diff --git a/docs/source/invalidation.rst b/docs/source/invalidation.rst index 7543eca01..56d0bf125 100644 --- a/docs/source/invalidation.rst +++ b/docs/source/invalidation.rst @@ -7,7 +7,7 @@ Quick reference of important files (all under src/snovault/) * indexing_views.py - contains the function that builds the object model and other information that is actually indexed. This view is in charge of generating invalidation information * resource_views.py - contains functions for all commonly-used views, including those used in indexing_views * embed.py - key functions used in indexing_views.py and resource_views.py -* utils.py - contains functions used in the selective embedding process (used for @@embedded view) +* utils.py - contains functions used in the selective embedding process (used for ``@@embedded view``) * resources.py - contains class definitions for the basic items in Snovault and controls adding linked and rev_linked items * elasticsearch/indexer.py - coordinates the whole indexing/invalidation process = * elasticsearch/indexer_utils.py - holds function used to run invalidation @@ -16,7 +16,7 @@ Quick reference of important files (all under src/snovault/) Keeping elasticsearch in sync ----------------------------- -The /_indexer wsgi app (es_index_listener.py) drives the incremental indexing process. Previously in the ENCODE setup, the listener was driven by database transactions. We have moved this to a queue-based setup that does not operate on DB snapshot. At a fixed, short time interval (at time of writing: 3 seconds), the index listener calls the /index view (indexer.py) which works out what needs to be reindexed. The actual reindexing happens in parallel in multiprocessing subprocesses (mpindexer.py.) +The ``/_indexer`` wsgi app (``es_index_listener.py``) drives the incremental indexing process. Previously in the ENCODE setup, the listener was driven by database transactions. We have moved this to a queue-based setup that does not operate on DB snapshot. At a fixed, short time interval (at time of writing: 3 seconds), the index listener calls the ``/index`` view (``indexer.py``) which works out what needs to be reindexed. The actual reindexing happens in parallel in multiprocessing subprocesses (``mpindexer.py``.) Keeping indexing on track requires a couple components: 1. keeping track of what needs to be invalidated @@ -25,40 +25,41 @@ Keeping indexing on track requires a couple components: Keeping track of what needs to be invalidated --------------------------------------------- -When rendering the view of an item to be indexed (@@index-data, see src/snovault/indexing_views.py), we record the set of uuids traversed when building the item. This is the _linked_uuids, which is stored as an reified attribute on the request used to build the item. These are the main source of information of what needs to be invalidated when items are updated. Whenever an item is changed, a search is performed to find all items that contain the changed item in their linked_uuids; these items are also reindexed. The function responsible for this is `find_uuids_for_indexing` in src/snovault/elasticsearch/indexer_utils.py. +When rendering the view of an item to be indexed (``@@index-data``, see ``src/snovault/indexing_views.py``), we record the set of uuids traversed when building the item. This is the ``_linked_uuids``, which is stored as an reified attribute on the request used to build the item. These are the main source of information of what needs to be invalidated when items are updated. Whenever an item is changed, a search is performed to find all items that contain the changed item in their ``linked_uuids``; these items are also reindexed. The function responsible for this is ``find_uuids_for_indexing`` in ``src/snovault/elasticsearch/indexer_utils.py``. -Items are added to the set of request._linked_uuids in the `item_with_links` function in src/snovault/resources.py. This is the function used to control the _linked_uuids because it is closely tied with the @@object view of an item (defined in resource_views.py). The embedding process traverses the `embedded_list` of an object and uses the @@object view to build the total embedded object by iteratively visiting all its component objects. See the `embedding-and-indexing.rst` document for more information. +Items are added to