Add labels collection and endpoints

tests/labels/test_api.py

@@ -0,0 +1,196 @@
+import pytest
+
+
+async def test_find(spawn_client):
+    """
+    Test that a ``GET /api/labels`` return a complete list of labels.
+
+    """
+    client = await spawn_client(authorize=True, administrator=True)
+    await client.db.labels.insert_many([
+        {
+            "_id": "test_1",
+            "name": "Bug",
+            "color": "#a83432"
+        },
+        {
+            "_id": "test_2",
+            "name": "Question",
+            "color": "#03fc20"
+        }
+    ])
+
+    resp = await client.get("/api/labels")
+    assert resp.status == 200
+
+    assert await resp.json() == [
+        {
+            "id": "test_1",
+            "name": "Bug",
+            "color": "#a83432"
+        },
+        {
+            "id": "test_2",
+            "name": "Question",
+            "color": "#03fc20"
+        }
+    ]
+
+
+@pytest.mark.parametrize("error", [None, "404"])
+async def test_get(error, spawn_client, all_permissions, resp_is):
+    """
+    Test that a ``GET /api/labels/:label_id`` return the correct label document.
+
+    """
+    client = await spawn_client(authorize=True, administrator=True)
+
+    if not error:
+        await client.db.labels.insert_one({
+            "_id": "test",
+            "name": "Bug",
+            "color": "#a83432"
+        })
+
+    resp = await client.get("/api/labels/test")
+
+    if error:
+        assert await resp_is.not_found(resp)
+        return
+
+    assert resp.status == 200
+
+    assert await resp.json() == {
+        "id": "test",
+        "name": "Bug",
+        "color": "#a83432"
+    }
+
+
+@pytest.mark.parametrize("error", [None, "400_exists", "422_color"])
+async def test_create(error, spawn_client, test_random_alphanumeric, resp_is):
+    """
+    Test that a label can be added to the database at ``POST /api/labels``.
+
+    """
+    client = await spawn_client(authorize=True, administrator=True)
+
+    if error == "400_exists":
+        await client.db.labels.insert_one({
+            "name": "Bug"
+        })
+
+    data = {
+        "name": "Bug",
+        "color": "#a83432",
+        "description": "This is a bug"
+    }
+
+    if error == "422_color":
+        data["color"] = "#1234567"
+
+    resp = await client.post("/api/labels", data)
+
+    if error == "400_exists":
+        assert await resp_is.bad_request(resp, "Label name already exists")
+        return
+
+    if error == "422_color":
+        assert resp.status == 422
+        return
+
+    assert resp.status == 201
+
+    expected_id = test_random_alphanumeric.history[0]
+    assert resp.headers["Location"] == "/api/labels/" + expected_id
+
+    assert await resp.json() == {
+        "id": expected_id,
+        "name": "Bug",
+        "color": "#a83432",
+        "description": "This is a bug"
+    }
+
+
+@pytest.mark.parametrize("error", [None, "404", "400_exists", "422_color"])
+async def test_edit(error, spawn_client, resp_is):
+    """
+        Test that a label can be edited to the database at ``PATCH /api/labels/:label_id``.
+
+    """
+    client = await spawn_client(authorize=True, administrator=True)
+
+    if error != "404":
+        await client.db.labels.insert_many([
+            {
+                "_id": "test_1",
+                "name": "Bug",
+                "color": "#a83432",
+                "description": "This is a bug"
+            },
+            {
+                "_id": "test_2",
+                "name": "Question",
+                "color": "#32a85f",
+                "description": "Question from a user"
+            }
+        ])
+
+    data = {
+        "name": "Bug",
+        "color": "#fc5203",
+        "description": "Need to be fixed"
+    }
+
+    if error == "400_exists":
+        data["name"] = "Question"
+
+    if error == "422_color":
+        data["color"] = "#123bzp"
+
+    resp = await client.patch("/api/labels/test_1", data=data)
+
+    if error == "404":
+        assert await resp_is.not_found(resp)
+        return
+
+    if error == "400_exists":
+        assert await resp_is.bad_request(resp, "Label name already exists")
+        return
+
+    if error == "422_color":
+        assert resp.status == 422
+        return
+
+    assert resp.status == 200
+    assert await resp.json() == {
+        "id": "test_1",
+        "name": "Bug",
+        "color": "#fc5203",
+        "description": "Need to be fixed"
+    }
+
+
+@pytest.mark.parametrize("error", [None, "400"])
+async def test_remove(error, spawn_client, resp_is):
+    """
+        Test that a label can be deleted to the database at ``DELETE /api/labels/:label_id``.
+
+    """
+    client = await spawn_client(authorize=True, administrator=True)
+
+    if not error:
+        await client.db.labels.insert_one({
+                "_id": "test",
+                "name": "Bug",
+                "color": "#a83432",
+                "description": "This is a bug"
+        })
+
+    resp = await client.delete("/api/labels/test")
+
+    if error:
+        assert await resp_is.not_found(resp)
+        return
+
+    assert await resp_is.no_content(resp)

virtool/db/core.py

@@ -299,6 +299,8 @@ def __init__(self, client, enqueue_change):
             silent=True
         )
 
