Merge branch 'main' into jdb/item-graph-configuration

.github/utils/update_docs.sh

@@ -11,7 +11,7 @@ pipenv run invoke dev.set-version -v ${GITHUB_REF#refs/tags/}
 
 echo "\n-o- Commit updates - Changelog -o-"
 git add pydatalab/__init__.py
-git commit -m "Release ${GITHUB_REF#refs/tags/}"
+git commit --allow-empty -m "Release ${GITHUB_REF#refs/tags/}"
 
 echo -e "\n-o- Update version tag -o-"
 git tag -f ${GITHUB_REF#refs/tags/}

.github/workflows/ci.yml

@@ -120,9 +120,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
-      max-parallel: 2
+      max-parallel: 3
       matrix:
-        browser-backend: ["electron", "chrome"]
+        browser-backend: ["electron", "chrome", "firefox"]
 
     steps:
       - uses: actions/checkout@v4
@@ -158,5 +158,19 @@ jobs:
           working-directory: ./webapp
           record: true
           browser: ${{ matrix.browser-backend }}
+          group: "End-to-end tests (${{ matrix.browser-backend }})"
+        env:
+          CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}
+
+      - name: Run component tests
+        uses: cypress-io/github-action@v6
+        with:
+          working-directory: ./webapp
+          record: true
+          install: false
+          component: true
+          publish-summary: false
+          browser: ${{ matrix.browser-backend }}
+          group: "Component tests (${{ matrix.browser-backend }})"
         env:
           CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}

CHANGELOG.md

@@ -1,5 +1,51 @@
 # Changelog
 
+## v0.4.3 (July 2024
+
+This release simply re-enables Firefox testing in the CI, and reorganises the associated cloud runs.
+
+## What's Changed
+* Re-enable Firefox e2e tests by @ml-evs in https://github.com/datalab-org/datalab/pull/711
+
+**Full Changelog**: https://github.com/datalab-org/datalab/compare/v0.4.2...v0.4.3
+
+
+## v0.4.2 (July 2024)
+
+This release adds an update to the batch item creation UI to include other item types, and includes a new preview of the tabular UI which can be accessed at the path `/next`, as well as several UI tweaks and fixes.
+
+## What's Changed
+
+* Rebrand repo to the group-agnostic gh organisation by @ml-evs in https://github.com/datalab-org/datalab/pull/809
+* Change docker compose restart policy to "unless-stopped" by @ml-evs in https://github.com/datalab-org/datalab/pull/810
+* Update INSTALL.md by @jdbocarsly in https://github.com/datalab-org/datalab/pull/816
+* Fix logo link taking full screen width by @ml-evs in https://github.com/datalab-org/datalab/pull/821
+* Improve sample table component by @BenjaminCharmes in https://github.com/datalab-org/datalab/pull/784
+* Add simple component test for `ChemFormInput` by @ml-evs in https://github.com/datalab-org/datalab/pull/743
+* Add ability to add batch of cells by @jdbocarsly in https://github.com/datalab-org/datalab/pull/797
+* Add config options to automatically activate accounts from GitHub, email or any auth source by @ml-evs in https://github.com/datalab-org/datalab/pull/822
+* Bump version number to 0.4.2 by @ml-evs in https://github.com/datalab-org/datalab/pull/824
+
+**Full Changelog**: https://github.com/datalab-org/datalab/compare/v0.4.1...v0.4.2
+
+## v0.4.1 (July 2024)
+
+This minor release adds some quality-of-life fixes to the UI, a new cell format type "in situ (optical)" and tweaks to our development workflow.
+
+## What's Changed
+
+* Run vue3-recommended linting by @jdbocarsly in https://github.com/the-grey-group/datalab/pull/756
+* Corrected blockInfo computed property value by @BenjaminCharmes in https://github.com/the-grey-group/datalab/pull/775
+* Changes to pre-commit  by @jdbocarsly in https://github.com/the-grey-group/datalab/pull/785
+* Add 'optical' cellFormat by @BenjaminCharmes in https://github.com/the-grey-group/datalab/pull/788
+* Remove cheminventory import task (which is now in `datalab-api`) by @ml-evs in https://github.com/the-grey-group/datalab/pull/793
+* Add gpt4o and other updated models by @jdbocarsly in https://github.com/the-grey-group/datalab/pull/736
+* Report runtime server config at `/info` and use this in UI by @ml-evs in https://github.com/the-grey-group/datalab/pull/801
+* Development docker, pre-commit and eslint updates & refactoring by @ml-evs in https://github.com/the-grey-group/datalab/pull/805
+* Disable `ChemicalFormula` component by @ml-evs in https://github.com/the-grey-group/datalab/pull/806
+
+**Full Changelog**: https://github.com/the-grey-group/datalab/compare/v0.4.0...v0.4.1
+
 ## v0.4.0 (June 2024)
 