the set of ``request._linked_uuids`` in the ``item_with_links`` function in ``src/snovault/resources.py``. This is the function used to control the ``_linked_uuids`` because it is closely tied with the ``@@object`` view of an item (defined in ``resource_views.py``). The embedding process traverses the ``embedded_list`` of an object and uses the ``@@object`` view to build the total embedded object by iteratively visiting all its component objects. See the ``embedding-and-indexing.rst`` document for more information. -Reverse links (rev_links) must also be kept track of in the invalidation process. In our system, we represent rev_links as linkTos; the ENCODE concept of a linkFrom has been removed. rev_links are added to a request much the same as items are added to _linked_uuids. See the get_rev_links function in src/snovault/resources.py. This function keeps track of information of where the rev_link originates from and what item it targets, which is important information because many rev links could be visited in the process of building an embedded item. +Reverse links (``rev_links``) must also be kept track of in the invalidation process. In our system, we represent ``rev_links`` as ``linkTos``; the ENCODE concept of a ``linkFrom`` has been removed. ``rev_links`` are added to a request much the same as items are added to ``_linked_uuids``. See the ``get_rev_links`` function in ``src/snovault/resources.py``. This function keeps track of information of where the ``rev_link`` originates from and what item it targets, which is important information because many rev links could be visited in the process of building an embedded item. -Both _linked_uuids and rev_links are only kept track of if we are indexing. This is done by setting request._indexing_view to True in indexing_views.py. The information about the linked uuids and uuids that reverse link to an item are stored in the Elasticsearch document for the item in the `linked_uuids` and `uuids_that_rev_link_to_me` fields, respectively. +Both ``_linked_uuids`` and ``rev_links`` are only kept track of if we are indexing. This is done by setting ``request._indexing_view`` to ``True`` in ``indexing_views.py``. The information about the linked uuids and uuids that reverse link to an item are stored in the Elasticsearch document for the item in the ``linked_uuids`` and ``uuids_that_rev_link_to_me`` fields, respectively. Finding items to invalidate --------------------------- -This has already been somewhat covered, but it's worth reiterating. Whenever an item is indexed, the `find_uuids_for_indexing` function is run to find all items in Elasticsearch that contain the indexed item in their linked_uuids. In addition to this, any items added from the `uuids_rev_linked_to_me` list generated from the @@index-data view are also invalidated, since new reverse links may have been created and those items need to be updated as well. All of these items are added to the secondary queue after a primary item has been indexed. +This has already been somewhat covered, but it's worth reiterating. Whenever an item is indexed, the ``find_uuids_for_indexing`` function is run to find all items in Elasticsearch that contain the indexed item in their linked_uuids. In addition to this, any items added from the ``uuids_rev_linked_to_me`` list generated from the ``@@index-data`` view are also invalidated, since new reverse links may have been created and those items need to be updated as well. All of these items are added to the secondary queue after a primary item has been indexed. Total Reindexing ---------------- -Cases can arise where a total reindexing needs to be triggered. This should be done by using `bin/create-mapping`, which executes code in create_mapping.py. The point of this code is primarily to build the mappings needed to make the indices in Elasticsearch. Secondarily, create-mapping also takes care of queueing objects for indexing. Check out the code in that file for more information. A total re-creation of Elasticsearch indices followed by reindexing can be triggered using: +Cases can arise where a total reindexing needs to be triggered. This should be done by using ``bin/create-mapping``, which executes code in create_mapping.py. The point of this code is primarily to build the mappings needed to make the indices in Elasticsearch. Secondarily, create-mapping