Merge pull request #107 from ScilifelabDataCentre/develop

Frontend testing and bug fixing

Dockerfiles/Dockerfile.frontend.dev

@@ -2,7 +2,8 @@ FROM node:14-alpine
 
 RUN yarn global add @quasar/cli
 
-COPY .frontend/package.json /package.json
+COPY ./frontend/package.json /package.json
+COPY ./frontend/yarn.lock /yarn.lock
 RUN yarn install
 
 ADD ./frontend  /code/

backend/collection.py

@@ -82,17 +82,23 @@ def add_collection():
     if not validation.result:
         flask.abort(status=validation.status)
 
-    # add current user to editors if no editors are defined
     if not indata.get("editors"):
         indata["editors"] = [flask.g.current_user["_id"]]
+    # add current user if missing and only DATA_EDIT
+    elif (
+        not utils.req_has_permission("DATA_MANAGEMENT")
+        and str(flask.g.current_user["_id"]) not in indata["editors"]
+    ):
+        indata["editors"].append(flask.g.current_user["_id"])
+
+    # convert all incoming uuids to uuid.UUID
+    indata = utils.prepare_for_db(indata)
 
     # convert entries to uuids
     for field in ("datasets", "editors"):
         if field in indata:
             indata[field] = [utils.str_to_uuid(value) for value in indata[field]]
 
-    collection["description"] = utils.secure_description(collection["description"])
-
     collection.update(indata)
 
     # add to db
@@ -177,14 +183,22 @@ def update_collection(identifier):
     if not validation.result:
         flask.abort(status=validation.status)
 
+    # DATA_EDIT may not delete itself from editors
+    if (
+        not utils.req_has_permission("DATA_MANAGEMENT")
+        and indata.get("editors")
+        and str(flask.g.current_user["_id"]) not in indata["editors"]
+    ):
+        flask.abort(status=400)
+
+    # convert all incoming uuids to uuid.UUID
+    indata = utils.prepare_for_db(indata)
+
     # convert entries to uuids
     for field in ("datasets", "editors"):
         if field in indata:
             indata[field] = [utils.str_to_uuid(value) for value in indata[field]]
 
-    if "description" in indata:
-        indata["description"] = utils.secure_description(indata["description"])
-
     is_different = False
     for field in indata:
         if indata[field] != collection[field]:

backend/dataset.py

@@ -227,35 +227,31 @@ def build_dataset_info(identifier: str):
     Returns:
         dict: The prepared dataset entry.
     """
-    try:
-        dataset_uuid = utils.str_to_uuid(identifier)
-    except ValueError:
-        return None
-    dataset = flask.g.db["datasets"].find_one({"_id": dataset_uuid})
+    dataset = utils.req_get_entry("datasets", identifier)
     if not dataset:
         return None
-    order = flask.g.db["orders"].find_one({"datasets": dataset_uuid})
+    order = flask.g.db["orders"].find_one({"datasets": dataset["_id"]})
+    if flask.g.current_user:
+        curr_user = flask.g.current_user["_id"]
+    else:
+        curr_user = None
 
-    if (
-        utils.req_has_permission("DATA_MANAGEMENT")
-        or flask.g.db.current_user["id"] in order["editors"]
-    ):
-        dataset["order"] = order["_id"]
+    if utils.req_has_permission("DATA_MANAGEMENT") or curr_user in order["editors"]:
+        dataset["order"] = {"_id": order["_id"], "title": order["title"]}
     dataset["related"] = list(
         flask.g.db["datasets"].find({"_id": {"$in": order["datasets"]}}, {"title": 1})
     )
     dataset["related"].remove({"_id": dataset["_id"], "title": dataset["title"]})
     dataset["collections"] = list(
-        flask.g.db["projects"].find({"datasets": dataset_uuid}, {"title": 1})
+        flask.g.db["collections"].find({"datasets": dataset["_id"]}, {"title": 1})
     )
     for field in ("editors", "generators", "authors"):
         if field == "editors" and (
-            not utils.req_has_permission("DATA_MANAGEMENT")
-            and flask.g.db.current_user["id"] not in order[field]
+            not utils.req_has_permission("DATA_MANAGEMENT") and curr_user not in order[field]
         ):
             continue
         dataset[field] = utils.user_uuid_data(order[field], flask.g.db)
 
