From d4681de20159494975e82bf3d0d1be8bb48f44f6 Mon Sep 17 00:00:00 2001 From: "Alan B. Christie" <29806285+alanbchristie@users.noreply.github.com> Date: Tue, 21 May 2024 14:14:28 +0100 Subject: [PATCH] Release latest staging code (#591) * build(deps): bump django from 3.2.24 to 3.2.25 Bumps [django](https://github.com/django/django) from 3.2.24 to 3.2.25. - [Commits](https://github.com/django/django/compare/3.2.24...3.2.25) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] * stashing * Target loader now accepts experiments marked as 'manual' * build(deps): bump pillow from 10.2.0 to 10.3.0 Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.2.0 to 10.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/10.2.0...10.3.0) --- updated-dependencies: - dependency-name: pillow dependency-type: indirect ... Signed-off-by: dependabot[bot] * Attempt to reduce pop-up "flicker" (1403) (#569) * fix: Attempt to debug timeout errors * fix: More logging on service_query * fix: Varioustimeout adjustments * fix: Removed exception during timeout * fix: Explit log on SSH connection error * fix: Retry attempts for MySQL connections * fix: Service timeout now 28 (was 17) * fix: Add pymysql read and write timeouts * fix: Quiter (expected) connection failure handling * fix: TIMEOUT now DEGRADED * fix: Fix while loop exit conditions * fix: Better loop logic * style: services logging reduced and back to debug * fix: SSHTunnel logging now ERROR (was DEBUG) * fix: Quieter securty * fix: More failures permitted (and debug tweaks) * fix: Leaner logging * fix: Leaner logging (only report when we're having topruble) * fix: Better constant name * fix: Reduced service logging * docs: Doc tweak * fix: Minor log tweak * fix: Fixed duplicate log content --------- Co-authored-by: Alan Christie * feat: endpoint to download first reference pdb from assemblies.yaml * stashing * stashing Changes so far: - removed endpoint FirstAssemblyview - moved the functionality to template_protein field in TargetSerializer - removed TargetMoleculesserializer - removed sequences field from TargetSerializer This is a result of Boris' comment in github (https://github.com/m2ms/fragalysis-frontend/issues/1373#issuecomment-2047417958) where he said the field isn't used and template_protein field is not used. Looking at the code where this may be used, revealed that Targetmoleculesserializer can be removed as well NB! they're not removed-removed right now, only commented in. This commit can be used to restore the code. * fix: removed code mentioned in previous commit * basic functionality TODO: add and test PATCH method on PoseSerializer * stashing * build(deps): bump idna from 3.6 to 3.7 Bumps [idna](https://github.com/kjd/idna) from 3.6 to 3.7. - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](https://github.com/kjd/idna/compare/v3.6...v3.7) --- updated-dependencies: - dependency-name: idna dependency-type: indirect ... Signed-off-by: dependabot[bot] * stashing * Added 'hidden' property to viewer.Tag model Also, added exclude directives to .pre-commit-config.yaml to not touch django migration files * Better user/proposal cache (#576) * refactor: Quieter ISPyB cache * refactor: Security cache log now quieter * fix: Better cache logic - and reduced log --------- Co-authored-by: Alan Christie * stashing Nested serializer for pose, but I don't think I can use them * feat: added compound_code to pose serializer * fix: deeper nesting level to site observaton in meta_aligner.yaml Data loads successfully but actual v2 upload has not been tested * fix: renamed panddas_event_files to ligand_binding_events in meta_al * fix: static resources are now loaded again Fixes bare html API pages * fix: fixed nginx config * Revert "Fix static ressources not being loaded" * stashing Added sorting keys for versioned key. V1 data loading, waiting for fixes in conf site presentation to continue with v2 * fix: more robust update method Allows sending incomplete requests (no idea why seralizer isn't populating fields). Also fixed a bug where field updates on poses with multiple observations where blocked. * feat: added pose tags * stashing Working on allowing incomplete requests payloads. Turns out to be quite tricky, may have to go back on this. * feat: fully functional versioned data Reads and processes upload_2+ data where version numbers are given in suffix * fix: removed some dead code * stashing * build(deps): bump tqdm from 4.66.1 to 4.66.3 Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3. - [Release notes](https://github.com/tqdm/tqdm/releases) - [Commits](https://github.com/tqdm/tqdm/compare/v4.66.1...v4.66.3) --- updated-dependencies: - dependency-name: tqdm dependency-type: indirect ... Signed-off-by: dependabot[bot] * feat: only non-superseded sites available from the api * build(deps-dev): bump black from 23.12.0 to 24.3.0 Bumps [black](https://github.com/psf/black) from 23.12.0 to 24.3.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.12.0...24.3.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] * chore: merged conflicting migrations from issue 1311 branch * fix: pose instance attributes updating successfully * fix: better check for already uploaded data * fix: merge conflicting migrations Not sure why the previous merge didn't work * Adds basic metrics (#588) * feat: Experiment with django prometheus * feat: Fix build * fix: Fix build (locking drf) * feat: Fix lock file * feat: Update to non-slim Python 3.11.9 * feat: Back to slim image * fix: Some basic internal metrics * fix: Removed rogue line * fix: Fix lint issues * fix: Removed custom metrics --------- Co-authored-by: Alan Christie * Attempt to add prometheus to DB (#589) Co-authored-by: Alan Christie --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kalev Takkis Co-authored-by: Alan Christie Co-authored-by: Kalev Takkis Co-authored-by: Warren Thompson --- .pre-commit-config.yaml | 4 + Dockerfile | 2 +- README.md | 6 +- api/security.py | 147 +- api/urls.py | 4 +- fragalysis/settings.py | 5 +- fragalysis/urls.py | 1 + poetry.lock | 1214 ++++++++--------- pyproject.toml | 7 +- viewer/filters.py | 14 + viewer/fixtures/tagcategories.json | 9 + viewer/managers.py | 32 + viewer/migrations/0050_auto_20240410_1125.py | 70 + viewer/migrations/0050_auto_20240412_0930.py | 23 + .../0051_alter_siteobservation_pose.py | 23 + viewer/migrations/0051_auto_20240425_0748.py | 23 + viewer/migrations/0052_auto_20240503_1255.py | 38 + viewer/migrations/0053_auto_20240503_1302.py | 28 + viewer/migrations/0054_auto_20240509_0838.py | 27 + viewer/migrations/0054_merge_20240507_1558.py | 14 + viewer/migrations/0055_merge_20240516_1003.py | 14 + viewer/models.py | 62 +- viewer/serializers.py | 461 ++++--- viewer/target_loader.py | 279 +++- viewer/views.py | 31 +- 25 files changed, 1539 insertions(+), 999 deletions(-) create mode 100644 viewer/migrations/0050_auto_20240410_1125.py create mode 100644 viewer/migrations/0050_auto_20240412_0930.py create mode 100644 viewer/migrations/0051_alter_siteobservation_pose.py create mode 100644 viewer/migrations/0051_auto_20240425_0748.py create mode 100644 viewer/migrations/0052_auto_20240503_1255.py create mode 100644 viewer/migrations/0053_auto_20240503_1302.py create mode 100644 viewer/migrations/0054_auto_20240509_0838.py create mode 100644 viewer/migrations/0054_merge_20240507_1558.py create mode 100644 viewer/migrations/0055_merge_20240516_1003.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 28c6663b..c532b9f0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -28,6 +28,7 @@ repos: rev: 5.13.1 hooks: - id: isort + exclude: 'migrations/' args: - --profile - black @@ -38,6 +39,7 @@ repos: rev: 23.12.0 hooks: - id: black + exclude: 'migrations/' args: - --skip-string-normalization - --target-version @@ -51,6 +53,7 @@ repos: rev: v1.7.1 hooks: - id: mypy + exclude: 'migrations/' additional_dependencies: - types-PyYAML - types-pymysql @@ -63,6 +66,7 @@ repos: rev: v3.0.3 hooks: - id: pylint + exclude: 'migrations/' additional_dependencies: - pylint-django args: diff --git a/Dockerfile b/Dockerfile index a9d037cf..6fd4be36 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.11.7-slim-bullseye AS python-base +FROM python:3.11.9-slim-bullseye AS python-base ENV PYTHONUNBUFFERED 1 ENV PYTHONDONTWRITEBYTECODE 1 diff --git a/README.md b/README.md index af572d65..808ec279 100644 --- a/README.md +++ b/README.md @@ -283,11 +283,9 @@ pre-commit documentation. Ideally from a Python environment... - python -m venv venv - source venv/bin/activate + poetry shell + poetry install --only dev - pip install --upgrade pip - pip install -r build-requirements.txt pre-commit install -t commit-msg -t pre-commit Now the project's rules will run on every commit and you can check the diff --git a/api/security.py b/api/security.py index 8773aa31..8ecf6976 100644 --- a/api/security.py +++ b/api/security.py @@ -1,9 +1,11 @@ # pylint: skip-file import logging import os +import threading from