 This release of *datalab* contains significant new functionality whilst broadly maintaining compatibility with the 0.3.x series.

README.md

@@ -1,7 +1,7 @@
 # <div align="center"><i>datalab</i></div>
 
 <div align="center" style="padding-bottom: 5px">
-<a href="https://public.datalab.odbx.science"><img src="https://img.shields.io/badge/try_it_out!-public_demo_server-orange?logo=firefox"></a>
+<a href="https://demo.datalab-org.io"><img src="https://img.shields.io/badge/try_it_out!-public_demo_server-orange?logo=firefox"></a>
 </div>
 
 <div align="center">

pydatalab/pydatalab/__init__.py

@@ -1 +1 @@
-__version__ = "0.4.1"
+__version__ = "0.4.3"

pydatalab/pydatalab/config.py

@@ -205,6 +205,21 @@ class ServerConfig(BaseSettings):
         description="Whether to automatically activate accounts created via ORCID registration.",
     )
 
+    GITHUB_AUTO_ACTIVATE_ACCOUNTS: bool = Field(
+        False,
+        description="Whether to automatically activate accounts created via GitHub registration.",
+    )
+
+    EMAIL_AUTO_ACTIVATE_ACCOUNTS: bool = Field(
+        False,
+        description="Whether to automatically activate accounts created via email registration.",
+    )
+
+    AUTO_ACTIVATE_ACCOUNTS: bool = Field(
+        False,
+        description="Whether to automatically activate accounts created via any registration method.",
+    )
+
     EMAIL_DOMAIN_ALLOW_LIST: Optional[List[str]] = Field(
         [],
         description="A list of domains for which users will be able to register accounts if they have a matching verified email address, which still need to be verified by an admin. Setting the value to `None` will allow any email addresses at any domain to register *and activate* an account, otherwise the default `[]` will not allow any email addresses registration.",

pydatalab/pydatalab/permissions.py

@@ -1,6 +1,7 @@
 from functools import wraps
 from typing import Any, Dict
 
+from bson import ObjectId
 from flask import request
 from flask_login import current_user
 
@@ -10,6 +11,8 @@
 from pydatalab.models.people import AccountStatus
 from pydatalab.mongo import get_database
 
+PUBLIC_USER_ID = ObjectId(24 * "0")
+
 
 def active_users_or_get_only(func):
     """Decorator to ensure that only active user accounts can access the route,
@@ -81,7 +84,13 @@ def get_default_permissions(user_only: bool = True) -> Dict[str, Any]:
     ):
         return {}
 