also takes care of queueing objects for indexing. Check out the code in that file for more information. A total re-creation of Elasticsearch indices followed by reindexing can be triggered using:: -`bin/create-mapping production.ini --app-name app` -NOTE: use `development.ini` locally + bin/create-mapping production.ini --app-name app + +NOTE: For local debugging, such as when you're running ``make deploy1`` or ``make deploy2``, use ``development.ini`` instead. Purging items ------------- -There is another spot `find_uuids_for_indexing` is used, and that is to find all linked items when attempting to "purge" an item (fully remove from postgresql and Elasticsearch). Before removing an item, it is crucial to ensure that all links to that item have been removed, which is why this function is used. +There is another spot ``find_uuids_for_indexing`` is used, and that is to find all linked items when attempting to "purge" an item (fully remove from postgresql and Elasticsearch). Before removing an item, it is crucial to ensure that all links to that item have been removed, which is why this function is used. Invalidation Scope ------------------------- -Previously, `find_uuids_for_indexing` would take the uuids from _linked_uuids as is. Now, if given a diff (passed from SQS on edit) the uuids returned will be pruned to determine whether or not they actually need to be invalidated. The indexer does this by examining the diff received from SQS and the embedded list of all invalidated item types. If it detects the diff modified something that is embedded in the invalidated item type, all uuids of this type are invalidated. If not, those uuids are not queued for reindexing since the edit does not change the embedded view of the item. The followind diagram serves as a visual aid. +Previously, ``find_uuids_for_indexing`` would take the uuids from ``_linked_uuids`` as is. Now, if given a diff (passed from SQS on edit) the uuids returned will be pruned to determine whether or not they actually need to be invalidated. The indexer does this by examining the diff received from SQS and the embedded list of all invalidated item types. If it detects the diff modified something that is embedded in the invalidated item type, all uuids of this type are invalidated. If not, those uuids are not queued for reindexing since the edit does not change the embedded view of the item. The following diagram serves as a visual aid. Note that the above behavior is ONLY activate upon receiving a diff, which is computed only on item edits. Upon item creation/deletion the process remains the same, since there is no diff. It is also very important to note that any additional fields used in calculated properties are embedded as well. If not, then a field could be modified that would affect an embedded field but such edit would be invisible because we did not know the field was used. diff --git a/poetry.lock b/poetry.lock index 35c92079e..0d561a56b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -48,18 +48,18 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.26.127" +version = "1.26.140" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.26.127-py3-none-any.whl", hash = "sha256:ded836536be41de9f9bd6a75e9feeb74d61b8c58ed7dc4ea89095082d7a616af"}, - {file = "boto3-1.26.127.tar.gz", hash = "sha256:ed31b2d35aad31418bd8093c5732c6296f785cc234333330df6b81396424d93b"}, + {file = "boto3-1.26.140-py3-none-any.whl", hash = "sha256:37eac5bbe87aad6d842dca139128d1254eac004cb9f16a89d054b3bf91dfd64d"}, + {file = "boto3-1.26.140.tar.gz", hash = "sha256:b36d223231dd8bd22a690dc10cd0f133266389ef116b82b7edec568275804938"}, ] [package.dependencies] 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"sha256:662fa444963eff9b68120d70cda1af5a5f2aa57900003c2006d7626450eaae5f"}, ] [[package]] @@ -2666,26 +2667,26 @@ types-awscrt = "*" [[package]] name = "typing-extensions" -version = "4.5.0" +version = "4.6.1" description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"}, - {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"}, + {file = "typing_extensions-4.6.1-py3-none-any.whl", hash = "sha256:6bac751f4789b135c43228e72de18637e9a6c29d12777023a703fd1a6858469f"}, + {file = "typing_extensions-4.6.1.tar.gz", hash = "sha256:558bc0c4145f01e6405f4a5fdbd82050bd221b119f4bf72a961a1cfd471349d6"}, ] [[package]] name = "urllib3" -version = "1.26.15" +version = "1.26.16" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ - {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"}, - {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"}, + {file = "urllib3-1.26.16-py2.py3-none-any.whl", hash = "sha256:8d36afa7616d8ab714608411b4a3b13e58f463aee519024578e062e141dce20f"}, + {file = "urllib3-1.26.16.tar.gz", hash = "sha256:8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14"}, ] [package.extras] @@ -2755,14 +2756,14 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] [[package]] name = "websocket-client" -version = "1.5.1" +version = "1.5.2" description = "WebSocket client for Python with low level API options" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "websocket-client-1.5.1.tar.gz", hash = "sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40"}, - {file = "websocket_client-1.5.1-py3-none-any.whl", hash = "sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e"}, + {file = "websocket-client-1.5.2.tar.gz", hash = "sha256:c7d67c13b928645f259d9b847ab5b57fd2d127213ca41ebd880de1f553b7c23b"}, + {file = "websocket_client-1.5.2-py3-none-any.whl", hash = "sha256:f8c64e28cd700e7ba1f04350d66422b6833b82a796b525a51e740b8cc8dab4b1"}, ] [package.extras] @@ -2794,14 +2795,14 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [[package]] name = "werkzeug" -version = "2.3.3" +version = "2.3.4" description = "The comprehensive WSGI web application library." category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "Werkzeug-2.3.3-py3-none-any.whl", hash = "sha256:4866679a0722de00796a74086238bb3b98d90f423f05de039abb09315487254a"}, - {file = "Werkzeug-2.3.3.tar.gz", hash = "sha256:a987caf1092edc7523edb139edb20c70571c4a8d5eed02e0b547b4739174d091"}, + {file = "Werkzeug-2.3.4-py3-none-any.whl", hash = "sha256:48e5e61472fee0ddee27ebad085614ebedb7af41e88f687aaf881afb723a162f"}, + {file = "Werkzeug-2.3.4.tar.gz", hash = "sha256:1d5a58e0377d1fe39d061a5de4469e414e78ccb1e1e59c0f5ad6fa1c36c52b76"}, ] [package.dependencies] @@ -2961,4 +2962,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.10" -content-hash = "95265c9058247ecaedc191b1a6a0a84b1231f85e3261ae79e750b3022539c090" +content-hash = "cd673581139368bb4498dfa95e010b623c75b90b0ab601518612d59cd7806942" diff --git a/pyproject.toml b/pyproject.toml index e9eef1d08..a4e27d782 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicsnovault" -version = "8.0.1.3b7" # to become 8.1.0 +version = "8.0.1.5b17" # to become 8.1.0 description = "Storage support for 4DN Data Portals." authors = ["4DN-DCIC Team "] license = "MIT" @@ -41,7 +41,7 @@ boto3 = "^1.26.124" # no particular version required, but this speeds up search botocore = "^1.19.124" # no particular version required, but this speeds up search elasticsearch = "7.13.4" # versions >= 7.14.0 lock out AWS ES elasticsearch_dsl = "^7.4.0" -dcicutils = "^7.0.0" +dcicutils = "^7.4.4.5b25" # "^7.0.0" future = ">=0.15.2,<1" html5lib = ">=1.1" # experimental, should be OK now that we're not using moto server humanfriendly = "^1.44.9" diff --git a/pytest.ini b/pytest.ini index e047a1b51..d47e76a3f 100644 --- a/pytest.ini +++ b/pytest.ini @@ -15,6 +15,7 @@ markers = integrated: an integration test integratedx: an excludable integration test, redundantly testing functionality also covered by a unit test performance: mark a test as a performance test (deselect with '-m "not performance"') + setone: (deprecated) instead of '-m "setone"', please use '-m "not indexing"', TODO: refs and scripts to be rewritten slow: mark a test as slow (deselect with '-m "not slow"') static: mark as a test that is testing the static form of code, not its runtime functionality storage: mark a test as about storage (deselect with '-m "not storage"') diff --git a/snovault/app.py b/snovault/app.py index 2e6ef36a5..caff3c669 100644 --- a/snovault/app.py +++ b/snovault/app.py @@ -4,6 +4,7 @@ import json import os import psycopg2 +import psycopg2.extensions import subprocess import zope.sqlalchemy @@ -13,7 +14,7 @@ from pyramid.session import SignedCookieSessionFactory from pyramid.settings import asbool from pyramid_localroles import LocalRolesAuthorizationPolicy -from sqlalchemy import engine_from_config, event, orm +from sqlalchemy import engine_from_config, event, orm # , text as psql_text from webob.cookies import JSONSerializer from .interfaces