Cleanup

Author: nichtich

.dockerignore

@@ -16,3 +16,4 @@ package-lock.json
 # local files
 config.yaml
 stage
+queries

README.md

@@ -64,17 +64,9 @@ A local file `config.yaml` is needed with configuration. See [`config.example.ya
 
 In addition the following environment variables can be used:
 
+- `SPARQL`: backend API endpoint. Default: `http://localhost:3030/n4o/`
 - `STAGE`: readable stage directory. Default: `stage`
-
-### SPARQL
-
-The default configuration expects a SPARL endpoint at <http://localhost:3030/n4o/>. This can be provided with Fuseki triple store and a database `n4o` locally created like this:
-
-~~~sh
-curl --data "dbName=n4o&dbType=tdb2" http://localhost:3030/$/datasets
-~~~
-
-Alternatively use the preconfigured Docker container [n4o-fuseki](https://github.com/nfdi4objects/n4o-fuseki#readme).
+- `QUERIES`: directory with sample SPARQL queries with file extension `.rq`. Default: `queries`
 
 The RDF database is expected to be grouped in named graphs:
 
@@ -84,7 +76,7 @@ The RDF database is expected to be grouped in named graphs:
 - Graphs `http://bartoc.org/en/node/X` where X is an integer contain information from individual terminologies
 - The default graph must be configured as union graph.
 
-See [n4o-graph-importer](https://github.com/nfdi4objects/n4o-graph-importer#readme) for a component to ensure RDF data is only imported into the triple store as expected.
+See [n4o-fuseki](https://github.com/nfdi4objects/n4o-fuseki#readme) for preconfigured Triple store and [n4o-graph-importer](https://github.com/nfdi4objects/n4o-graph-importer#readme) for a component to ensure RDF data is only imported into the triple store as expected.
 