datetime import datetime, timedelta +from functools import cache from pathlib import Path -from typing import Any, Dict, Optional, Union +from typing import Any, Dict, List, Optional, Union from wsgiref.util import FileWrapper from django.conf import settings @@ -19,32 +21,49 @@ logger: logging.Logger = logging.getLogger(__name__) -# Sets of cached query results, indexed by username. -# The cache uses the key 'RESULTS' and the collection time uses the key 'TIMESTAMP'. -# and the time the cache is expires is in 'EXPIRES_AT' -USER_PROPOSAL_CACHE: Dict[str, Dict[str, Any]] = {} -# Period to cache user lists in seconds (on successful reads from the connector) -USER_PROPOSAL_CACHE_MAX_AGE: timedelta = timedelta( - minutes=settings.SECURITY_CONNECTOR_CACHE_MINUTES -) -# A short period, used when caching of results fails. -# This ensures a rapid retry on failure. -USER_PROPOSAL_CACHE_RETRY_TIMEOUT: timedelta = timedelta(seconds=7) - -# example test: -# from rest_framework.test import APIRequestFactory -# -# from rest_framework.test import force_authenticate -# from viewer.views import TargetView -# from django.contrib.auth.models import User -# -# factory = APIRequestFactory() -# view = TargetView.as_view({'get': 'list'}) -# user = User.objects.get(username='uzw12877') -# # Make an authenticated request to the view... -# request = factory.get('/api/targets/') -# force_authenticate(request, user=user) -# response = view(request) + +@cache +class CachedContent: + """A static class managing caches proposals/visits for each user. + Proposals should be collected when has_expired() returns True. + Content can be written (when the cache for the user has expired) + and read using the set/get methods. + """ + + _timers: Dict[str, datetime] = {} + _content: Dict[str, List[str]] = {} + _cache_period: timedelta = timedelta( + minutes=settings.SECURITY_CONNECTOR_CACHE_MINUTES + ) + _cache_lock: threading.Lock = threading.Lock() + + @staticmethod + def has_expired(username) -> bool: + assert username + with CachedContent._cache_lock: + has_expired = False + now = datetime.now() + if username not in CachedContent._timers: + # User's not known, + # initialise an entry that will automatically expire + CachedContent._timers[username] = now + if CachedContent._timers[username] <= now: + has_expired = True + # Expired, reset the expiry time + CachedContent._timers[username] = now + CachedContent._cache_period + return has_expired + + @staticmethod + def get_content(username): + with CachedContent._cache_lock: + if username not in CachedContent._content: + CachedContent._content[username] = [] + return CachedContent._content[username] + + @staticmethod + def set_content(username, content) -> None: + with CachedContent._cache_lock: + CachedContent._content[username] = content.copy() def get_remote_conn(force_error_display=False) -> Optional[SSHConnector]: @@ -197,57 +216,6 @@ def _get_proposals_for_user_from_django(self, user): ) return prop_ids - def _cache_needs_updating(self, user): - """True of the data for a user now needs to be collected - (e.g. the cache is out of date). The response is also True for the first - call for each user. When data is successfully collected you need to - call '_populate_cache()' with the user and new cache content. - This will set the cache content and the cache timestamp. - """ - now = datetime.now() - if user.username not in USER_PROPOSAL_CACHE: - # Unknown user - initilise the entry for this user. - # And make suer it immediately expires! - USER_PROPOSAL_CACHE[user.username] = { - "RESULTS": set(), - "TIMESTAMP": None, - "EXPIRES_AT": now, - } - - # Has the cache expired? - return now >= USER_PROPOSAL_CACHE[user.username]["EXPIRES_AT"] - - def _populate_cache(self, user, new_content): - """Called by code that collects content to replace the cache with new content, - this is typically from '_get_proposals_from_connector()'. The underlying map's - TIMESTAMP for the user will also be set (to 'now') to reflect the time the - cache was most recently populated. - """ - username = user.username - USER_PROPOSAL_CACHE[username]["RESULTS"] = new_content.copy() - # Set the timestamp (which records when the cache was populated with 'stuff') - # and ensure it will now expire after USER_PROPOSAL_CACHE_SECONDS. - now = datetime.now() - USER_PROPOSAL_CACHE[username]["TIMESTAMP"] = now - USER_PROPOSAL_CACHE[username]["EXPIRES_AT"] = now + USER_PROPOSAL_CACHE_MAX_AGE - logger.info( - "USER_PROPOSAL_CACHE populated for '%s' (expires at %s)", - username, - USER_PROPOSAL_CACHE[username]["EXPIRES_AT"], - ) - - def _mark_cache_collection_failure(self, user): - """Called by code that collects content to indicate that although the cache - should have been collected it has not (trough some other problem). - Under these circumstances the cache will not be updated but we have the opportunity - to set a new, short, 'expiry' time. In this way, cache collection will occur - again soon. The cache and its timestamp are left intact. - """ - now = datetime.now() - USER_PROPOSAL_CACHE[user.username]["EXPIRES_AT"] = ( - now + USER_PROPOSAL_CACHE_RETRY_TIMEOUT - ) - def _run_query_with_connector(self, conn, user): core = conn.core try: @@ -262,8 +230,8 @@ def _run_query_with_connector(self, conn, user): return rs def _get_proposals_for_user_from_ispyb(self, user): - if self._cache_needs_updating(user): - logger.info("user='%s' (needs_updating)", user.username) + if CachedContent.has_expired(user.username): + logger.info("Cache has expired for '%s'", user.username) if conn := get_configured_connector(): logger.debug("Got a connector for '%s'", user.username) self._get_proposals_from_connector(user, conn) @@ -272,15 +240,16 @@ def _get_proposals_for_user_from_ispyb(self, user): self._mark_cache_collection_failure(user) # The cache has either been updated, has not changed or is empty. - # Return what we have for the user. If required, public (open) proposals - # will be added to what we return. - cached_prop_ids = USER_PROPOSAL_CACHE[user.username]["RESULTS"] - logger.info( - "Got %s proposals for '%s': %s", + # Return what we have for the user. Public (open) proposals + # will be added to what we return if necessary. + cached_prop_ids = CachedContent.get_content(user.username) + logger.debug( + "Have %s cached Proposals for '%s': %s", len(cached_prop_ids), user.username, cached_prop_ids, ) + return cached_prop_ids def _get_proposals_from_connector(self, user, conn): @@ -342,9 +311,7 @@ def _get_proposals_from_connector(self, user, conn): user.username, prop_id_set, ) - - # Replace the cache with what we've collected - self._populate_cache(user, prop_id_set) + CachedContent.set_content(user.username, prop_id_set) def get_proposals_for_user(self, user, restrict_to_membership=False): """Returns a list of proposals that the user has access to. @@ -369,10 +336,10 @@ def get_proposals_for_user(self, user, restrict_to_membership=False): ) if ispyb_user: if user.is_authenticated: - logger.info("Getting proposals from ISPyB...") + logger.debug("Getting proposals from ISPyB...") proposals = self._get_proposals_for_user_from_ispyb(user) else: - logger.info("Getting proposals from Django...") + logger.debug("Getting proposals from Django...") proposals = self._get_proposals_for_user_from_django(user) # We have all the proposals where the user has authority. diff --git a/api/urls.py b/api/urls.py index 229efc95..8f4d38ea 100644 --- a/api/urls.py +++ b/api/urls.py @@ -88,9 +88,6 @@ viewer_views.SessionProjectTagView, basename='session_project_tag', ) -router.register( - "target_molecules", viewer_views.TargetMoleculesView, basename='target_molecules' -) # Download a zip file of the requested contents router.register( @@ -125,6 +122,7 @@ "canon_site_confs", viewer_views.CanonSiteConfs, basename='canon_site_confs' ) router.register("xtalform_sites", viewer_views.XtalformSites, basename='xtalform_sites') +router.register("poses", viewer_views.PoseView, basename='poses') # Squonk Jobs router.register( diff --git a/fragalysis/settings.py b/fragalysis/settings.py index cfef3208..ef3775f1 100644 --- a/fragalysis/settings.py +++ b/fragalysis/settings.py @@ -153,6 +153,7 @@ "webpack_loader", "django_cleanup", "simple_history", + "django_prometheus", ] LANGUAGE_CODE = "en-us" @@ -167,6 +168,7 @@ LOGOUT_REDIRECT_URL = "/viewer/react/landing" MIDDLEWARE = [ + "django_prometheus.middleware.PrometheusBeforeMiddleware", "django.middleware.security.SecurityMiddleware", "django.contrib.sessions.middleware.SessionMiddleware", "django.middleware.common.CommonMiddleware", @@ -175,6 +177,7 @@ "django.contrib.messages.middleware.MessageMiddleware", "django.middleware.clickjacking.XFrameOptionsMiddleware", "mozilla_django_oidc.middleware.SessionRefresh", + "django_prometheus.middleware.PrometheusAfterMiddleware", ] PROJECT_ROOT = os.path.abspath(os.path.join(BASE_DIR, "..")) @@ -331,7 +334,7 @@ DATABASES = { "default": { - "ENGINE": "django.db.backends.postgresql_psycopg2", + "ENGINE": "django_prometheus.db.backends.postgresql", "NAME": os.environ.get("POSTGRESQL_DATABASE", "frag"), "USER": os.environ.get("POSTGRESQL_USER", "fragalysis"), "PASSWORD": os.environ.get("POSTGRESQL_PASSWORD", "fragalysis"), diff --git a/fragalysis/urls.py b/fragalysis/urls.py index c54cff4e..048f1252 100644 --- a/fragalysis/urls.py +++ b/fragalysis/urls.py @@ -49,4 +49,5 @@ mozilla_django_oidc.views.OIDCAuthenticationCallbackView.as_view(), name="keycloak_callback", ), + path("", include("django_prometheus.urls")), ] diff --git a/poetry.lock b/poetry.lock index 306d4ce0..4bcad13d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "amqp" @@ -30,13 +30,13 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] [[package]] name = "asgiref" -version = "3.7.2" +version = "3.8.1" description = "ASGI specs, helper code, and adapters" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "asgiref-3.7.2-py3-none-any.whl", hash = "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e"}, - {file = "asgiref-3.7.2.tar.gz", hash = "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed"}, + {file = "asgiref-3.8.1-py3-none-any.whl", hash = "sha256:3e1e3ecc849832fe52ccf2cb6686b7a55f82bb1d6aee72a58826471390335e47"}, + {file = "asgiref-3.8.1.tar.gz", hash = "sha256:c343bd80a0bec947a9860adb4c432ffa7db769836c64238fc34bdc3fec84d590"}, ] [package.extras] @@ -44,13 +44,13 @@ tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"] [[package]] name = "astroid" -version = "3.0.2" +version = "3.2.1" description = "An abstract 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brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -2894,13 +2892,13 @@ files = [ [[package]] name = "virtualenv" -version = "20.25.0" +version = "20.26.2" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"}, - {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"}, + {file = "virtualenv-20.26.2-py3-none-any.whl", hash = "sha256:a624db5e94f01ad993d476b9ee5346fdf7b9de43ccaee0e0197012dc838a0e9b"}, + {file = "virtualenv-20.26.2.tar.gz", hash = "sha256:82bf0f4eebbb78d36ddaee0283d43fe5736b53880b8a8cdcd37390a07ac3741c"}, ] [package.dependencies] @@ -2909,18 +2907,18 @@ filelock = ">=3.12.2,<4" platformdirs = ">=3.9.1,<5" [package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] name = "wcwidth" -version = "0.2.12" +version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" files = [ - {file = "wcwidth-0.2.12-py2.py3-none-any.whl", hash = "sha256:f26ec43d96c8cbfed76a5075dac87680124fa84e0855195a6184da9c187f133c"}, - {file = "wcwidth-0.2.12.tar.gz", hash = "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"}, + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, ] [[package]] @@ -3020,4 +3018,4 @@ test = ["coverage"] [metadata] lock-version = "2.0" python-versions = "^3.11.3" -content-hash = "0936ef1db7e8ceefe1856aca7ee387a034af454ba5935f6cd46c669aa7c84953" +content-hash = "f5ab769523c6d0b223a4020f92f5929d919472c348a5d08767a88f3570e85e8f" diff --git a/pyproject.toml b/pyproject.toml index 6d13000e..ca0f367e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,16 +14,17 @@ python = "^3.11.3" # Do not change these without careful thought! rdkit = "2023.3.2" xchem-db = "0.1.26b0" +djangorestframework = "3.14.0" # Less strict (flexible dependency) packages... celery = "^5.3.1" deepdiff = "^6.2.0" -djangorestframework = "^3.14.0" django-bootstrap3 = "^23.4" django-cleanup = "^8.0.0" django-extensions = "^3.2.3" django-filter = "^23.2" django-guardian = "^2.4.0" +django-prometheus = "^2.3.1" django-simple-history = "^3.3.0" django-webpack-loader = "^0.7.0" django-rest-swagger = "^2.2.0" @@ -53,7 +54,7 @@ bcrypt = "4.0.1" # Django will (probably) need work in the code to support v4. # Simply changing to django 4 results in errors # like "CSRF Failed: Origin checking failed" -django = "3.2.24" +django = "3.2.25" # We're stuck on ISPyB 4.x to avoid the error: - # ImportError: cannot import name 'ISPyBNoResultException' from 'ispyb.connector.mysqlsp.main' ispyb = "4.13.2" @@ -65,7 +66,7 @@ pre-commit = "^3.3.3" pylint = "^3.0.3" pylint-django = "^2.5.5" httpie = "^3.2.2" -black = "^23.12.0" +black = "^24.3.0" mypy = "^1.7.1" [build-system] diff --git a/viewer/filters.py b/viewer/filters.py index 0cfe82ff..d5e62e03 100644 --- a/viewer/filters.py +++ b/viewer/filters.py @@ -5,6 +5,8 @@ CanonSite, CanonSiteConf, Compound, + Pose, + QuatAssembly, SiteObservation, Snapshot, XtalformSite, @@ -100,3 +102,15 @@ class CompoundFilter(TargetFilterMixin): class Meta: model = Compound fields = ("smiles", "current_identifier", "inchi") + + +class PoseFilter(TargetFilterMixin): + class Meta: + model = Pose + fields = ("target", "canon_site", "compound", "main_site_observation") + + +class AssemblyFilter(TargetFilterMixin): + class Meta: + model = QuatAssembly + fields = ("target",) diff --git a/viewer/fixtures/tagcategories.json b/viewer/fixtures/tagcategories.json index 9a002bba..e502eb50 100644 --- a/viewer/fixtures/tagcategories.json +++ b/viewer/fixtures/tagcategories.json @@ -70,5 +70,14 @@ "colour": "000000", "description": null } +}, +{ + "model": "viewer.tagcategory", + "pk": 9, + "fields": { + "category": "Pose", + "colour": "ff0000", + "description": null + } } ] diff --git a/viewer/managers.py b/viewer/managers.py index 7a1a4826..12d9937d 100644 --- a/viewer/managers.py +++ b/viewer/managers.py @@ -283,3 +283,35 @@ def filter_qs(self): def by_target(self, target): return self.get_queryset().filter_qs().filter(target=target.id) + + +class PoseQueryset(QuerySet): + def filter_qs(self): + Pose = apps.get_model("viewer", "Pose") + CanonSite = apps.get_model("viewer", "CanonSite") + + canonsite_qs = CanonSite.filter_manager.filter_qs() + + qs = Pose.objects.annotate( + target=Subquery( + canonsite_qs.filter( + pk=OuterRef("canon_site__pk"), + ).values( + "target" + )[:1], + ), + upload_name=F("main_site_observation__code"), + ) + + return qs + + +class PoseDataManager(Manager): + def get_queryset(self): + return PoseQueryset(self.model, using=self._db) + + def filter_qs(self): + return self.get_queryset().filter_qs() + + def by_target(self, target): + return self.get_queryset().filter_qs().filter(target=target.id) diff --git a/viewer/migrations/0050_auto_20240410_1125.py b/viewer/migrations/0050_auto_20240410_1125.py new file mode 100644 index 00000000..d9ca2e10 --- /dev/null +++ b/viewer/migrations/0050_auto_20240410_1125.py @@ -0,0 +1,70 @@ +# Generated by Django 3.2.24 on 2024-04-10 11:25 + +import django.db.models.deletion +from django.db import migrations, models + + +class Migration(migrations.Migration): + dependencies = [ + ('viewer', '0049_auto_20240307_1344'), + ] + + operations = [ + migrations.CreateModel( + name='Pose', + fields=[ + ( + 'id', + models.BigAutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name='ID', + ), + ), + ('display_name', models.TextField(null=True)), + ( + 'canon_site', + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to='viewer.canonsite', + ), + ), + ( + 'compound', + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to='viewer.compound', + ), + ), + ( + 'main_site_observation', + models.OneToOneField( + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name='main_pose', + to='viewer.siteobservation', + ), + ), + ], + ), + migrations.AddField( + model_name='historicalsiteobservation', + name='pose', + field=models.ForeignKey( + blank=True, + db_constraint=False, + null=True, + on_delete=django.db.models.deletion.DO_NOTHING, + related_name='+', + to='viewer.pose', + ), + ), + migrations.AddField( + model_name='siteobservation', + name='pose', + field=models.ForeignKey( + null=True, on_delete=django.db.models.deletion.CASCADE, to='viewer.pose' + ), + ), + ] diff --git a/viewer/migrations/0050_auto_20240412_0930.py b/viewer/migrations/0050_auto_20240412_0930.py new file mode 100644 index 00000000..51b27993 --- /dev/null +++ b/viewer/migrations/0050_auto_20240412_0930.py @@ -0,0 +1,23 @@ +# Generated by Django 3.2.24 on 2024-04-12 09:30 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0049_auto_20240307_1344'), + ] + + operations = [ + migrations.AddField( + model_name='sessionprojecttag', + name='hidden', + field=models.BooleanField(default=False), + ), + migrations.AddField( + model_name='siteobservationtag', + name='hidden', + field=models.BooleanField(default=False), + ), + ] diff --git a/viewer/migrations/0051_alter_siteobservation_pose.py b/viewer/migrations/0051_alter_siteobservation_pose.py new file mode 100644 index 00000000..fa965898 --- /dev/null +++ b/viewer/migrations/0051_alter_siteobservation_pose.py @@ -0,0 +1,23 @@ +# Generated by Django 3.2.24 on 2024-04-10 15:30 + +import django.db.models.deletion +from django.db import migrations, models + + +class Migration(migrations.Migration): + dependencies = [ + ('viewer', '0050_auto_20240410_1125'), + ] + + operations = [ + migrations.AlterField( + model_name='siteobservation', + name='pose', + field=models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name='site_observations', + to='viewer.pose', + ), + ), + ] diff --git a/viewer/migrations/0051_auto_20240425_0748.py b/viewer/migrations/0051_auto_20240425_0748.py new file mode 100644 index 00000000..0c7b4f7a --- /dev/null +++ b/viewer/migrations/0051_auto_20240425_0748.py @@ -0,0 +1,23 @@ +# Generated by Django 3.2.24 on 2024-04-25 07:48 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0050_auto_20240412_0930'), + ] + + operations = [ + migrations.AddField( + model_name='historicalsiteobservation', + name='version', + field=models.PositiveSmallIntegerField(default=1), + ), + migrations.AddField( + model_name='siteobservation', + name='version', + field=models.PositiveSmallIntegerField(default=1), + ), + ] diff --git a/viewer/migrations/0052_auto_20240503_1255.py b/viewer/migrations/0052_auto_20240503_1255.py new file mode 100644 index 00000000..7001e499 --- /dev/null +++ b/viewer/migrations/0052_auto_20240503_1255.py @@ -0,0 +1,38 @@ +# Generated by Django 3.2.24 on 2024-05-03 12:55 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0051_auto_20240425_0748'), + ] + + operations = [ + migrations.AddField( + model_name='canonsite', + name='superseded', + field=models.BooleanField(default=False), + ), + migrations.AddField( + model_name='canonsiteconf', + name='superseded', + field=models.BooleanField(default=False), + ), + migrations.AddField( + model_name='historicalsiteobservation', + name='superseded', + field=models.BooleanField(default=False), + ), + migrations.AddField( + model_name='siteobservation', + name='superseded', + field=models.BooleanField(default=False), + ), + migrations.AddField( + model_name='xtalformsite', + name='superseded', + field=models.BooleanField(default=False), + ), + ] diff --git a/viewer/migrations/0053_auto_20240503_1302.py b/viewer/migrations/0053_auto_20240503_1302.py new file mode 100644 index 00000000..05da4c5f --- /dev/null +++ b/viewer/migrations/0053_auto_20240503_1302.py @@ -0,0 +1,28 @@ +# Generated by Django 3.2.24 on 2024-05-03 13:02 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0052_auto_20240503_1255'), + ] + + operations = [ + migrations.AddField( + model_name='canonsite', + name='version', + field=models.PositiveSmallIntegerField(default=1), + ), + migrations.AddField( + model_name='canonsiteconf', + name='version', + field=models.PositiveSmallIntegerField(default=1), + ), + migrations.AddField( + model_name='xtalformsite', + name='version', + field=models.PositiveSmallIntegerField(default=1), + ), + ] diff --git a/viewer/migrations/0054_auto_20240509_0838.py b/viewer/migrations/0054_auto_20240509_0838.py new file mode 100644 index 00000000..bd4cf0e0 --- /dev/null +++ b/viewer/migrations/0054_auto_20240509_0838.py @@ -0,0 +1,27 @@ +# Generated by Django 3.2.24 on 2024-05-09 08:38 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0053_auto_20240503_1302'), + ] + + operations = [ + migrations.RemoveField( + model_name='experiment', + name='version', + ), + migrations.AddField( + model_name='experimentupload', + name='upload_data_dir', + field=models.TextField(null=True), + ), + migrations.AddField( + model_name='experimentupload', + name='upload_version', + field=models.PositiveSmallIntegerField(default=1), + ), + ] diff --git a/viewer/migrations/0054_merge_20240507_1558.py b/viewer/migrations/0054_merge_20240507_1558.py new file mode 100644 index 00000000..8c98b007 --- /dev/null +++ b/viewer/migrations/0054_merge_20240507_1558.py @@ -0,0 +1,14 @@ +# Generated by Django 3.2.24 on 2024-05-07 15:58 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0051_alter_siteobservation_pose'), + ('viewer', '0053_auto_20240503_1302'), + ] + + operations = [ + ] diff --git a/viewer/migrations/0055_merge_20240516_1003.py b/viewer/migrations/0055_merge_20240516_1003.py new file mode 100644 index 00000000..2280e1eb --- /dev/null +++ b/viewer/migrations/0055_merge_20240516_1003.py @@ -0,0 +1,14 @@ +# Generated by Django 3.2.25 on 2024-05-16 10:03 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('viewer', '0054_auto_20240509_0838'), + ('viewer', '0054_merge_20240507_1558'), + ] + + operations = [ + ] diff --git a/viewer/models.py b/viewer/models.py index 31336fa4..0d38914f 100644 --- a/viewer/models.py +++ b/viewer/models.py @@ -1,6 +1,7 @@ import logging import uuid from dataclasses import dataclass +from pathlib import Path from django.conf import settings from django.contrib.auth.models import User @@ -17,6 +18,7 @@ CanonSiteDataManager, CompoundDataManager, ExperimentDataManager, + PoseDataManager, QuatAssemblyDataManager, SiteObservationDataManager, XtalformDataManager, @@ -171,6 +173,8 @@ class ExperimentUpload(models.Model): reference_structure_transforms = models.FileField( upload_to="experiment-upload/", max_length=255 ) + upload_data_dir = models.TextField(null=True) + upload_version = models.PositiveSmallIntegerField(default=1) def __str__(self) -> str: return f"{self.project}" @@ -178,12 +182,20 @@ def __str__(self) -> str: def __repr__(self) -> str: return "" % (self.id, self.project, self.target) + def get_upload_path(self): + return ( + Path(settings.MEDIA_ROOT) + .joinpath(settings.TARGET_LOADER_MEDIA_DIRECTORY) + .joinpath(self.task_id) + .joinpath(Path(str(self.file)).stem) + .joinpath(self.upload_data_dir) + ) + class Experiment(models.Model): experiment_upload = models.ForeignKey(ExperimentUpload, on_delete=models.CASCADE) code = models.TextField(null=True) status = models.IntegerField(null=True) - version = models.IntegerField(null=True) pdb_info = models.FileField( upload_to="target_loader_data/", null=True, max_length=255 ) @@ -360,7 +372,15 @@ class Meta: ] -class CanonSite(models.Model): +class Versionable(models.Model): + superseded = models.BooleanField(null=False, default=False) + version = models.PositiveSmallIntegerField(null=False, default=1) + + class Meta: + abstract = True + + +class CanonSite(Versionable, models.Model): name = models.TextField() residues = models.JSONField(encoder=DjangoJSONEncoder) # TODO: missing in db, check if correct, (might be correct, but might not) @@ -381,7 +401,7 @@ def __repr__(self) -> str: return "" % (self.id, self.name) -class XtalformSite(models.Model): +class XtalformSite(Versionable, models.Model): xtalform = models.ForeignKey(Xtalform, on_delete=models.CASCADE) canon_site = models.ForeignKey(CanonSite, on_delete=models.CASCADE) lig_chain = models.CharField(max_length=1) @@ -408,7 +428,7 @@ def __repr__(self) -> str: ) -class CanonSiteConf(models.Model): +class CanonSiteConf(Versionable, models.Model): canon_site = models.ForeignKey(CanonSite, on_delete=models.CASCADE) # TODO: name not present in metadata atm name = models.TextField(null=True) @@ -427,13 +447,44 @@ def __repr__(self) -> str: return "" % (self.id, self.name, self.canon_site) -class SiteObservation(models.Model): +class Pose(models.Model): + canon_site = models.ForeignKey(CanonSite, on_delete=models.CASCADE) + compound = models.ForeignKey(Compound, on_delete=models.CASCADE) + main_site_observation = models.OneToOneField( + "SiteObservation", + null=True, + on_delete=models.CASCADE, + related_name="main_pose", + ) + display_name = models.TextField(null=True) + + objects = models.Manager() + filter_manager = PoseDataManager() + + def __str__(self) -> str: + return f"{self.main_site_observation.code}" + + def __repr__(self) -> str: + return "" % ( + self.id, + self.main_site_observation.code, + self.display_name, + ) + + +class SiteObservation(Versionable, models.Model): code = models.TextField(null=True) longcode = models.TextField(null=True) experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE) cmpd = models.ForeignKey(Compound, null=True, on_delete=models.CASCADE) xtalform_site = models.ForeignKey(XtalformSite, on_delete=models.CASCADE) canon_site_conf = models.ForeignKey(CanonSiteConf, on_delete=models.CASCADE) + pose = models.ForeignKey( + Pose, + on_delete=models.CASCADE, + null=True, + related_name="site_observations", + ) bound_file = models.FileField( upload_to="target_loader_data/", null=True, max_length=255 ) @@ -1206,6 +1257,7 @@ class Tag(models.Model): null=True, help_text="Optional JSON field containing name/value pairs for future use", ) + hidden = models.BooleanField(default=False) def __str__(self) -> str: return f"{self.tag}" diff --git a/viewer/serializers.py b/viewer/serializers.py index a029267b..41252d89 100644 --- a/viewer/serializers.py +++ b/viewer/serializers.py @@ -1,11 +1,12 @@ import logging -import os +from pathlib import Path from urllib.parse import urljoin +import yaml from django.conf import settings from django.contrib.auth.models import User -from django.contrib.postgres.aggregates import ArrayAgg -from django.db.models import F +from django.db import IntegrityError, transaction +from django.db.models import Count from frag.network.decorate import get_3d_vects_for_mol, get_vect_indices_for_mol from frag.network.query import get_full_graph from rdkit import Chem @@ -14,8 +15,8 @@ from api.security import ISpyBSafeQuerySet from api.utils import draw_mol, validate_tas -from scoring.models import SiteObservationGroup from viewer import models +from viewer.target_loader import XTALFORMS_FILE from viewer.target_set_upload import sanitize_mol from viewer.utils import get_https_host @@ -30,100 +31,6 @@ class Meta: fields = "__all__" -def get_protein_sequences(pdb_block): - sequence_list = [] - aa = { - 'CYS': 'C', - 'ASP': 'D', - 'SER': 'S', - 'GLN': 'Q', - 'LYS': 'K', - 'ILE': 'I', - 'PRO': 'P', - 'THR': 'T', - 'PHE': 'F', - 'ASN': 'N', - 'GLY': 'G', - 'HIS': 'H', - 'LEU': 'L', - 'ARG': 'R', - 'TRP': 'W', - 'ALA': 'A', - 'VAL': 'V', - 'GLU': 'E', - 'TYR': 'Y', - 'MET': 'M', - } - - current_chain = 'A' - current_sequence = '' - current_number = 0 - - for line in pdb_block.split('\n'): - if line[0:4] == 'ATOM': - residue = line[17:20].strip() - chain = line[21].strip() - n = int(line[22:26].strip()) - - if chain != current_chain: - chain_dict = {'chain': current_chain, 'sequence': current_sequence} - sequence_list.append(chain_dict) - current_sequence = '' - current_chain = chain - if not n == current_number: - if n == current_number + 1: - try: - seqres = aa[residue] - except: - seqres = 'X' - current_sequence += seqres - else: - if not current_number == 0: - gap = n - current_number - gap_str = '' - for _ in range(gap): - gap_str += 'X' - current_sequence += gap_str - current_number = n - - if not sequence_list: - chain_dict = {'chain': current_chain, 'sequence': current_sequence} - sequence_list.append(chain_dict) - - return sequence_list - - -def protein_sequences(obj): - """Common enabler code for Target-related serializers""" - proteins = models.SiteObservation.filter_manager.by_target(target=obj) - protein_file = None - for protein in proteins: - if protein.apo_file: - if not os.path.isfile(protein.apo_file.path): - continue - protein_file = protein.apo_file - break - if not protein_file: - return [{'chain': '', 'sequence': ''}] - - protein_file.open(mode='r') - pdb_block = protein_file.read() - protein_file.close() - - sequences = get_protein_sequences(pdb_block) - return sequences - - -def template_protein(obj): - """Common enabler code for Target-related serializers""" - - proteins = models.SiteObservation.filter_manager.by_target(target=obj) - for protein in proteins: - if protein.apo_file: - return protein.apo_file.url - return "NOT AVAILABLE" - - class CompoundIdentifierTypeSerializer(serializers.ModelSerializer): class Meta: model = models.CompoundIdentifierType @@ -140,10 +47,69 @@ class TargetSerializer(serializers.ModelSerializer): template_protein = serializers.SerializerMethodField() zip_archive = serializers.SerializerMethodField() metadata = serializers.SerializerMethodField() - sequences = serializers.SerializerMethodField() def get_template_protein(self, obj): - return template_protein(obj) + exp_upload = ( + models.ExperimentUpload.objects.filter( + target=obj, + ) + .order_by('-commit_datetime') + .first() + ) + + yaml_path = exp_upload.get_upload_path() + + # last components of path, need for reconstruction later + comps = yaml_path.parts[-2:] + + # and the file itself + yaml_path = yaml_path.joinpath(XTALFORMS_FILE) + logger.debug("assemblies path: %s", yaml_path) + if yaml_path.is_file(): + with open(yaml_path, "r", encoding="utf-8") as file: + contents = yaml.safe_load(file) + try: + assemblies = contents["assemblies"] + except KeyError: + logger.error("No 'assemblies' section in '%s'", XTALFORMS_FILE) + return '' + + try: + first = list(assemblies.values())[0] + except IndexError: + logger.error("No assemblies in 'assemblies' section") + return '' + + try: + reference = first["reference"] + except KeyError: + logger.error("No assemblies in 'assemblies' section") + return '' + + ref_path = ( + Path(settings.TARGET_LOADER_MEDIA_DIRECTORY) + .joinpath(exp_upload.task_id) + .joinpath(comps[0]) + .joinpath(comps[1]) + .joinpath("crystallographic_files") + .joinpath(reference) + .joinpath(f"{reference}.pdb") + ) + logger.debug('ref_path: %s', ref_path) + if Path(settings.MEDIA_ROOT).joinpath(ref_path).is_file(): + request = self.context.get('request', None) + if request is not None: + return request.build_absolute_uri( + Path(settings.MEDIA_URL).joinpath(ref_path) + ) + else: + return '' + else: + logger.error("Reference pdb file doesn't exist") + return '' + else: + logger.error("'%s' missing", XTALFORMS_FILE) + return '' def get_zip_archive(self, obj): # The if-check is because the filefield in target has null=True. @@ -157,9 +123,6 @@ def get_metadata(self, obj): return urljoin(get_https_host(self.context["request"]), obj.metadata.url) return - def get_sequences(self, obj): - return protein_sequences(obj) - class Meta: model = models.Target # TODO: it's missing protein_set. is it necessary anymore? @@ -173,7 +136,6 @@ class Meta: "metadata", "zip_archive", "upload_status", - "sequences", ) extra_kwargs = { "id": {"read_only": True}, @@ -184,7 +146,6 @@ class Meta: "metadata": {"read_only": True}, "zip_archive": {"read_only": True}, "upload_status": {"read_only": True}, - "sequences": {"read_only": True}, } @@ -731,107 +692,6 @@ class Meta: fields = '__all__' -class TargetMoleculesSerializer(serializers.ModelSerializer): - template_protein = serializers.SerializerMethodField() - zip_archive = serializers.SerializerMethodField() - metadata = serializers.SerializerMethodField() - sequences = serializers.SerializerMethodField() - molecules = serializers.SerializerMethodField() - tags_info = serializers.SerializerMethodField() - tag_categories = serializers.SerializerMethodField() - - def get_template_protein(self, obj): - return template_protein(obj) - - def get_zip_archive(self, obj): - # The if-check is because the filefield in target has null=True. - # Note that this link will not work on local - if hasattr(obj, 'zip_archive') and obj.zip_archive.name: - return urljoin(get_https_host(self.context["request"]), obj.zip_archive.url) - return - - def get_metadata(self, obj): - if hasattr(obj, 'metadata') and obj.metadata.name: - return urljoin(get_https_host(self.context["request"]), obj.metadata.url) - return - - def get_sequences(self, obj): - return protein_sequences(obj) - - def get_molecules(self, obj): - mols = models.SiteObservation.objects.filter( - experiment__experiment_upload__target__id=obj.id - ).annotate( - # NB! some of the fields are just renamed here, avoiding - # that would simplify things here and remove some lines of - # code. but that means front-end code needs to know about - # the changes - protein_code=F('code'), - molecule_protein=F('experiment__pdb_info'), - sdf_info=F('ligand_mol_file'), - lig_id=F('seq_id'), - tags_set=ArrayAgg("siteobservationtag__pk"), - ) - fields = [ - "id", - "smiles", - "cmpd", - "protein_code", - "molecule_protein", - "lig_id", - "chain_id", - "sdf_info", - "tags_set", - ] - - logger.debug("%s", mols) - logger.debug("%s", mols.values(*fields)) - - molecules = [ - {'data': k, 'tags_set': k['tags_set']} for k in mols.values(*fields) - ] - - return molecules - - def get_tags_info(self, obj): - tags = models.SiteObservationTag.objects.filter(target_id=obj.id) - tags_info = [] - for tag in tags: - tag_data = models.SiteObservationTag.objects.filter(id=tag.id).values() - tag_coords = SiteObservationGroup.objects.filter( - id=tag.mol_group_id - ).values('x_com', 'y_com', 'z_com') - tag_dict = {'data': tag_data, 'coords': tag_coords} - tags_info.append(tag_dict) - - return tags_info - - def get_tag_categories(self, obj): - tag_categories = ( - models.TagCategory.objects.filter(siteobservationtag__target_id=obj.id) - .distinct() - .values() - ) - return tag_categories - - class Meta: - model = models.Target - fields = ( - "id", - "title", - "project_id", - "default_squonk_project", - "template_protein", - "metadata", - "zip_archive", - "upload_status", - "sequences", - "molecules", - "tags_info", - "tag_categories", - ) - - class DownloadStructuresSerializer(serializers.Serializer): target_name = serializers.CharField(max_length=200, default=None, allow_blank=True) proteins = serializers.CharField(max_length=5000, default='', allow_blank=True) @@ -982,3 +842,192 @@ class XtalformSiteReadSerializer(serializers.ModelSerializer): class Meta: model = models.XtalformSite fields = '__all__' + + +class PoseSerializer(serializers.ModelSerializer): + site_observations = serializers.PrimaryKeyRelatedField( + many=True, + queryset=models.SiteObservation.objects.all(), + ) + main_site_observation = serializers.PrimaryKeyRelatedField( + required=False, default=None, queryset=models.SiteObservation.objects.all() + ) + main_site_observation_cmpd_code = serializers.SerializerMethodField() + + def get_main_site_observation_cmpd_code(self, obj): + return obj.main_site_observation.cmpd.compound_code + + def update_pose_main_observation(self, main_obvs): + if main_obvs.pose.site_observations.count() == 1: + main_obvs.pose.delete() + + def