import DBSESSION @@ -82,7 +83,13 @@ def connect(dbapi_connection, connection_record): timeout_ms = int(timeout_ms) cursor = dbapi_connection.cursor() try: - cursor.execute("SET statement_timeout TO %d" % timeout_ms) + # cursor: psycopg2.extensions.cursor + # This call to psycopg2.extensions.cursor.execute expects a real string. Giving it an sqlalchemy.text + # object will fail because something will try to do a boolean test, probably "if thing_to_execute:..." + # and __bool__ is not defined on sqlalchemy.txt + # Bottom line: Cannot wrap this string with psql_text(...) like we do elsewhere. It's not ready. + # Might be we could do such a wrapper if we called execute on some other object. + cursor.execute("SET statement_timeout = %d;" % timeout_ms) except psycopg2.Error: dbapi_connection.rollback() finally: diff --git a/snovault/commands/clear_db_es_contents.py b/snovault/commands/clear_db_es_contents.py index eebe73d52..7bc947d46 100644 --- a/snovault/commands/clear_db_es_contents.py +++ b/snovault/commands/clear_db_es_contents.py @@ -7,6 +7,7 @@ from dcicutils.lang_utils import disjoined_list from pyramid.paster import get_app from snovault import DBSESSION +from sqlalchemy import text as psql_text from ..storage import Base from ..elasticsearch.create_mapping import run as run_create_mapping from sqlalchemy import MetaData @@ -40,8 +41,8 @@ def clear_db_tables(app): try: # truncate tables by only deleting contents (sqlalchemy 1.4+ compliant) table_names = ','.join(table.name for table in reversed(Base.metadata.sorted_tables)) - connection.execute('SET statement_timeout = 300000;') # give 5 mins for DB clear - connection.execute(f'TRUNCATE {table_names} RESTART IDENTITY;') + connection.execute(psql_text('SET statement_timeout = 300000;')) # give 5 mins for DB clear + connection.execute(psql_text(f'TRUNCATE {table_names} RESTART IDENTITY;')) except Exception as e: log.error(f"clear_db_es_contents: Error on DB drop_all/create_all. {type(e)}: {e}") transaction.abort() diff --git a/snovault/commands/list_db_tables.py b/snovault/commands/list_db_tables.py index e5639c628..cd4fcd079 100644 --- a/snovault/commands/list_db_tables.py +++ b/snovault/commands/list_db_tables.py @@ -14,8 +14,8 @@ from typing import Optional, List # from zope.sqlalchemy import mark_changed from .. import configure_dbsession +from ..project_defs import app_project from ..sqlalchemy_tools import PyramidAppManager -from ..project import app_project logger = structlog.getLogger(__name__) @@ -115,7 +115,7 @@ def main(simulated_args=None): log = args.log logging.basicConfig() - project = app_project(initialize=True) + project = app_project() # Loading app will have configured from config file. Reconfigure here: if log: logging.getLogger(project.NAME).setLevel(logging.DEBUG) diff --git a/snovault/dev_servers.py b/snovault/dev_servers.py index 4c894f292..97c5cb2e6 100644 --- a/snovault/dev_servers.py +++ b/snovault/dev_servers.py @@ -19,7 +19,7 @@ from pyramid.paster import get_app, get_appsettings from pyramid.path import DottedNameResolver from .elasticsearch import create_mapping -from .project import app_project, project_filename +from .project_defs import app_project from .tests import elasticsearch_fixture, postgresql_fixture @@ -31,7 +31,7 @@ def nginx_server_process(prefix='', echo=False): args = [ os.path.join(prefix, 'nginx'), - '-c', project_filename('nginx-dev.conf'), + '-c', app_project().project_filename('nginx-dev.conf'), '-g', 'daemon off;' ] process = subprocess.Popen( @@ -114,7 +114,7 @@ def main(): def run(app_name, config_uri, datadir, clear=False, init=False, load=False, ingest=True): - project = app_project(initialize=True) + project = app_project() logging.basicConfig(format='') # Loading app will have configured from config file. Reconfigure here: diff --git a/snovault/loadxl.py b/snovault/loadxl.py index c558fb475..bb659d4f9 100644 --- a/snovault/loadxl.py +++ b/snovault/loadxl.py @@ -20,7 +20,7 @@ from pyramid.view import view_config from snovault.util import debug_log -from .project import project_filename +from .project_defs import app_project from .server_defaults import add_last_modified @@ -117,7 +117,7 @@ def load_data_view(context, request): inserts = None from_json = False if fdn_dir: - inserts = project_filename('tests/data/' + fdn_dir + '/') + inserts = app_project().project_filename('tests/data/' + fdn_dir + '/') elif local_path: inserts = local_path elif store: @@ -517,7 +517,7 @@ def load_data(app, indir='inserts', docsdir=None, overwrite=False, testapp = webtest.TestApp(app, environ) # load master-inserts by default if indir != 'master-inserts' and use_master_inserts: - master_inserts = project_filename('tests/data/master-inserts/') + master_inserts = app_project().project_filename('tests/data/master-inserts/') master_res = load_all(testapp, master_inserts, [], skip_types=skip_types) if master_res: # None if successful print(LOAD_ERROR_MESSAGE) @@ -526,13 +526,13 @@ def load_data(app, indir='inserts', docsdir=None, overwrite=False, if not indir.endswith('/'): indir += '/' - inserts = project_filename('tests/data/' + indir) + inserts = app_project().project_filename('tests/data/' + indir) if docsdir is None: docsdir = [] else: if not docsdir.endswith('/'): docsdir += '/' - docsdir = [project_filename('tests/data/' + docsdir)] + docsdir = [app_project().project_filename('tests/data/' + docsdir)] res = load_all(testapp, inserts, docsdir, overwrite=overwrite) if res: # None if successful print(LOAD_ERROR_MESSAGE) @@ -568,7 +568,7 @@ def load_local_data(app, overwrite=False): ] for test_insert_dir in test_insert_dirs: - chk_dir = project_filename("tests/data/" + test_insert_dir) + chk_dir = app_project().project_filename("tests/data/" + test_insert_dir) for (dirpath, dirnames, filenames) in os.walk(chk_dir): if any([fn for fn in filenames if fn.endswith('.json') or fn.endswith('.json.gz')]): logger.info('Loading inserts from "{}" directory.'.format(test_insert_dir)) @@ -711,7 +711,7 @@ def load_data_by_type(app, indir='master-inserts', overwrite=True, itype=None): if not indir.endswith('/'): indir += '/' - inserts = project_filename('tests/data/' + indir) + inserts = app_project().project_filename('tests/data/' + indir) res = load_all(testapp, inserts, docsdir=[], overwrite=overwrite, itype=itype) if res: # None if successful diff --git a/snovault/project.py b/snovault/project.py deleted file mode 100644 index 43bd30f6f..000000000 --- a/snovault/project.py +++ /dev/null @@ -1,216 +0,0 @@ -import os -import toml - -from pkg_resources import resource_filename -from dcicutils.env_utils import EnvUtils -from dcicutils.misc_utils import classproperty - - -# This isn't the home of snovault, but the home of the snovault-based application. -# So in CGAP, for example, this would want to be the home of the CGAP application. -# If not set, it will be assumed that the current working directory is that. -APPLICATION_PROJECT_HOME = os.environ.get("APPLICATION_PROJECT_HOME", os.path.abspath(os.curdir)) -_PYPROJECT_TOML_FILE = os.path.join(APPLICATION_PROJECT_HOME, "pyproject.toml") -PYPROJECT_TOML_FILE = _PYPROJECT_TOML_FILE if os.path.exists(_PYPROJECT_TOML_FILE) else None -PYPROJECT_TOML = toml.load(PYPROJECT_TOML_FILE) if PYPROJECT_TOML_FILE else None -POETRY_DATA = PYPROJECT_TOML['tool']['poetry'] if PYPROJECT_TOML else None - -_DECLARED_PYPROJECT_NAME = os.environ.get("APPLICATION_PYPROJECT_NAME") -_INFERRED_PYPROJECT_NAME = POETRY_DATA['name'] if POETRY_DATA else None -if _DECLARED_PYPROJECT_NAME and _INFERRED_PYPROJECT_NAME and _DECLARED_PYPROJECT_NAME != _INFERRED_PYPROJECT_NAME: - raise RuntimeError(f"APPLICATION_PYPROJECT_NAME={_DECLARED_PYPROJECT_NAME!r} but {PYPROJECT_TOML_FILE}" - f" says it should be {_INFERRED_PYPROJECT_NAME!r}") -PYPROJECT_NAME = _DECLARED_PYPROJECT_NAME or _INFERRED_PYPROJECT_NAME - - -def project_filename(filename): - # TODO: In fact we should do this based on the working dir so that when this is imported to another repo, - # it gets the inserts out of that repo's tests, not our own. - return resource_filename(Project.PACKAGE_NAME, filename) - - -class ProjectRegistry: - - REGISTERED_PROJECTS = {} - - @classmethod - def register(cls, name): - """ - Registers a class to be used based on the name in the top of pyproject.toml. - Note that this means that cgap-portal and fourfront will both register as 'encoded', - as in: - - @Project.register('encoded') - class FourfrontProject(EncodedCoreProject): - PRETTY_NAME = "Fourfront" - - Since fourfront and cgap-portal don't occupy the same space, no confusion should result. - """ - def _wrap_class(the_class): - the_class_name = the_class.