snovault

Change Log

11.22.0

2024-09-03/dmichaels - Fix in snovault/tests/elasticsearch_fixture.py (use only for local/dev deploy) for

strange (new as of 2024-09-02) behavior where it was hanging on startup during ElasticSearch index mapping creation, related to ElasticSearch logging output, and the way we were using subprocess.Popen and reading the subprocess output; more correct way is to inherit stdout/stderr of the partent.

11.21.1

Minor changes to allow running (for example) both cgap-portal and smaht-portal simultaneously locally, for localhost/dev purposes only: - Minor updates to dev_servers.py and tests/elasticsearch_fixture.py

to allow defining transport_port for elasticsearch.
- Minor updates to dev_servers.py and tests/postgresql_fixture.py to allow parsing sqlalchemy.url in the ini file (e.g. development.ini) for the postgres port and temporary directory path.

11.21.0

Fix in indexing_views.py for frame=raw not including the uuid.

11.20.0

Bug fix: use loadxl_order() in staggered reindexing
Add B-tree index to rid column in propsheets to optimize revision history retrieval

11.19.0

Fix for revision history - deepcopy history as to not modify props in place

11.18.0

Dropped support for Python 3.8.
Updates related to Python 3.12. - Had to update venusian (from 1.2.0) to 3.1.0. - Had to update pyramid (from 1.10.4) to 1.10.8 (for imp import not found).
- Had to add pmdarima (no module pyramid.compat).
- Had to define/update numpy (to 1.26.4) for this as it was implicitly, due to something else, using 1.24.4 which failed to build with Python 3.12. - And had to update lower bound of Python (from 3.8.1) to 3.9 for this.
- Had to update dcicutils (from 8.11.0) to 8.13.0 (for pyramid update for imp import not found).
Minor change to dev_servers.py to facilitate running a local ElasticSearch proxy to observe traffic (resquests/responses) between the portal and ElasticSearch with a tool like mitmproxy or mitmweb; see comments in dev_server.py.

11.17.0

Add /routes endpoint to return all routes and select item views in the application

11.16.0

Update /submission-schemas/ to capture required prop via new key in property schema

11.15.1

Update drs_download to not guard on Authentication, as this check is superfluous since @@drs as_user is evaluated

11.15.0

Update drs primitive to only return JSON

11.14.3

Fix update-inserts-from-server command to display --help option

11.14.2

Fix update-inserts-from-server command to move away from direct ES interaction * Rewrite signicantly * Add new options to allow for more flexible use

11.14.1

Create constants for submission-schemas endpoint to share with downstream portals

11.14.0

2024-03-25
Changes to loadxl to support tracking ingestion progess for smaht-submitr (via Redis).
Changed dev_servers.py

11.13.0

Fix in loadxl to PATCH on validate_only for items which already exist; discovered during smaht-submitr testing.
Fix in loadxl.normalize_deleted_properties which was creating/returning a new (an_item) item, which was messing up determination of identifying path for patch (as second_round_items comes from store but we had set uuid in an_item which, without this fix, became a different object).
Added skip_links feature to loadxl which will cause reference/link integrity checking to be skipped altogether; this is (currently) only set by smaht-portal/ ingestion/loadxl_extensions.py for smaht-submitr, since that process already does thorough reference integrity checking anyways (via structured_data).

11.12.4

Remove restricted permissions for AccessKey status to enable non-admins to delete access keys

11.12.3

Changed ACCESSION_PREFIX in server_defaults.py to GET_ACCESSION_PREFIX() function; called only within snovault (and only from schema_formats.py); to get around app_project call at file scope (came up as circular import in smaht ingester).

11.12.2

Gets total results from ES, then try to get exact count if total hits ES_MAX_HIT_TOTAL limitation

11.12.1

Repairs schema format validation

11.12.0

Change the exception message for a unresolved object reference (linkTo) in schema_validation.normalize_links.
Added instance info to ERROR in loadxl.load_all_gen.
Both of above in support of reference integrity validation code within smaht-submitr.

11.11.0

Removes strip of role. permissions so smaht-portal roles work

11.10.0

Version updates to dcicutils. Changes to itemize SMaHT submission ingestion create/update/diff situation.

11.9.0

Added support for an optional gitinfo.json file (deployed via portal buildspec.yml).

11.8.0

Add submission-schemas api

11.7.0

Updated dcicutils to 8.6.0 (with minor fixes related to structured_data and SMaHT ingestion).

11.6.0

Updated dcicutils to 8.4.1 (with structured_data).
Updated loadxl to pass "filename" in yields (for smaht-portal/ingester).

11.5.0

More work related to SMaHT ingestion.

11.4.0

RAS updates

11.3.1

Broaden schema $merge regex to allow mixin and other references

11.3.0

Another thug commit to add CHANGELOG for below.