-    dataset["organisation"] = utils.user_uuid_data(order[field], flask.g.db)
+    dataset["organisation"] = utils.user_uuid_data(order["organisation"], flask.g.db)
     dataset["organisation"] = dataset["organisation"][0] if dataset["organisation"] else ""
     return dataset

backend/order.py

@@ -136,7 +136,7 @@ def add_order():
     # add current user if missing and only DATA_EDIT
     elif (
         not utils.req_has_permission("DATA_MANAGEMENT")
-        and flask.g.current_user["_id"] not in indata["editors"]
+        and str(flask.g.current_user["_id"]) not in indata["editors"]
     ):
         indata["editors"].append(flask.g.current_user["_id"])
 

backend/tests/test_datasets.py

@@ -102,7 +102,7 @@ def test_get_dataset(mdb):
       * Confirm that the dataset is not listed in ``related``
     """
     session = requests.Session()
-    for _ in range(10):
+    for _ in range(2):
         orig = mdb["datasets"].aggregate([{"$sample": {"size": 1}}]).next()
         response = helpers.make_request(session, f'/api/v1/dataset/{orig["_id"]}')
         assert response[1] == 200

backend/validate.py

@@ -187,7 +187,7 @@ def validate_orcid(data: str) -> bool:
     """
     if not isinstance(data, str):
         raise ValueError(f"Not a str ({data})")
-    if not ORCID_REGEX.fullmatch(data):
+    if data and not ORCID_REGEX.fullmatch(data):
         raise ValueError(f"Not an orcid ({data})")
     return True
 

docs/build/html/code.app.html

@@ -148,6 +148,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.collection.html

@@ -149,6 +149,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.config.html

@@ -100,6 +100,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.dataset.html

@@ -164,6 +164,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.db_management.html

@@ -116,6 +116,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.developer.html

@@ -160,6 +160,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.migrations.html

@@ -51,6 +51,15 @@
 </ul>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="migrations.migrate_v2_to_v3">
+<span class="sig-prename descclassname"><span class="pre">migrations.</span></span><span class="sig-name descname"><span class="pre">migrate_v2_to_v3</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">db</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="modules/migrations.html#migrate_v2_to_v3"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#migrations.migrate_v2_to_v3" title="Permalink to this definition">¶</a></dt>
+<dd><p>Update the database fields to match the changes in the data structure.</p>
+<ul class="simple">
+<li><p>Remove the <code class="docutils literal notranslate"><span class="pre">DATA_LIST</span></code> and <code class="docutils literal notranslate"><span class="pre">STATISTICS</span></code> permissions from all users.</p></li>
+</ul>
+</dd></dl>
+
 </div>
 
 
@@ -80,6 +89,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.order.html

@@ -198,6 +198,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.schema.html

@@ -126,6 +126,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.structure.html

@@ -135,6 +135,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.user.html

@@ -295,6 +295,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.utils.html

@@ -752,6 +752,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/code.validate.html

@@ -367,6 +367,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/development.html

@@ -42,6 +42,11 @@ <h1>Development<a class="headerlink" href="#development" title="Permalink to thi
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html#add-test-data">Add test data</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="development.testing.html">Testing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html#backend">Backend</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html#frontend">Frontend</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">Code reference</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="code.app.html">app.py</a></li>
 <li class="toctree-l2"><a class="reference internal" href="code.collection.html">collection.py</a></li>
@@ -89,6 +94,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Development</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="development.quick_environment.html">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>

docs/build/html/development.quick_environment.html

@@ -14,7 +14,7 @@
     <script src="static/doctools.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Code reference" href="modules.html" />
+    <link rel="next" title="Testing" href="development.testing.html" />
     <link rel="prev" title="Development" href="development.html" />
 
   <link rel="stylesheet" href="static/custom.css" type="text/css" />
@@ -88,6 +88,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="development.html">Development</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">System for development</a></li>
+<li class="toctree-l2"><a class="reference internal" href="development.testing.html">Testing</a></li>
 <li class="toctree-l2"><a class="reference internal" href="modules.html">Code reference</a></li>
 </ul>
 </li>
@@ -99,7 +100,7 @@ <h3>Related Topics</h3>
   <li><a href="index.html">Documentation overview</a><ul>
   <li><a href="development.html">Development</a><ul>
       <li>Previous: <a href="development.html" title="previous chapter">Development</a></li>
-      <li>Next: <a href="modules.html" title="next chapter">Code reference</a></li>
+      <li>Next: <a href="development.testing.html" title="next chapter">Testing</a></li>
   </ul></li>
   </ul></li>
 </ul>