-    null_perm = {"$or": [{"creator_ids": {"$size": 0}}, {"creator_ids": {"$exists": False}}]}
+    null_perm = {
+        "$or": [
+            {"creator_ids": {"$size": 0}},
+            {"creator_ids": {"$in": [PUBLIC_USER_ID]}},
+            {"creator_ids": {"$exists": False}},
+        ]
+    }
     if current_user.is_authenticated and current_user.person is not None:
         # find managed users under the given user (can later be expanded to groups)
         managed_users = list(

pydatalab/pydatalab/routes/v0_1/auth.py

@@ -373,7 +373,11 @@ def email_logged_in():
         raise UserRegistrationForbidden
 
     create_account = AccountStatus.UNVERIFIED
-    if CONFIG.EMAIL_DOMAIN_ALLOW_LIST is None:
+    if (
+        CONFIG.EMAIL_DOMAIN_ALLOW_LIST is None
+        or CONFIG.EMAIL_AUTO_ACTIVATE_ACCOUNTS
+        or CONFIG.AUTO_ACTIVATE_ACCOUNTS
+    ):
         create_account = AccountStatus.ACTIVE
 
     find_create_or_modify_user(
@@ -426,6 +430,9 @@ def github_logged_in(blueprint, token):
     elif CONFIG.GITHUB_ORG_ALLOW_LIST is None:
         create_account = True
 
+    if CONFIG.GITHUB_AUTO_ACTIVATE_ACCOUNTS or CONFIG.AUTO_ACTIVATE_ACCOUNTS:
+        create_account = AccountStatus.ACTIVE
+
     find_create_or_modify_user(
         github_user_id,
         IdentityType.GITHUB,
@@ -452,7 +459,7 @@ def orcid_logged_in(_, token):
 
     # New ORCID accounts must be activated by an admin unless configured otherwise
     create_account = AccountStatus.UNVERIFIED
-    if CONFIG.ORCID_AUTO_ACTIVATE_ACCOUNTS:
+    if CONFIG.ORCID_AUTO_ACTIVATE_ACCOUNTS or CONFIG.AUTO_ACTIVATE_ACCOUNTS:
         create_account = AccountStatus.ACTIVE
 
     find_create_or_modify_user(

pydatalab/pydatalab/routes/v0_1/collections.py

@@ -112,9 +112,7 @@ def create_collection():
 
     if CONFIG.TESTING:
         data["creator_ids"] = [24 * "0"]
-        data["creators"] = [
-            {"display_name": "Public testing user", "contact_email": "datalab@odbx.science"}
-        ]
+        data["creators"] = [{"display_name": "Public testing user"}]
     else:
         data["creator_ids"] = [current_user.person.immutable_id]
         data["creators"] = [

pydatalab/pydatalab/routes/v0_1/items.py

@@ -16,7 +16,7 @@
 from pydatalab.models.relationships import RelationshipType
 from pydatalab.models.utils import generate_unique_refcode
 from pydatalab.mongo import flask_mongo
-from pydatalab.permissions import active_users_or_get_only, get_default_permissions
+from pydatalab.permissions import PUBLIC_USER_ID, active_users_or_get_only, get_default_permissions
 
 ITEMS = Blueprint("items", __name__)
 
@@ -396,17 +396,16 @@ def _create_sample(
                 "negative_electrode",
                 "electrolyte",
             ):
-                if copied_doc.get(component):
-                    existing_consituent_ids = [
-                        constituent["item"].get("item_id", None)
-                        for constituent in copied_doc[component]
-                    ]
-                    copied_doc[component] += [
-                        constituent
-                        for constituent in sample_dict.get(component, [])
-                        if constituent["item"].get("item_id", None) is None
-                        or constituent["item"].get("item_id") not in existing_consituent_ids
-                    ]
+                existing_consituent_ids = [
+                    constituent["item"].get("item_id", None)
+                    for constituent in copied_doc[component]
+                ]
+                copied_doc[component] += [
+                    constituent
+                    for constituent in sample_dict.get(component, [])
+                    if constituent["item"].get("item_id", None) is None
+                    or constituent["item"].get("item_id") not in existing_consituent_ids
+                ]
 
             sample_dict = copied_doc
 
@@ -424,10 +423,10 @@ def _create_sample(
         )
 
     sample_dict.pop("refcode", None)
-    type = sample_dict["type"]
-    if type not in ITEM_MODELS:
+    type_ = sample_dict["type"]
+    if type_ not in ITEM_MODELS:
         raise RuntimeError("Invalid type")
-    model = ITEM_MODELS[type]
+    model = ITEM_MODELS[type_]
 
