From 64e78f452932c7fddde9580d8a7a0149ec6d34d0 Mon Sep 17 00:00:00 2001
From: Dario <d.eltzner@gmx.de>
Date: Mon, 19 Aug 2024 18:52:44 +0200
Subject: [PATCH] example configs + compose

---
 docker-compose.yml           | 42 ++++++++++++++++++----------
 examples/compose-config.json | 53 ++++++++++++++++++++++++++++++++++++
 examples/config.json         |  2 +-
 3 files changed, 82 insertions(+), 15 deletions(-)
 create mode 100644 examples/compose-config.json

diff --git a/docker-compose.yml b/docker-compose.yml
index 3145ed6f..affac9cb 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,22 +1,36 @@
+configs:
+  model-polisher-config:
+    # you may want to adapt this your config
+    - file: ./examples/config.json
+  
 services:
 
+  polisher:
+    image: mephenor/modelpolisher:2.1-beta
+    depends_on:
+      - biggdb
+      - adb
+    configs:
+      - source: model-polisher-config
+        target: /config.json
+    command: ['--config-file', '/config.json']
+    volumes:
+      # you may want to adapt these to your local input
+      # and output directories
+      - "input:/input-dir"
+      - "output:/output-dir"
+
   biggdb:
     image: schmirgel/bigg_db:1.6
-    container_name: modelpolisher_biggdb
-    ports:
-      - 127.0.0.1:1310:5432
+    hostname: bigg
+    networks:
+      - dbs
 
   adb:
     image: schmirgel/annotatedb:0.1.1
-    container_name: modelpolisher_adb
-    ports:
-      - 127.0.0.1:1013:5432
+    hostname: adb
+    networks:
+      - dbs
 
-  polisher:
-    image: mephenor/modelpolisher:2.1-beta
-    depends_on:
-      - biggdb
-      - adb
-    container_name: modelpolisher_java
-    stdin_open: true
-    tty: true
+networks:
+  - dbs
diff --git a/examples/compose-config.json b/examples/compose-config.json
new file mode 100644
index 00000000..1fdbc7a1
--- /dev/null
+++ b/examples/compose-config.json
@@ -0,0 +1,53 @@
+{
+    "input": "input-dir",
+    "output": "output-dir",
+    "output-type": "xml",
+    
+    "fixing": {
+	"dont-fix": false,
+	"fix-flux-objectives": {
+	    "flux-coefficients": [],
+	    "flux-objectives": []
+	}
+    },
+    
+    "polishing": {
+	"polish-even-if-model-invalid": false
+    },
+    
+    "annotation": {
+	"bigg": {
+	    "annotate-with-bigg": true,
+	    "include-any-uri": true,
+	    "document-title-pattern": "[biggId] - [organism]",
+	    "notes": {
+		"no-model-notes": true,
+		"model-notes-file": null,
+		"document-notes-file": null
+	    },
+	    "db-config": {
+		"db-name": "bigg",
+		"host": "bigg",
+		"password": "postgres",
+		"user": "postgres",
+		"port": 5432
+	    }
+	},
+	"annotatedb": {
+	    "annotate-with-adb": true,
+	    "db-config": {
+		"db-name": "adb",
+		"host": "adb",
+		"password": "postgres",
+		"user": "postgres",
+		"port": 5432
+	    }
+	}
+    },
+    
+    "sbo-terms": {
+	"add-generic-terms": false
+    },
+    
+    "sbml-validation": false
+}
diff --git a/examples/config.json b/examples/config.json
index 18768283..f82a4273 100644
--- a/examples/config.json
+++ b/examples/config.json
@@ -1,5 +1,5 @@
 {
-    "input": "examples",
+    "input": "examples/input",
     "output": "examples/output",
     "output-type": "xml",