Adding index with services included in BioAPI

omics-datascience · Nov 4, 2024 · 0699470 · 0699470
1 parent ba5f1a2
commit 0699470
Show file tree

Hide file tree

Showing 3 changed files with 66 additions and 21 deletions.
diff --git a/README.md b/README.md
@@ -761,7 +761,7 @@ For a given gene, this service gets from the String database a list of genes and
 
 Service that takes gene symbol and returns a link to <https://go.drugbank.com> with all the drugs that upregulate and down regulate its expresion. Useful for embeding.
 
-- URL: drugs-regulating-gene/*gene_id*
+- URL: /drugs-regulating-gene/*gene_id*
   - `gene_id` is the identifier of the gene.
 - Method: GET
 - Params: -
@@ -800,7 +800,7 @@ All kind of contribution is welcome! If you want to contribute just:
 ### Run Flask dev server
 
 1. Start up Docker services like MongoDB: `docker compose -f docker-compose.dev.yml up -d`.
-2. Go to the `bioapi` folder.
+2. Go to the `bio-api` folder.
 3. Run Flask server: `python3 bioapi.py`.
 
 **NOTE:** If you are looking for documentation for a production deployment see [DEPLOYING.md](DEPLOYING.md).

diff --git a/bio-api/bioapi.py b/bio-api/bioapi.py
@@ -643,32 +643,40 @@ def associated_string_genes(gene_symbol: str, min_combined_score: int = 400) ->
     return res
 
 
+# Documentation of included services
+services = [
+    {"name": "Genes symbols validator", "url": "[POST] /gene-symbols"},
+    {"name": "Genes symbols finder", "url": "[GET] /gene-symbols-finder"},
+    {"name": "Genes information", "url": "[POST] /information-of-genes"},
+    {"name": "Gene Groups", "url": "[GET] /genes-of-its-group/<gene_id>"},
+    {"name": "Genes of a metabolic pathway", "url": "[GET] /pathway-genes/<source>/<external_id>"},
+    {"name": "Metabolic pathways from different genes", "url": "[POST] /pathways-in-common"},
+    {"name": "Gene expression", "url": "[POST] /expression-of-genes"},
+    {"name": "Therapies and actionable genes in cancer", "url": "[POST] /information-of-oncokb"},
+    {"name": "Gene Ontology terms related to a list of genes", "url": "[POST] /genes-to-terms"},
+    {"name": "Gene Ontology terms related to another specific term", "url": "[POST] /related-terms"},
+    {"name": "Cancer related drugs", "url": "[POST] /drugs-pharm-gkb"},
+    {"name": "Predicted functional associations network", "url": "[POST] /string-relations"},
+    {"name": "Drugs that regulate a gene", "url": "[GET] /drugs-regulating-gene/<gene_id>"}
+]
+
+
 def create_app():
     # Creates and configures the app
     flask_app = Flask(__name__, instance_relative_config=True)
 
     # Endpoints
     @flask_app.route("/")
     def homepage():
-        return render_template('homepage.html', version=VERSION)
+        # return render_template('index.html', title=f"API v{VERSION}", services=services)
+        return render_template('homepage.html', version=VERSION, services=services)
 
     @flask_app.route("/ping")
     def ping_ok():
         """To use as healthcheck by Docker"""
         output = "ok"
         return make_response(output, 200, headers)
 
-    @flask_app.route("/bioapi-map")
-    def list_routes():
-        """Lists all BioAPI endpoints"""
-        output = {"endpoints": []}
-        for rule in flask_app.url_map.iter_rules():
-            methods = ','.join(rule.methods)
-            line = urllib.parse.unquote(
-                "{:50s} {:20s} {}".format(rule.endpoint, methods, rule))
-            output["endpoints"].append(line)
-        return make_response(output, 200, headers)
-
     @flask_app.route("/gene-symbols", methods=['POST'])
     def gene_symbols():
         """Receives a list of gene IDs in any standard and returns the standardized corresponding gene IDs.

diff --git a/bio-api/templates/homepage.html b/bio-api/templates/homepage.html
@@ -1,17 +1,54 @@
+<!-- templates/index.html -->
 <!DOCTYPE html>
-<html lang="en" dir="ltr">
+<html lang="es">
 <head>
-    <meta charset="utf-8">
-    <title>BioAPI</title>
-
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>BioAPI v{{ version }}</title>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet">
     <style>
         body {
-            background-color: #f5f5f5;
-            font-family: Arial, Helvetica, sans-serif;
+            background-color: #f8f9fa;
+            font-family: Arial, sans-serif;
+            padding-top: 50px;
+            padding: 10px 15px;
+        }
+        .container {
+            max-width: 600px;
+        }
+        h1 {
+            color: #343a40;
+            margin-bottom: 20px;
+        }
+        h2 {
+            color: #6c757d;
+            margin-top: 30px;
+        }
+        .service-list .service-item {
+            padding: 5px 5px;
+            border-bottom: 1px solid #dee2e6;
+            text-align: left; /* Alinea el contenido a la izquierda */
+        }
+        .service-item span {
+            display: block; /* Coloca el nombre y el endpoint en líneas separadas */
+        }
+        .service-item code {
+            color: #6c757d;
+            font-size: 0.9em;
         }
     </style>
 </head>
 <body>
-    <h1>BioAPI {{ version }}</h1>
+    <h1>BioAPI v{{ version }}</h1>
+    <h2 class="mb-4">Servicios incluidos:</h2>
+    <ul class="list-group service-list">
+        {% for service in services %}
+            <li class="service-item">
+                <span>{{ service.name }}</span>
+                <code>{{ service.url }}</code>
+            </li>
+        {% endfor %}
+    </ul>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap/5.3.0/js/bootstrap.bundle.min.js"></script>
 </body>
 </html>