remove_empty_poses(self, pose): + # fmt: off + empty_poses = models.Pose.objects.filter( + canon_site=pose.canon_site, + compound=pose.compound, + ).annotate( + num_obvs=Count('site_observations'), + ).filter( + num_obvs=0, + ) + # fmt: on + logger.debug('empty_poses: %s', empty_poses) + empty_poses.delete() + + def create(self, validated_data): + logger.debug('validated_data: %s', validated_data) + try: + with transaction.atomic(): + # only situation with suggested main being a main in + # other pose is when it's the only observation in + # pose, the other cases must have been caught by + # validation + self.update_pose_main_observation( + validated_data['main_site_observation'] + ) + pose = super().create(validated_data) + self.remove_empty_poses(pose) + return pose + + except IntegrityError as exc: + raise serializers.ValidationError({'errors': exc.args[0]}) + + def update(self, instance, validated_data): + logger.debug('validated_data: %s', validated_data) + + try: + with transaction.atomic(): + # TODO: func here to release the main + pose = super().update(instance, validated_data) + pose.save() + self.remove_empty_poses(pose) + return pose + + except IntegrityError as exc: + raise serializers.ValidationError({'errors': exc.args[0]}) + + def validate(self, data): + """Validate data sent to create or update pose. + + First look at the main_site_observation. If this is not set, + try to find a suitable one from the list of observations. If + is given, check if it already isn't a main observation to some + othe pose. + + Then check observation and make sure that: + - they have the same canon_site and compound as the pose being created + - the pose they're being removed from is deleted when empty + + """ + logger.info('+ validate: %s', data) + + template = ( + "Site observation {} cannot be assigned to pose because " + + "pose's {} ({}) doesn't match with observation's ({})" + ) + + messages: dict[str, list[str]] = { + 'site_observations': [], + 'main_site_observation': [], + } + validated_observations = [] + + # populate data struct with missing attributes but only when + # they're missing, not simply undefined. not sure why the + # serializer isn't doing this here + instance = getattr(self, 'instance', None) + if 'site_observations' not in data.keys(): + data['site_observations'] = ( + instance.site_observations.all() if instance else [] + ) + if 'main_site_observation' not in data.keys(): + data['main_site_observation'] = ( + instance.main_site_observation if instance else None + ) + if 'compound' not in data.keys(): + data['compound'] = instance.compound if instance else None + if 'canon_site' not in data.keys(): + data['canon_site'] = instance.canon_site if instance else None + + if not data['site_observations']: + if hasattr(self, 'instance'): + messages['site_observations'].append( + 'Cannot remove all site observations from pose' + ) + else: + messages['site_observations'].append('Cannot create empty pose') + + if data['main_site_observation']: + logger.debug('main observation given, trying to set one') + main_pose = getattr(data['main_site_observation'], 'main_pose', None) + if ( + main_pose + and main_pose != instance + and main_pose.site_observations.count() > 1 + ): + # checking length, because if single observation in + # pose, it would leave an empty pose which will be + # deleted. otherwise don't allow setting main + messages['main_site_observation'].append( + 'Requested main_site_observation already the main observation ' + + f'in pose {main_pose.display_name}' + ) + + for so in data['site_observations']: + all_good = True + + # only try to set one if not given in request data + if not data['main_site_observation']: + logger.debug('no main observation given, trying to find one') + if not hasattr(so, 'main_pose'): + data['main_site_observation'] = so + + logger.debug('processing observation: %s', so) + if so.canon_site_conf.canon_site != data['canon_site']: + all_good = False + messages['site_observations'].append( + template.format( + so.code, + 'canonical site', + data['canon_site'].name, + so.canon_site_conf.canon_site.name, + ) + ) + if so.cmpd != data['compound']: + all_good = False + messages['site_observations'].append( + template.format( + so.code, + 'compound', + data['compound'].compound_code, + so.cmpd.compound_code, + ) + ) + logger.debug('accumulated messages: %s', messages) + if all_good: + validated_observations.append(so) + + # did we get main observaton? + if not data['main_site_observation']: + messages['main_site_observation'].append( + 'No suitable observation found to set as main_site_observation' + ) + + if any(messages.values()): + raise serializers.ValidationError(messages) + else: + data['site_observations'] = validated_observations + return data + + class Meta: + model = models.Pose + fields = ( + 'id', + 'display_name', + 'canon_site', + 'compound', + 'main_site_observation', + 'site_observations', + 'main_site_observation_cmpd_code', + ) diff --git a/viewer/target_loader.py b/viewer/target_loader.py index ba4aaa19..26e3719d 100644 --- a/viewer/target_loader.py +++ b/viewer/target_loader.py @@ -35,6 +35,7 @@ Compound, Experiment, ExperimentUpload, + Pose, Project, QuatAssembly, SiteObservation, @@ -97,6 +98,8 @@ class MetadataObject: """ instance: Model + key: str + versioned_key: str index_data: dict = field(default_factory=dict) new: bool = False @@ -118,7 +121,7 @@ class ProcessedObject: key: str defaults: dict = field(default_factory=dict) index_data: dict = field(default_factory=dict) - identifier: Optional[str] = "" + versioned_key: Optional[str] = "" @dataclass @@ -298,10 +301,10 @@ def alphanumerator(start_from: str = "") -> Generator[str, None, None]: return generator -def strip_version(s: str) -> str: +def strip_version(s: str, separator: str = "/") -> Tuple[str, int]: # format something like XX01ZVNS2B-x0673/B/501/1 - # remove tailing '/1' - return s[0 : s.rfind('/')] + # remove tailing '1' + return s[0 : s.rfind(separator)], int(s[s.rfind(separator) + 1 :]) def create_objects(func=None, *, depth=math.inf): @@ -328,7 +331,8 @@ def wrapper_create_objects( flattened_data = flatten_dict(yaml_data, depth=depth) result = {} - created, existing, failed = 0, 0, 0 + created, existing, failed, updated = 0, 0, 0, 0 + for item in flattened_data: logger.debug("flattened data item: %s", item) instance_data = func( @@ -377,10 +381,7 @@ def wrapper_create_objects( instance_data.model_class._meta.object_name, # pylint: disable=protected-access obj, ) - if new: - created = created + 1 - else: - existing = existing + 1 + except MultipleObjectsReturned: msg = "{}.get_or_create in {} returned multiple objects for {}".format( instance_data.model_class._meta.object_name, # pylint: disable=protected-access @@ -397,7 +398,12 @@ def wrapper_create_objects( self.report.log(logging.ERROR, msg) failed = failed + 1 - if not obj: + if obj: + # update any additional fields + instance_qs = instance_data.model_class.objects.filter(pk=obj.pk) + instance_qs.update(**instance_data.defaults) + obj.refresh_from_db() + else: # create fake object so I can just push the upload # through and compile report for user feedback obj = instance_data.model_class( @@ -409,11 +415,30 @@ def wrapper_create_objects( obj, ) + if new: + created = created + 1 + # check if old versions exist and mark them as superseded + if "version" in instance_data.fields.keys(): + del instance_data.fields["version"] + superseded = instance_data.model_class.objects.filter( + **instance_data.fields, + ).exclude( + pk=obj.pk, + ) + updated += superseded.update(superseded=True) + + else: + existing = existing + 1 + m = MetadataObject( - instance=obj, index_data=instance_data.index_data, new=new + instance=obj, + key=instance_data.key, + versioned_key=instance_data.versioned_key, + index_data=instance_data.index_data, + new=new, ) # index data here probs - result[instance_data.key] = m + result[instance_data.versioned_key] = m msg = "{} {} objects processed, {} created, {} fetched from database".format( created + existing + failed, @@ -425,6 +450,19 @@ def wrapper_create_objects( ) # pylint: disable=protected-access self.report.log(logging.INFO, msg) + # refresh all objects to make sure they're up to date. + # this is specifically because of the superseded flag above - + # I'm setting this in separate queryset, the db rows are + # updated, but the changes are not being propagated to the + # objects in result dict. Well aware that this isn't efficient + # but I don't have access to parent's versioned key here, (and + # even if I did, there's no guarantee that they would have + # already been processd), so that's why updating every single + # object. + if updated > 0: + for k in result.values(): + k.instance.refresh_from_db() + return result return wrapper_create_objects @@ -446,7 +484,7 @@ def __init__( self.tempdir = tempdir self.raw_data = Path(self.tempdir).joinpath(self.bundle_name) self.task = task - self.version_number = None + self.version_number = 1 self.version_dir = None self.previous_version_dirs = None self.user_id = user_id @@ -764,14 +802,14 @@ def process_experiment( ) try: - panddas_files = data["crystallographic_files"]["panddas_event_files"] + event_files = data["crystallographic_files"]["ligand_binding_events"] except KeyError: - panddas_files = [] + event_files = [] map_info_files = self.validate_map_files( - key="panddas_event_files", + key="ligand_binding_events", obj_identifier=experiment_name, - file_struct=panddas_files, + file_struct=event_files, validate_files=validate_files, ) @@ -810,10 +848,6 @@ def process_experiment( except KeyError: smiles = "" - # TODO: unhandled atm - # version int old versions are kept target loader - version = 1 - # if empty or key missing entirely, ensure code_prefix returns empty code_prefix = extract(key="code_prefix", level=logging.INFO) # ignoring type because tooltip dict can legitimately be empty @@ -832,7 +866,6 @@ def process_experiment( defaults = { "experiment_upload": self.experiment_upload, "status": status, - "version": version, "type": exp_type, "pdb_info": str(self._get_final_path(pdb_info)), "mtz_info": str(self._get_final_path(mtz_info)), @@ -855,6 +888,7 @@ def process_experiment( model_class=Experiment, fields=fields, key=experiment_name, + versioned_key=experiment_name, defaults=defaults, index_data=index_fields, ) @@ -916,6 +950,7 @@ def process_compound( fields={}, defaults=defaults, key=protein_name, + versioned_key=protein_name, ) @create_objects(depth=1) @@ -969,6 +1004,7 @@ def process_xtalform( model_class=Xtalform, fields=fields, key=xtalform_name, + versioned_key=xtalform_name, defaults=defaults, ) @@ -1010,6 +1046,7 @@ def process_quat_assembly( model_class=QuatAssembly, fields=fields, key=assembly_name, + versioned_key=assembly_name, ) @create_objects(depth=3) @@ -1059,6 +1096,7 @@ def process_xtalform_quatassembly( model_class=XtalformQuatAssembly, fields=fields, key=xtalform_id, + versioned_key=xtalform_id, ) @create_objects(depth=1) @@ -1082,7 +1120,9 @@ def process_canon_site( """ del kwargs assert item_data - canon_site_id, data = item_data + v_canon_site_id, data = item_data + + canon_site_id, version = strip_version(v_canon_site_id, separator="+") extract = functools.partial( self._extract, @@ -1095,6 +1135,10 @@ def process_canon_site( fields = { "name": canon_site_id, + "version": version, + } + + defaults = { "residues": residues, } @@ -1112,6 +1156,8 @@ def process_canon_site( fields=fields, index_data=index_data, key=canon_site_id, + versioned_key=v_canon_site_id, + defaults=defaults, ) @create_objects(depth=1) @@ -1134,8 +1180,10 @@ def process_canon_site_conf( """ del kwargs assert item_data - conf_site_name, data = item_data - canon_site = canon_sites[conf_site_name] + v_conf_site_name, data = item_data + conf_site_name, version = strip_version(v_conf_site_name, separator="+") + + canon_site = canon_sites[v_conf_site_name] extract = functools.partial( self._extract, @@ -1149,11 +1197,16 @@ def process_canon_site_conf( fields = { "name": conf_site_name, - "residues": residues, "canon_site": canon_site, + "version": version, + } + + defaults = { + "residues": residues, } members = extract(key="members") + ref_ligands = extract(key="reference_ligand_id") index_fields = { @@ -1166,6 +1219,8 @@ def process_canon_site_conf( fields=fields, index_data=index_fields, key=conf_site_name, + versioned_key=v_conf_site_name, + defaults=defaults, ) @create_objects(depth=1) @@ -1189,7 +1244,8 @@ def process_xtalform_site( """ del kwargs assert item_data - xtalform_site_name, data = item_data + v_xtalform_site_name, data = item_data + xtalform_site_name, version = strip_version(v_xtalform_site_name) extract = functools.partial( self._extract, @@ -1212,6 +1268,7 @@ def process_xtalform_site( "xtalform_site_id": xtalform_site_name, "xtalform": xtalform, "canon_site": canon_site, + "version": version, } defaults = { @@ -1228,19 +1285,21 @@ def process_xtalform_site( fields=fields, defaults=defaults, key=xtalform_site_name, + versioned_key=v_xtalform_site_name, index_data=index_data, ) - @create_objects(depth=5) + @create_objects(depth=6) def process_site_observation( self, experiments: dict[int | str, MetadataObject], compounds: dict[int | str, MetadataObject], xtalform_sites: dict[str, Model], canon_site_confs: dict[int | str, MetadataObject], - item_data: tuple[str, str, str, int | str, int | str, dict] | None = None, + item_data: tuple[str, str, str, int | str, int, str, dict] | None = None, # chain: str, # ligand: str, + # version: int, # idx: int | str, # data: dict, validate_files: bool = True, @@ -1265,11 +1324,12 @@ def process_site_observation( del kwargs assert item_data try: - experiment_id, _, chain, ligand, idx, data = item_data + experiment_id, _, chain, ligand, version, v_idx, data = item_data except ValueError: # wrong data item return None + idx, _ = strip_version(v_idx, separator="+") extract = functools.partial( self._extract, data=data, @@ -1282,6 +1342,7 @@ def process_site_observation( longcode = f"{experiment.code}_{chain}_{str(ligand)}_{str(idx)}" key = f"{experiment.code}/{chain}/{str(ligand)}" + v_key = f"{experiment.code}/{chain}/{str(ligand)}/{version}" smiles = extract(key="ligand_smiles_string") @@ -1293,7 +1354,6 @@ def process_site_observation( # the first. try: logger.debug('exp: %s, %s', experiment, experiments[experiment_id].new) - # logger.debug('exp compounds: %s', experiment.compounds) compound = experiment.compounds.get( smiles=experiments[experiment_id].index_data["smiles"] ) @@ -1314,8 +1374,8 @@ def process_site_observation( f"Multiple compounds for experiment {experiment.code}", ) - canon_site_conf = canon_site_confs[idx].instance - xtalform_site = xtalform_sites[key] + canon_site_conf = canon_site_confs[v_idx].instance + xtalform_site = xtalform_sites[v_key] ( # pylint: disable=unbalanced-tuple-unpacking bound_file, @@ -1367,6 +1427,7 @@ def process_site_observation( fields = { # Code for this protein (e.g. Mpro_Nterm-x0029_A_501_0) "longcode": longcode, + "version": version, "experiment": experiment, "cmpd": compound, "xtalform_site": xtalform_site, @@ -1397,6 +1458,7 @@ def process_site_observation( fields=fields, defaults=defaults, key=key, + versioned_key=v_key, ) def process_bundle(self): @@ -1473,6 +1535,12 @@ def process_bundle(self): # add upload as anonymous user committer = get_user_model().objects.get(pk=settings.ANONYMOUS_USER) + # collect top level info + self.version_number = int(meta["version_number"]) + self.version_dir = meta["version_dir"] + self.previous_version_dirs = meta["previous_version_dirs"] + prefix_tooltips = meta.get("code_prefix_tooltips", {}) + # TODO: is it here where I can figure out if this has already been uploaded? if self._is_already_uploaded(target_created, project_created): # remove uploaded file @@ -1490,12 +1558,6 @@ def process_bundle(self): assert self.target self.target.project_id.add(self.project) - # collect top level info - self.version_number = meta["version_number"] - self.version_dir = meta["version_dir"] - self.previous_version_dirs = meta["previous_version_dirs"] - prefix_tooltips = meta.get("code_prefix_tooltips", {}) - # check transformation matrix files ( # pylint: disable=unbalanced-tuple-unpacking trans_neighbourhood, @@ -1525,6 +1587,8 @@ def process_bundle(self): self.experiment_upload.reference_structure_transforms = str( self._get_final_path(trans_ref_struct) ) + self.experiment_upload.upload_data_dir = self.version_dir + self.experiment_upload.upload_version = self.version_number self.experiment_upload.save() ( # pylint: disable=unbalanced-tuple-unpacking @@ -1641,6 +1705,7 @@ def process_bundle(self): # now can update CanonSite with ref_conf_site # also, fill the canon_site_num field + # TODO: ref_conf_site is with version, object's key isn't for val in canon_site_objects.values(): # pylint: disable=no-member val.instance.ref_conf_site = canon_site_conf_objects[ val.index_data["reference_conformer_site_id"] @@ -1654,8 +1719,7 @@ def process_bundle(self): xtalform_site_by_tag = {} for val in xtalform_sites_objects.values(): # pylint: disable=no-member for k in val.index_data["residues"]: - # strip the version number from tag - xtalform_site_by_tag[strip_version(k)] = val.instance + xtalform_site_by_tag[k] = val.instance site_observation_objects = self.process_site_observation( yaml_data=crystals, @@ -1666,12 +1730,18 @@ def process_bundle(self): ) values = ["experiment"] - qs = ( - SiteObservation.objects.values(*values) - .order_by(*values) - .annotate(obvs=ArrayAgg("id")) - .values_list("obvs", flat=True) - ) + # fmt: off + qs = SiteObservation.objects.filter( + experiment__experiment_upload__target=self.target, + code__isnull=True, + ).values( + *values, + ).order_by( + *values, + ).annotate( + obvs=ArrayAgg("id"), + ).values_list("obvs", flat=True) + # fmt: on for elem in qs: # fmt: off @@ -1702,6 +1772,7 @@ def process_bundle(self): # 