11.2.0

Thug commit to change dcictuils from 8.2.0 to ^8.2.0.

11.1.0

Merging in Doug's drr_schema_updates branch with new types.
Added limited support to loadxl for required properties within anyOf of data type schemas.
Merged in load_data_fix branch.
Update dcicutils to 8.2.0
2023-11-02

11.0.1

Repair reference to load_data_by_type to resolve correctly when loadxl is absent entirely from the application repo

11.0.0

Upgrade to Python 3.11.
Fixed access of user in types/access_key.py in access_key_add WRT request.validated['user'].
Added identifyingProperties with just uuid in schemas/access_key.json.
Fix in setup_eb.py to handle jsonschema in pyproject.toml like {extras = ..., version = ...}.
Added snovault/commands/generate_local_access_key.py script; originally just for smaht-portal to create access-key for local dev/testing because doing it via UI not yet fully supported; but generally convenient for cgap-portal and fourfront as well. * Minor changes (e.g. create_testapp) to loadxl.py to help load data from a specified directory;
called from dev_server.py; for creating access-keys on the fly after startup for local dev/testing. * Enhancement in load_data in loadxl.py to respect a fully qualified data directory path name,

i.e. do not make it relative to the current working directory if it is fully qualified.
- Updates to load_all_gen to allow object create/update with no uuid.
Added snovault/commands/view_local_object.py script for dev/testing to retrieve and output a given object (uuid) from a locally running portal.
Added support for consortia and submission_centers in ingestion_listener.py.
Added unique_key to types/access_key.py (helps get rid of this in cgap-portal/fourfront).

10.0.5

Bug fix in schema reference resolution when the schema is loaded from a file

10.0.4

Bug fix in access key refresh to predicate on whether

expiration is enabled

10.0.3

Update drs primitive to resolve specific access types with preferential defaulting to https, http

10.0.2

Repair bug in permission implementation involving restricted fields
Repair bug in user registration, allowing customization through app_project definition

10.0.1

Extend FormatChecker to ensure date and date-time validation

10.0.0

Updates jsonschema version, removing dependency on jsonschema-serialize-fork and allowing us to use $merge refs. * Breaking Change: dependencies --> dependentRequired in schema * Breaking Change: object serialization in schema no longer valid

9.1.1

Small fix for JWT Decode incompatible change

9.1.0

Fix for MIME type ordering in renderers.py (differs between cgap and fourfront).

9.0.0

Merge/unify ingestion and other code from cgap-portal and fourfront.

8.1.0

Add several modules/commands from upstream portals that are generic enough to live in this repository (to reduce code/library maintenace overhead)
Port support for make deploy1 from the portals:
- In Makefile:
  - Support for make deploy1
  - Support for make psql-dev
  - Support for make psql-test
  - Support for make kibana-start (commented out for now, pending testing)
  - Support for make kibana-start-test (commented out)
  - Support for make kibana-stop (commented out)
- In pyproject.toml:
  - Template file development.ini.template
  - Template file test.ini.template
  - Support for prepare-local-dev script, which creates development.ini from development.ini.template and test.ini from test.ini.template.

Port the dev_servers.py support from CGAP.

In the scripts/ dir:

Add scripts/psql-start in support of make psql-dev and make psql-test.

8.0.1

Fix some warnings from pytest
- If a method has "test" in its name but isn't a test, it needs a prefix "_"
Fix some warnings from sqlalchemy
- session.connection() doesn't need to .connect()
- .join(x, y, ...) should be .join(x).join(y)...
- session.query(Foo).get(bar) should be session.get(Foo, bar)

8.0.0

Redis support, adding /callback info to /auth0_config if a Redis server is configured

7.3.1

Change pytest.yield_fixture to pytest.yield. This is techinically incompatible since it would break downstream portals if they were below pytest 6, but they are both at pytest 7 now, so they should be unaffected.
Address some places involving .execute(raw_string) that should be .execute(text(raw_string)).

7.3.0

In Makefile:
- Make sure make test and make test-full also run make test-static.
In snovault/storage.py:
- Add POSTGRES_COMPATIBLE_MAJOR_VERSIONS (moved from snovault/tests/test_storage.py)
In snovault/elasticsearch/create_mapping.py:
- Per Will's direction, replace a call to run_index_data with a vapp creation and a call to an index post with given uuids.
In snovault/elasticsearch/mpindexer.py:
- Very minor syntactic refactor to make a use of global more clear.
In snovault/tools.py:
- Reimplement index_n_items_for_testing for better clarity and to fix a potential bug.
In snovault/tests/test_indexing.py
- Various test optimizations using better synchronization for robustness.

7.2.1

In Makefile:
- New make target test-one.
- Separate testing of indexing tests from other unit tests, renaming the "npm" tests to "indexing" tests.
Make github workflow main.yml consistent with Makefile changes.
In pyproject.toml:
- Use pytest 7.2.2.