__name__ - if not issubclass(the_class, Project): - raise ValueError(f"The class {the_class_name} must inherit from Project.") - lower_registry_name = name.lower() - for x in ['cgap-portal', 'fourfront', 'smaht']: - if x in lower_registry_name: - # It's an easy error to make, but the name of the project from which we're gaining foothold - # in pyproject.toml is 'encoded', not 'cgap-portal', etc., so the name 'encoded' will be - # needed for bootstrapping. So it should look like - # -kmp 15-May-2023 - raise ValueError(f"Please use ProjectRegistry.register('encoded')," - f" not ProjectRegistry.register({name!r})." - f" This registration is just for bootstrapping." - f" The class can still be {the_class_name}.") - cls.REGISTERED_PROJECTS[name] = the_class - return the_class - return _wrap_class - - @classmethod - def _lookup(cls, name): - """ - Returns the project object with the given name. - - :param name: a string name that was used in a ProjectRegistry.register decorator - - NOTE: There is no need for this function to be called outside of this class except for testing. - Really only one of these should be instantiated per running application, and that's - done automatically by this class. - """ - project_class = cls.REGISTERED_PROJECTS.get(name) - return project_class - - @classmethod - def _make_project(cls): - """ - Creates and returns an instantiated project object for the current project. - - The project to use can be specified by setting the environment variable APPLICATION_PROJECT_HOME - to a particular directory that contains the pyproject.toml file to use. - If no such variable is set, the current working directory is used. - - NOTE: There is no need for this function to be called outside of this class except for testing. - Really only one of these should be instantiated per running application, and that's - done automatically by this class. - """ - project_class = cls._lookup(PYPROJECT_NAME) - assert issubclass(project_class, Project) - project: Project = project_class() - return project # instantiate and return - - _app_project = None - _initialized = False - - @classmethod - def initialize(cls): - if cls._initialized: - raise RuntimeError(f"{cls.__name__}.initialize() was called more than once.") - cls._app_project = cls._make_project() - cls._initalized = True - app_project: Project = cls.app_project - return app_project # It's initialized now, so we use the proper interface - - @classproperty - def app_project(cls): # noQA - PyCharm thinks we should use 'self' - """ - Once the project is initialized, ProjectRegistry.app_project returns the application object - that should be used to dispatch project-dependent behavior. - """ - if cls._app_project is None: - # You need to put a call to - raise RuntimeError(f"Attempt to access {cls.__name__}.project before .initialize() called.") - return cls._app_project - - -class Project: - """ - A class that should be a superclass of all classes registered using ProjectRegistry.register - - All such classes have these names: - .NAME - The name of the project in pyproject.toml - .PACKAGE_NAME - The pypi name of the project, useful for pkg_resources, for example. - .PRETTY_NAME - The pretty name of the package name - .APP_NAME - The ame of the project application (see dcicutils.common and the orchestrated app in EnvUtils) - .APP_PRETTY_NAME - The pretty name of the project application. - - Some sample usess of pre-defined attributes of a Project that may help motivate the choice of attribute names: - - registered | - name | NAME | PACKAGE_NAME | PRETTY NAME | APP_NAME | APP_PRETTY_NAME - -------------+--------------+----------------+--------------+-----------+---------------- - snovault | dcicsnovault | snovault | Snovault | snovault | Snovault - encoded-core | encoded-core | encoded-core | Encoded Core | core | Core - encoded | cgap-portal | cgap-portal | CGAP Portal | cgap | CGAP - encoded | fourfront | fourfront | Fourfront | fourfront | Fourfront - encoded | smaht-portal | smaht-portal | SMaHT Portal | smaht | SMaHT - - The registered name is the one used with the ProjectRegistry.register() decorator. - """ - - NAME = 'project' - - @classmethod - def _prettify(cls, name): - return name.title().replace("Cgap", "CGAP").replace("Smaht", "SMaHT").replace("-", " ") - - @classproperty - def PACKAGE_NAME(cls): # noQA - PyCharm wants the variable name to be self - return