEM_PASSWORD=admin

.docs/concepts/index.md

@@ -18,10 +18,10 @@ environments.
 ## Architecture
 
 The repository is designed as a service-based architecture to ensure scalability and the utilization of various
-technologies. The conceptualized microservices operate the basic database operations, data versioning as well as
+technologies. The conceptualized microservices (c.f. [Fig. 1](#fig1)) operate the basic database operations, data versioning as well as
 *findability*, *accessability*, *interoperability* and *reuseability* (FAIR).
 
-<figure markdown>
+<figure id="fig1" markdown>
 ![DBRepo architecture](../images/architecture-docker-compose.svg)
-<figcaption>Architecture of the services deployed via Docker Compose</figcaption>
+<figcaption>Fig. 1: Architecture of the services deployed via Docker Compose</figcaption>
 </figure>
\ No newline at end of file

.docs/stylesheets/extra.css

 :root,
 [data-md-color-accent=indigo] {
-  --md-hue: 230;
-  --md-default-bg-color: hsla(230, 15%, 21%, 1);
   --md-primary-fg-color: #006699;
   --md-accent-fg-color: #005c8a;
   /* darken 10% */
   --md-primary-fg-color--dark: #00537c;
   /* darken 10% */ }
 
+[data-md-color-scheme="slate"] {
+  --md-hue: 230;
+  --md-default-bg-color: hsla(230, 15%, 21%, 1); }
+
 img.img-border {
   border: 1px solid #b3b3b3; }
 
@@ -30,3 +32,5 @@ img.img-border {
 
 .md-banner {
   background-color: var(--md-primary-fg-color--dark); }
+
+/*# sourceMappingURL=extra.css.map */

.docs/stylesheets/extra.css.map

 {
 "version": 3,
-"mappings": "AAAA;6BAC8B;EAC5B,qBAAqB,CAAC,QAAQ;EAC9B,oBAAoB,CAAC,QAAQ;EAAE,gBAAgB;EAC/C,2BAA2B,CAAC,QAAQ;EAAE,gBAAgB;;AAGxD,cAAe;EACb,MAAM,EAAE,iBAAiB;;AAG3B,yCAA0C;EACxC,KAAK,EAAE,gBAAgB;;AAIvB,oGACQ;EACN,KAAK,EAAE,gCAAgC;EACvC,UAAU,EAAE,OAAO;;AAIvB;0DAC2D;EACzD,KAAK,EAAE,0BAA0B;EACjC,aAAa,EAAE,oCAAoC;EAEnD;;kEACQ;IACN,KAAK,EAAE,gCAAgC;IACvC,aAAa,EAAE,0CAA0C;;AAK7D,UAAW;EACT,gBAAgB,EAAE,gCAAgC",
+"mappings": "AAAA;6BAC8B;EAC5B,qBAAqB,CAAC,QAAQ;EAC9B,oBAAoB,CAAC,QAAQ;EAAE,gBAAgB;EAC/C,2BAA2B,CAAC,QAAQ;EAAE,gBAAgB;;AAGxD,8BAA+B;EAC7B,QAAQ,CAAC,IAAI;EACb,qBAAqB,CAAC,uBAAuB;;AAG/C,cAAe;EACb,MAAM,EAAE,iBAAiB;;AAG3B,yCAA0C;EACxC,KAAK,EAAE,gBAAgB;;AAIvB,oGACQ;EACN,KAAK,EAAE,gCAAgC;EACvC,UAAU,EAAE,OAAO;;AAIvB;0DAC2D;EACzD,KAAK,EAAE,0BAA0B;EACjC,aAAa,EAAE,oCAAoC;EAEnD;;kEACQ;IACN,KAAK,EAAE,gCAAgC;IACvC,aAAa,EAAE,0CAA0C;;AAK7D,UAAW;EACT,gBAAgB,EAAE,gCAAgC",
 "sources": ["extra.scss"],
 "names": [],
 "file": "extra.css"

.docs/stylesheets/extra.scss

 :root,
 [data-md-color-accent=indigo] {
-  --md-hue: 230;
-  --md-default-bg-color: hsla(230, 15%, 21%, 1);
   --md-primary-fg-color: #006699;
   --md-accent-fg-color: #005c8a; /* darken 10% */
   --md-primary-fg-color--dark: #00537c; /* darken 10% */
 }
 
+[data-md-color-scheme="slate"] {
+  --md-hue: 230;
+  --md-default-bg-color: hsla(230, 15%, 21%, 1);
+}
+
 img.img-border {
   border: 1px solid #b3b3b3;
 }

.gitignore

@@ -55,9 +55,8 @@ fda-ui/
 # Generated
 ready
 
-# crt
+# Certificates
 *.crt
-*.key
 *.p12
 
 # Environment

dbrepo-search-service/.gitignore

@@ -7,16 +7,10 @@ __pycache__/
 *.so
 
 # Generated
+/clients/
 coverage.txt
 report.xml
-clients/
-omlib/
-
-# Libraries
-./lib/dbrepo-1.4.4*
-./lib/dbrepo-1.4.5*
-./lib/dbrepo-1.4.6*
-./lib/dbrepo-1.4.7rc*
+/omlib/
 
 # Distribution / packaging
 .Python

dbrepo-search-service/app.py

+import logging
 import math
 import os
-import logging
-from ast import literal_eval
 from json import dumps
 from typing import List, Any
 
 import requests
+from clients.keycloak_client import User, KeycloakClient
+from clients.opensearch_client import OpenSearchClient
 from dbrepo.api.dto import Database, ApiError
 from flasgger import LazyJSONEncoder, Swagger, swag_from
 from flask import Flask, request
 from flask_cors import CORS
 from flask_httpauth import HTTPTokenAuth, HTTPBasicAuth, MultiAuth
 from jwt.exceptions import JWTDecodeError
-from opensearchpy import TransportError, NotFoundError
+from opensearchpy import NotFoundError
 from prometheus_flask_exporter import PrometheusMetrics
 from pydantic import ValidationError
 
-from clients.keycloak_client import User, KeycloakClient
-from clients.opensearch_client import OpenSearchClient
-
 logging.addLevelName(level=logging.NOTSET, levelName='TRACE')
 logging.basicConfig(level=logging.DEBUG)
 

dbrepo-search-service/init/.gitignore

-# Libraries
-./lib/dbrepo-1.4.4*
-./lib/dbrepo-1.4.5*
-./lib/dbrepo-1.4.6*
-./lib/dbrepo-1.4.7rc*
\ No newline at end of file

dbrepo-search-service/init/Pipfile

@@ -9,7 +9,7 @@ opensearch-py = "~=2.2"
 python-dotenv = "~=1.0"
 testcontainers-opensearch = "*"
 pytest = "*"
-dbrepo = {path = "./lib/dbrepo-1.5.0.tar.gz"}
+dbrepo = {path = "./lib/dbrepo-1.5.1.tar.gz"}
 rdflib = "*"
 
 [dev-packages]

mkdocs.yml

@@ -17,7 +17,6 @@ nav:
   - Concepts:
     - Overview: concepts/index.md
     - Authentication: concepts/authentication.md
-    - Database: concepts/database.md
     - Messaging: concepts/messaging.md
     - Monitoring: concepts/monitoring.md
     - Persistent Identifier: concepts/pid.md