 ### Tools
 
@@ -140,6 +132,8 @@ To locally build the Docker image run `make docker`. The container is named `n4o
 docker run --rm --net=host -p 8000:8000 -v ./config.yaml:/app/config.yaml:ro n4o-graph-apis
 ~~~
 
+To use custom queries, mount your local directory to `/app/queries`
+
 ## License
 
 MIT License

app.py

@@ -37,7 +37,7 @@ def jsonify(data, status=200, indent=3, sort_keys=False):
 def render(template, **vars):
     # TODO: better title?
     title = template.split(".")[0]
-    return render_template(template, title=title, githash=app.config["githash"], **vars)
+    return render_template(template, title=title, **vars)
 
 
 @app.errorhandler(ApiError)
@@ -95,10 +95,10 @@ def terminology():
     return render('terminologies.html')
 
 
-@app.route('/repository')
-@app.route('/repository/')
-def repository():
-    return render('repositories.html')
+@app.route('/mappings')
+@app.route('/mappings/')
+def mappings():
+    return render('mappings.html')
 
 
 @app.route('/collection', defaults={'id': None, 'path': None})
@@ -156,9 +156,6 @@ def collection(id, path):
                 format = "turtle"
                 mimetype = "text/turtle"
 
-        print("Format, mimetype")
-        print(format, mimetype)
-
         response = make_response("Not found", 404)
         response.mimetype = "text/plain"
         if len(graph) > 0:
@@ -175,7 +172,7 @@ def sparql_api():
 
 @app.route('/sparql')
 def sparql_form():
-    return render('sparql.html', **config["sparql"])
+    return render('sparql.html', **config)
 
 
 @app.route('/tools')
@@ -192,7 +189,7 @@ def init(**config):
     for key in config.keys():
         app.config[key] = config[key]
 
-    endpoint = config["sparql"]["endpoint"]
+    endpoint = config["sparql"]
     app.config["sparql-proxy"] = SparqlProxy(endpoint, config["debug"])
 
     stage = config.get("stage")

config.example.yaml

@@ -1,17 +1,6 @@
 # run in debug mode to emit more debugging information
 debug: false
 
-# SPARQL endpoint and examples (required)
-sparql:
-  endpoint: http://localhost:3030/n4o
-  examples:
-    # examples given in files
-    - queries/*.rq
-    # example given in config file
-    - name: List all classes
-      query: |
-        SELECT DISTINCT ?class WHERE { [] a ?class }  examples:
-
 # Links to tools and references (optional)
 tools:
   - name: LIDO-Schulung

lib/config.py

@@ -1,25 +1,21 @@
 from collections import UserDict
 import yaml
+from pathlib import Path
 import glob
 import re
 import os
 import subprocess
 
 
-def extend_examples(api):
-    if "examples" in api:
-        extended = []
-        for ex in api["examples"]:
-            if isinstance(ex, str):
-                for file in glob.glob(ex):
-                    lines = open(file).read().split("\n")
-                    name = re.sub(r"^#\s*", "", lines[0])
-                    extended.append({"name": name, "query": "\n".join(lines)})
-            else:
-                extended.append(ex)
-        api["examples"] = extended
-    else:
-        api["examples"] = []
+def get_queries(path):
+    path = Path(path)
+    queries = []
+    if path.is_dir():
+        for file in path.glob('*.rq'):
+            lines = open(file).read().split("\n")
+            name = re.sub(r"^#\s*", "", lines[0])
+            queries.append({"name": name, "query": "\n".join(lines)})
+    return queries
 
 
 class Config(UserDict):
@@ -38,35 +34,15 @@ def __init__(self, file=None, debug=False):
         else:
             self.data = {}
 
-        if not self.get("stage", None):
-            self.data["stage"] = os.getenv('STAGE', 'stage')
-        if not self.data.get("sparql", None):
-            self.data["sparql"] = {
-                "endpoint": os.getenv('SPARQL', "http://localhost:3030/n4o")
-            }
+        self.data["stage"] = os.getenv('STAGE', 'stage')
+        self.data["sparql"] = os.getenv('SPARQL', "http://localhost:3030/n4o")
 
         if debug:
             self.data["debug"] = True
         elif "debug" not in self.data:
             self.data["debug"] = False
 
-        if "import" in self.data:
-            for name in ["collections", "terminologies"]:
-                if name in self.data["import"]:
-                    path = self.data["import"][name]
-                    if not os.path.isdir(path):
-                        raise Exception(f"Missing {name} path: {path}")
-        else:
-            self.data["import"] = {}
-
-        extend_examples(self.data["sparql"])
+        self.data["queries"] = get_queries(os.getenv('QUERIES', 'queries'))
 
         if "tools" not in self.data:
             self.data["tools"] = []
-
-        try:
-            self.data["githash"] = subprocess.run(['git', 'rev-parse', '--short=8', 'HEAD'],
-                                                  stdout=subprocess.PIPE).stdout.decode('utf-8').strip()
-        except Exception:
-            self.data["githash"] = None
-            pass

templates/base.html

@@ -13,7 +13,6 @@
     <script src="{{url_for('static',filename='codemirror/codemirror.js')}}"></script>
     <script src="{{url_for('static',filename='codemirror/runmode.js')}}"></script>
     <script src="{{url_for('static',filename='codemirror/javascript.js')}}"></script>
-    <script src="{{url_for('static',filename='codemirror/pg.js')}}"></script>
     <script src="{{url_for('static',filename='common.js')}}"></script>
     <meta name="msapplication-TileImage" content="{{url_for('static',filename='nfdi4objects-logo.png')}}" />
     <title>N4O Graph: {{title}}</title>
@@ -50,10 +49,10 @@
           			{% endif %}
         			</li>
         			<li>
-          			{% if request.path.startswith("/repository") %}
-            		<a href="{{url_for('repository')}}"><span><strong>Repositories</strong></span></a>
+          			{% if request.path.startswith("/mappings") %}
+            		<a href="{{url_for('mappings')}}"><span><strong>Mappings</strong></span></a>
           			{% else %}
-            		<a href="{{url_for('repository')}}"><span>Repositories</span></a>
+            		<a href="{{url_for('mappings')}}"><span>Mappings</span></a>
           			{% endif %}
         			</li>
         			{% if config.tools %}
@@ -80,9 +79,6 @@
       <div style="float:right;">
         web interface:
         <a href="https://github.com/nfdi4objects/n4o-graph-apis">sources</a>
-        {% if githash %} 
-        (<a href="https://github.com/nfdi4objects/n4o-graph-apis/commit/{{ githash }}">{{ githash }}</a>)
-        {% endif %}
         |
         <a href="https://github.com/nfdi4objects/n4o-graph-apis/issues">issues</a>
       </div>

templates/examples.html

@@ -2,8 +2,7 @@
 
 {% block content %}
   <p>
-    Data about <a href="/collection/">collections</a> and
-    <a href="/repository/">repositories</a> can be used freely without
+    Data about <a href="/collection/">collections</a> and can be used freely without
     any restrictions (<a href="https://creativecommons.org/publicdomain/zero/1.0/">CC Zero</a>).
   </p>
   <p>

templates/license.html

@@ -4,7 +4,9 @@
 
 <script src="{{url_for('static',filename='yasr.min.js')}}"></script>
 
-<p>
+<p>This page needs to be filled.</p>
+
+<!--p>
   All research data in the knowledge graph must be published in a trusted
   research data repository. These include selected repositories listed in
   <a href="https://www.re3data.org/">re3data</a> and some repositories of
@@ -24,6 +26,6 @@
       OPTIONAL { ?repo foaf:homepage ?url }
     }
   }
-} GROUP BY ?repo ?url"></div>
+} GROUP BY ?repo ?url"></div-->
 
 {% endblock %}

templates/repositories.html templates/mappings.htmltemplates/repositories.html renamed to templates/mappings.html

@@ -1,20 +1,25 @@
 {% extends 'base.html' %}
 
 {% block content %}
- <script src="{{url_for('static',filename='yasr.min.js')}}"></script>
- <script src="{{url_for('static',filename='yasqe.min.js')}}"></script>
- <script src="{{url_for('static',filename='sparql-gui.js')}}"></script>
+<script src="{{url_for('static',filename='yasr.min.js')}}"></script>
+<script src="{{url_for('static',filename='yasqe.min.js')}}"></script>
+<script src="{{url_for('static',filename='sparql-gui.js')}}"></script>
 
-  {% if 'examples' in config.sparql %}
-    {% set examples = config.sparql.examples %}
-    {% include 'examples.html' %}
-  {% endif %}
+<div style="float:right;">
+  <label for="examples">Example queries:</label>
+  <select id="examples">
+    <option value="">Please select!</option>
+    {% for q in config.queries %}
+      <option value="{{q.query}}">{{q.name}}</option>
+    {% endfor %}
+  </select>
+</div>
 
-  <p>
-    SPARQL endpoint <code>/api/sparql</code>
-    (see <a href="https://www.w3.org/TR/2013/REC-sparql11-protocol-20130321/#query-operation">documentation</a>)
-  </p>
+ <p>
+   SPARQL endpoint <code>/api/sparql</code>
+   (see <a href="https://www.w3.org/TR/2013/REC-sparql11-protocol-20130321/#query-operation">documentation</a>)
+ </p>
 
-  <div id="yasqe"></div>
-  <div id="yasr"></div>
+ <div id="yasqe"></div>
+ <div id="yasr"></div>
 {% endblock %}