     ## the following code was used previously to explicitely check schema properties.
     ## it doesn't seem to be necessary now, with extra = "ignore" turned on in the pydantic models,
@@ -437,19 +436,18 @@ def _create_sample(
     # new_sample = {k: sample_dict[k] for k in schema["properties"] if k in sample_dict}
     new_sample = sample_dict
 
-    if type in ("starting_materials", "equipment"):
+    if type_ in ("starting_materials", "equipment"):
         # starting_materials and equipment are open to all in the deploment at this point,
         # so no creators are assigned
         new_sample["creator_ids"] = []
         new_sample["creators"] = []
     elif CONFIG.TESTING:
         # Set fake ID to ObjectId("000000000000000000000000") so a dummy user can be created
         # locally for testing creator UI elements
-        new_sample["creator_ids"] = [24 * "0"]
+        new_sample["creator_ids"] = [PUBLIC_USER_ID]
         new_sample["creators"] = [
             {
                 "display_name": "Public testing user",
-                "contact_email": "datalab@odbx.science",
             }
         ]
     else:
@@ -632,10 +630,13 @@ def delete_sample():
     )
 
 
+@ITEMS.route("/items/<refcode>", methods=["GET"])
 @ITEMS.route("/get-item-data/<item_id>", methods=["GET"])
-def get_item_data(item_id, load_blocks: bool = False):
+def get_item_data(
+    item_id: str | None = None, refcode: str | None = None, load_blocks: bool = False
+):
     """Generates a JSON response for the item with the given `item_id`,
-    additionally resolving relationships to files and other items.
+    or `refcode` additionally resolving relationships to files and other items.
 
     Parameters:
        load_blocks: Whether to regenerate any data blocks associated with this
@@ -644,12 +645,30 @@ def get_item_data(item_id, load_blocks: bool = False):
 
     """
 
+    if item_id:
+        match = {"item_id": item_id}
+    elif refcode:
+        if not len(refcode.split(":")) == 2:
+            refcode = f"{CONFIG.IDENTIFIER_PREFIX}:{refcode}"
+
+        match = {"refcode": refcode}
+    else:
+        return (
+            jsonify(
+                {
+                    "status": "error",
+                    "message": "No item_id or refcode provided.",
+                }
+            ),
+            400,
+        )
+
     # retrieve the entry from the database:
     cursor = flask_mongo.db.items.aggregate(
         [
             {
                 "$match": {
-                    "item_id": item_id,
+                    **match,
                     **get_default_permissions(user_only=False),
                 }
             },
@@ -673,7 +692,7 @@ def get_item_data(item_id, load_blocks: bool = False):
             jsonify(
                 {
                     "status": "error",
-                    "message": f"No matching item {item_id=} with current authorization.",
+                    "message": f"No matching items for {match=} with current authorization.",
                 }
             ),
             404,

pydatalab/pydatalab/send_email.py

@@ -2,6 +2,7 @@
 
 from flask_mail import Mail, Message
 
+from pydatalab.config import CONFIG
 from pydatalab.logger import LOGGER
 
 MAIL = Mail()
@@ -22,8 +23,12 @@ def send_mail(recipient: str, subject: str, body: str):
     """
     LOGGER.debug("Sending email to %s", recipient)
 
+    sender = None
+    if CONFIG.EMAIL_AUTH_SMTP_SETTINGS is not None:
+        sender = CONFIG.EMAIL_AUTH_SMTP_SETTINGS.MAIL_DEFAULT_SENDER
+
     message = Message(
-        sender="datalab@odbx.science",
+        sender=sender,
         recipients=[recipient],
         body=body,
         subject=subject,