+        self.labels = self.bind_collection("labels")
+
         self.otus = self.bind_collection(
             "otus",
             projection=virtool.otus.db.PROJECTION

virtool/dispatcher.py

@@ -31,6 +31,7 @@
     "hmm",
     "indexes",
     "jobs",
+    "labels",
     "otus",
     "processes",
     "references",

virtool/labels/api.py

@@ -0,0 +1,138 @@
+import virtool.http.routes
+import virtool.utils
+import virtool.validators
+import virtool.db.utils
+from virtool.api.response import bad_request, json_response, no_content, not_found
+
+routes = virtool.http.routes.Routes()
+
+
+@routes.get("/api/labels")
+async def find(req):
+    """
+        Get a list of all label documents in the database.
+
+    """
+    db = req.app["db"]
+
+    cursor = db.labels.find()
+
+    return json_response([virtool.utils.base_processor(d) async for d in cursor])
+
+
+@routes.get("/api/labels/{label_id}")
+async def get(req):
+    """
+        Get a complete label document.
+
+    """
+    document = await req.app["db"].labels.find_one(req.match_info["label_id"])
+
+    if document is None:
+        return not_found()
+
+    return json_response(virtool.utils.base_processor(document))
+
+
+@routes.post("/api/labels", schema={
+    "name": {
+        "type": "string",
+        "coerce": virtool.validators.strip,
+        "required": True,
+        "empty": False
+    },
+    "color": {
+        "type": "string",
+        "coerce": virtool.validators.strip,
+        "validator": virtool.validators.is_valid_hex_color,
+    },
+    "description": {
+        "type": "string",
+        "coerce": virtool.validators.strip,
+        "default": ""
+    }
+})
+async def create(req):
+    """
+        Add a new label to the labels database.
+
+    """
+    db = req.app["db"]
+    data = req["data"]
+
+    if await db.labels.count_documents({'name': data['name']}):
+        return bad_request("Label name already exists")
+
+    label_id = await virtool.db.utils.get_new_id(db.labels)
+
+    document = {
+        "_id": label_id,
+        "name": data["name"],
+        "color": data["color"],
+        "description": data["description"]
+    }
+
+    await db.labels.insert_one(document)
+
+    headers = {
+        "Location": f"/api/labels/{label_id}"
+    }
+
+    return json_response(virtool.utils.base_processor(document), status=201, headers=headers)
+
+
+@routes.patch("/api/labels/{label_id}", schema={
+    "name": {
+        "type": "string",
+        "coerce": virtool.validators.strip,
+    },
+    "color": {
+        "type": "string",
+        "coerce": virtool.validators.strip,
+        "validator": virtool.validators.is_valid_hex_color,
+    },
+    "description": {
+        "type": "string",
+        "coerce": virtool.validators.strip,
+    }
+})
+async def edit(req):
+    """
+        Edit an existing label.
+
+    """
+    db = req.app["db"]
+    data = req["data"]
+
+    label_id = req.match_info["label_id"]
+
+    if "name" in data and await db.labels.count_documents({"_id": {"$ne": label_id}, "name": data["name"]}):
+        return bad_request("Label name already exists")
+
+    document = await db.labels.find_one_and_update({"_id": label_id}, {
+        "$set": data
+    })
+
+    if document is None:
+        return not_found()
+
+    return json_response(virtool.utils.base_processor(document))
+
+
+@routes.delete("/api/labels/{label_id}")
+async def remove(req):
+    """
+        Remove a label.
+
+    """
+    db = req.app["db"]
+
+    label_id = req.match_info["label_id"]
+
+    delete_result = await db.labels.delete_one({"_id": label_id})
+
+    if delete_result.deleted_count == 0:
+        return not_found()
+
+    return no_content()
+

virtool/routes.py

@@ -16,6 +16,7 @@
 import virtool.http.ws
 import virtool.indexes.api
 import virtool.jobs.api
+import virtool.labels.api
 import virtool.otus.api
 import virtool.processes.api
 import virtool.references.api
@@ -54,6 +55,7 @@
     virtool.hmm.api.routes,
     virtool.indexes.api.routes,
     virtool.jobs.api.routes,
+    virtool.labels.api.routes,
     virtool.otus.api.routes,
     virtool.processes.api.routes,
     virtool.references.api.routes,

virtool/validators.py

@@ -1,5 +1,8 @@
+import re
 import virtool.users.utils
 
+RE_HEX_COLOR = re.compile("^#([A-Fa-f0-9]{6}|[A-Fa-f0-9]{3})$")
+
 
 def strip(value: str) -> str:
     """
@@ -20,3 +23,8 @@ def is_permission_dict(field, value, error):
 def has_unique_segment_names(field, value, error):
     if len({seg["name"] for seg in value}) != len(value):
         error(field, "list contains duplicate names")
+
+
+def is_valid_hex_color(field, value, error):
+    if not RE_HEX_COLOR.match(value):
+        error(field, "This is not a valid Hexadecimal color")