cls.NAME.replace('dcic', '') - - @classproperty - def PRETTY_NAME(cls): # noQA - PyCharm wants the variable name to be self - return cls._prettify(cls.PACKAGE_NAME) - - @classproperty - def APP_NAME(cls): # noQA - PyCharm wants the variable name to be self - return cls.PACKAGE_NAME.replace('-portal', '').replace('encoded-', '') - - @classproperty - def APP_PRETTY_NAME(cls): # noQA - PyCharm wants the variable name to be self - return cls._prettify(cls.APP_NAME) - - @classproperty - def app_project(cls): # noQA - PyCharm wants the variable name to be self - """ - Project.app_project returns the actual instantiated project for app-specific behavior, - which might be of this class or one of its subclasses. - - This access will fail if the project has not been initialized. - """ - return ProjectRegistry.app_project - - @classmethod - def initialize_app_project(cls, initialize_env_utils=True): - if initialize_env_utils: - EnvUtils.init() - project: Project = ProjectRegistry.initialize() - cls.show_herald() - return project - - @classmethod - def show_herald(cls): - print("=" * 80) - print(f"APPLICATION_PROJECT_HOME == {APPLICATION_PROJECT_HOME!r}") - print(f"PYPROJECT_TOML_FILE == {PYPROJECT_TOML_FILE!r}") - print(f"PYPROJECT_NAME == {PYPROJECT_NAME!r}") - the_app_project = Project.app_project - the_app_project_class = the_app_project.__class__ - the_app_project_class_name = the_app_project_class.__name__ - assert (Project.app_project - == app_project() - == the_app_project_class.app_project - == the_app_project.app_project), ( - "Project consistency check failed." - ) - print(f"{the_app_project_class_name}.app_project == Project.app_project == app_project() == {app_project()!r}") - print(f"app_project().NAME == {app_project().NAME!r}") - print(f"app_project().PRETTY_NAME == {app_project().PRETTY_NAME!r}") - print(f"app_project().PACKAGE_NAME == {app_project().PACKAGE_NAME!r}") - print(f"app_project().APP_NAME == {app_project().APP_NAME!r}") - print(f"app_project().APP_PRETTY_NAME == {app_project().APP_PRETTY_NAME!r}") - print("=" * 80) - - -def app_project(initialize=False): - if initialize: - Project.initialize_app_project() - return ProjectRegistry.app_project diff --git a/snovault/project_defs.py b/snovault/project_defs.py index d53be98fe..585f9ee42 100644 --- a/snovault/project_defs.py +++ b/snovault/project_defs.py @@ -1,10 +1,9 @@ -from .project import ( - ProjectRegistry, - Project as _Project # renamed to avoid confusing programmers using discovery into thinking this is an export -) +from dcicutils.project_utils import C4ProjectRegistry, C4Project - -@ProjectRegistry.register('dcicsnovault') -class SnovaultProject(_Project): - NAME = 'dcicsnovault' +@C4ProjectRegistry.register('dcicsnovault') +class SnovaultProject(C4Project): + NAMES = {'NAME': 'snovault', 'PYPI_NAME': 'dcicsnovault'} ACCESSION_PREFIX = 'SNO' + + +app_project = C4ProjectRegistry.app_project_maker() diff --git a/snovault/project_start.py b/snovault/project_start.py deleted file mode 100644 index f30b06cd1..000000000 --- a/snovault/project_start.py +++ /dev/null @@ -1,3 +0,0 @@ -from .project_defs import SnovaultProject - -SnovaultProject.initialize_app_project() diff --git a/snovault/server_defaults.py b/snovault/server_defaults.py index a439143e5..0799cab85 100644 --- a/snovault/server_defaults.py +++ b/snovault/server_defaults.py @@ -8,7 +8,7 @@ from snovault.schema_utils import server_default from snovault import COLLECTIONS # , ROOT from string import digits # , ascii_uppercase -from .project import app_project +from .project_defs import app_project ACCESSION_FACTORY = __name__ + ':accession_factory' diff --git a/snovault/tests/conftest.py b/snovault/tests/conftest.py index a06fb284f..ad0a63677 100644 --- a/snovault/tests/conftest.py +++ b/snovault/tests/conftest.py @@ -1,11 +1,14 @@ import logging import pytest -from ..project_defs import SnovaultProject +from ..project_defs import C4ProjectRegistry from ..elasticsearch.indexer_queue import QueueManager -SnovaultProject.initialize_app_project(initialize_env_utils=False) +# This might not be needed because it should demand-initialize, but there's a chance that the +# demand-initialization would happen in some weird state of mocking, so rather than risk that, +# we force it here. +C4ProjectRegistry.initialize() # required so that db transactions are properly rolled back in tests