2024-03-04, if you need to check for so in so_group.filter(code__isnull=True): + logger.debug("processing so: %s", so.longcode) if so.experiment.type == 1: # manual. code is pdb code code = f"{so.experiment.code}-{next(suffix)}" @@ -1725,12 +1796,17 @@ def process_bundle(self): # TODO: this should ideally be solved by db engine, before # rushing to write the trigger, have think about the # loader concurrency situations - if SiteObservation.objects.filter( + code_qs = SiteObservation.objects.filter( experiment__experiment_upload__target=self.target, code=code, - ).exists(): + ) + # if code exists and the experiment is new + logger.debug( + 'checking code uniq: %s, %s', code, so.experiment.status + ) + if code_qs.exists() and so.experiment.status == 0: msg = ( - f"short code {code} already exists for this target; " + f"short code {code} already exists for this target; " + "specify a code_prefix to resolve this conflict" ) self.report.log(logging.ERROR, msg) @@ -1738,11 +1814,22 @@ def process_bundle(self): so.code = code so.save() + # site_observations_versioned = {} + # for val in site_observation_objects.values(): # pylint: disable=no-member + # site_observations_versioned[val.versioned_key] = val.instance + # final remaining fk, attach reference site observation to canon_site_conf for val in canon_site_conf_objects.values(): # pylint: disable=no-member val.instance.ref_site_observation = site_observation_objects[ - strip_version(val.index_data["reference_ligands"]) + val.index_data["reference_ligands"] ].instance + logger.debug("attaching canon_site_conf: %r", val.instance) + logger.debug( + "attaching canon_site_conf: %r", + site_observation_objects[ + val.index_data["reference_ligands"] + ].instance.longcode, + ) val.instance.save() logger.debug("data read and processed, adding tags") @@ -1768,8 +1855,10 @@ def process_bundle(self): ) tag = val.instance.name.split('+')[0] so_list = [ - site_observation_objects[strip_version(k)].instance + site_observation_objects[k].instance for k in val.index_data["members"] + # site_observations_versioned[k] + # for k in val.index_data["members"] ] self._tag_observations(tag, prefix, "ConformerSites", so_list) @@ -1804,13 +1893,27 @@ def process_bundle(self): ) tag = f"{val.instance.xtalform.name} - {val.instance.xtalform_site_id}" so_list = [ - site_observation_objects[strip_version(k)].instance - for k in val.index_data["residues"] + site_observation_objects[k].instance for k in val.index_data["residues"] ] self._tag_observations(tag, prefix, "CrystalformSites", so_list) logger.debug("xtalform_sites objects tagged") + self._generate_poses() + + # tag all new observations, so that the curator can find and + # re-pose them + self._tag_observations( + "New", + "", + "Other", + [ + k.instance + for k in site_observation_objects.values() # pylint: disable=no-member + if k.new + ], + ) + def _load_yaml(self, yaml_file: Path) -> dict | None: contents = None try: @@ -1859,6 +1962,60 @@ def _extract( return result + def _generate_poses(self): + values = ["canon_site_conf__canon_site", "cmpd"] + # fmt: off + pose_groups = SiteObservation.objects.exclude( + canon_site_conf__canon_site__isnull=True, + ).exclude( + cmpd__isnull=True, + ).values( + *values + ).order_by( + "canon_site_conf__canon_site", + ).annotate( + obvs=ArrayAgg('id'), + ).values_list("obvs", flat=True) + # fmt: on + + for group in pose_groups: + pose_items = SiteObservation.objects.filter(pk__in=group) + sample = pose_items.first() + # check for existing group + try: + pose = Pose.objects.get( + canon_site=sample.canon_site_conf.canon_site, + compound=sample.cmpd, + ) + except Pose.DoesNotExist: + # create new, add random observation as main + pose = Pose( + canon_site=sample.canon_site_conf.canon_site, + compound=sample.cmpd, + main_site_observation=sample, + display_name=sample.code, + ) + pose.save() + except MultipleObjectsReturned: + # must be a follow-up upload. create new pose, but + # only add observatons that are not yet assigned + pose_items = pose_items.filter(pose__isnull=True) + sample = pose_items.first() + pose = Pose( + canon_site=sample.canon_site_conf.canon_site, + compound=sample.cmpd, + main_site_observation=sample, + display_name=sample.code, + ) + pose.save() + + # finally add observations to the (new or existing) pose + for obvs in pose_items: + obvs.pose = pose + obvs.save() + + self._tag_observations(pose.display_name, "P", "Pose", pose_items) + def _tag_observations(self, tag, prefix, category, so_list): try: # memo to self: description is set to tag, but there's @@ -1885,9 +2042,10 @@ def _tag_observations(self, tag, prefix, category, so_list): so_group = SiteObservationGroup(target=self.target) so_group.save() + name = f"{prefix} - {tag}" if prefix else tag try: so_tag = SiteObservationTag.objects.get( - upload_name=f"{prefix} - {tag}", target=self.target + upload_name=name, target=self.target ) # Tag already exists # Apart from the new mol_group and molecules, we shouldn't be @@ -1897,7 +2055,7 @@ def _tag_observations(self, tag, prefix, category, so_list): so_tag = SiteObservationTag() so_tag.tag = tag so_tag.tag_prefix = prefix - so_tag.upload_name = f"{prefix} - {tag}" + so_tag.upload_name = name so_tag.category = TagCategory.objects.get(category=category) so_tag.target = self.target so_tag.mol_group = so_group @@ -1911,15 +2069,12 @@ def _is_already_uploaded(self, target_created, project_created): if target_created or project_created: return False else: - uploaded_files = ExperimentUpload.objects.filter( + uploaded = ExperimentUpload.objects.filter( target=self.target, project=self.project, - ).values_list("file", flat=True) - - # TODO: this just tests the target-project-filename combo, - # which may not be enough + ).values_list("upload_data_dir", flat=True) - return self.data_bundle in uploaded_files + return self.version_dir in uploaded def _get_final_path(self, path: str | None) -> Path | None: """Update relative path to final storage path diff --git a/viewer/views.py b/viewer/views.py index 91f91fbb..523ab9d9 100644 --- a/viewer/views.py +++ b/viewer/views.py @@ -1360,6 +1360,15 @@ class SiteObservationTagView(viewsets.ModelViewSet): ) +class PoseView(viewsets.ModelViewSet): + """Set up/retrieve information about Poses (api/poses)""" + + queryset = models.Pose.filter_manager.filter_qs() + serializer_class = serializers.PoseSerializer + filterset_class = filters.PoseFilter + http_method_names = ('get', 'post', 'patch') + + class SessionProjectTagView(viewsets.ModelViewSet): """Set up/retrieve information about tags relating to Session Projects.""" @@ -1368,18 +1377,6 @@ class SessionProjectTagView(viewsets.ModelViewSet): filterset_fields = ('id', 'tag', 'category', 'target', 'session_projects') -class TargetMoleculesView(ISpyBSafeQuerySet): - """Retrieve all Molecules and Tag information relating - to a Target. The idea is that a single call can return all target related - information needed by the React front end in a single call. - """ - - queryset = models.Target.objects.all() - serializer_class = serializers.TargetMoleculesSerializer - filter_permissions = "project_id" - filterset_fields = ("title",) - - class DownloadStructures(ISpyBSafeQuerySet): """Uses a selected subset of the target data (proteins and booleans with suggested files) and creates a Zip file @@ -1680,7 +1677,9 @@ class TargetExperimentUploads(ISpyBSafeQuerySet): class SiteObservations(viewsets.ModelViewSet): - queryset = models.SiteObservation.filter_manager.filter_qs() + queryset = models.SiteObservation.filter_manager.filter_qs().filter( + superseded=False + ) serializer_class = serializers.SiteObservationReadSerializer permission_class = [permissions.IsAuthenticated] filterset_class = filters.SiteObservationFilter @@ -1689,7 +1688,7 @@ class SiteObservations(viewsets.ModelViewSet): class CanonSites(viewsets.ModelViewSet): - queryset = models.CanonSite.filter_manager.filter_qs() + queryset = models.CanonSite.filter_manager.filter_qs().filter(superseded=False) serializer_class = serializers.CanonSiteReadSerializer permission_class = [permissions.IsAuthenticated] filterset_class = filters.CanonSiteFilter @@ -1697,7 +1696,7 @@ class CanonSites(viewsets.ModelViewSet): class CanonSiteConfs(viewsets.ModelViewSet): - queryset = models.CanonSiteConf.filter_manager.filter_qs() + queryset = models.CanonSiteConf.filter_manager.filter_qs().filter(superseded=False) serializer_class = serializers.CanonSiteConfReadSerializer filterset_class = filters.CanonSiteConfFilter permission_class = [permissions.IsAuthenticated] @@ -1705,7 +1704,7 @@ class CanonSiteConfs(viewsets.ModelViewSet): class XtalformSites(viewsets.ModelViewSet): - queryset = models.XtalformSite.filter_manager.filter_qs() + queryset = models.XtalformSite.filter_manager.filter_qs().filter(superseded=False) serializer_class = serializers.XtalformSiteReadSerializer filterset_class = filters.XtalformSiteFilter permission_class = [permissions.IsAuthenticated]