7.2.0

In Makefile:
- Add make test-full to test like make test but without the instafail option.
- Add make test-static to run static checks.
- Add make test-one TEST_NAME=<test_name_or_filename_base> so you can test a single file or test from make. This is not so important in snovault as in cgap-portal but I want the interface to be uniform.
- In all testing, added SQLALCHEMY_WARN_20=1 at start of command line to enable SQLAlchemy 2.0 compatibility warnings, since we're using SQLAlchemy 1.4, which has those warnings.
In pyproject.toml: * Require dcicutils 6,7 for fixes to Eventually.
- Include pipdeptree as a dev dependency for debugging.
- Remove "backports.statistics", needed for Python 3.3 support and earlier.
- Bump python_magic foothold (no effective change, just faster locking)
- Update some comments.
In snovault/updater.py:
- Better error message for UUID integrity errors, noting they might not be conflits but just maybe also UUID missing.
- Rearrange imports for clarity.
In new file snovault/tools.py:
- New functions make_testapp, make_htmltestapp, make_authenticated_testapp, make_submitter_testapp, make_indexer_testapp, and make_embed_testapp.
- New context managers being_nested and local_collections.
- New function index_n_items_for_testing.
These functions are potentially useful in the portal repos, so are not part of the test files.
In file snovault/tests/serverfixtures.py:
- New fixture engine
In file snovault/tests/test_indexing.py:
- Material changes to testing to use better storage synchronization (semaphor-style rather than sleep-style), hopefully achieving fewer intermittent errors in testing both locally and in GA.
- Bug fixes in a few tests that were assigning settings or other dictionary structures but not assuring an undo was done if the test failed.
In files snovault/util.py, snovault/tests/test_embedding.py, snovault/tests/test_storage.py:
- Various changes for PEP8 or other readability reasons, including to satisfy PyCharm linters.
- Allow Postgres 14 to be used.

7.1.3

In upgrader.py, default parse_version argument to '0', rather than '1' when None or the empty string is given.
Remove the Python 3.7 classifier in pyproject.toml.
Add make clear-poetry-cache in Makefile.
Misc PEP8.

7.1.2

Fix C4-984:
- Add pip install wheel in make configure.
- Remove dependency in pyproject.toml on futures library.
Fix C4-985:
- Make a wrapper for pkg_resources.parse_version in upgrader.py that parses the empty string as if '1' had been supplied.
Fix C4-987:
- Use in str(exc.value) rather than in str(exc) after with pytest.raises(....) as exc:

7.1.1

Small fix/adjustment to snapshot related error handling when re-mapping

7.1.0

Supress log errors from skip_indexing
Suppress errors from SQLAlchemy relationship overlap
Add reindex_by_type capabilities
Small changes to indexing tests to speed them up

7.0.0

Upgrades ElasticSearch to version 7 (OpenSearch 1.3 in production)
Upgrades SQLAlchemy to 1.4.41 (and other associated versions)
Adds B-Tree index on max_sid to optimize retrieval of this value in indexing
Drop support for Python 3.7

6.0.8

Environment variable NO_SERVER_FIXTURES suppresses creation of server fixtures during testing.

6.0.7

Miscellaneous PEP8.

6.0.6

Evaluate KMS args as truthy for blob storage to avoid errors for empty string KMS key

6.0.5

Add a CHANGELOG.rst file.
Add tests for consistency of version and changelog.
Make dev dependency on docutils explicit, adding a constraint that gets rid of a deprecation warning.

6.0.4

6.0.3

PR 225 Genelist upload (C4-875)

Instrumentation added to help debug C4-875.

Improved error messages for ValidationFailure in attachment.py.

Actual proposed fix:

In attachment.py, replaced mimetypes.guess_type with new function guess_mime_type (adjusting the receipt of return value, since I adjusted that slightly to return the mime type, not a tuple of mime type and encoding).
Make sure that we have useful return values for common file extensions.

Opportunistic:

Better .flake8 file excluding a bunch of whitespace-related issues we don't need to care about yet.
Add a lint target to the Makefile.
Suppress an annoying warning from the jose package (included by moto 1.3.7) about how it's not going to work in Python 3.9.
Do keyword-calling of ValidationFailure in attachment.py just to clarify what the weird args are.
Add an extra warning message in create_mapping.py for certain unusual argument combinations. (This had come up elsewhere in a discussion I had with Will and was just waiting for a PR to ride in on.)

6.0.2

PR 223 Index Delete Retry

Retry delete_index in case of an error, likely related to a snapshot occurring at the same time as the delete operation. Give it two minutes (12 tries) to succeed.

6.0.1

6.0.0

PR 224 Use dcicutils 4.0

NOTE: The breaking change here is the use of dcicutils 4.x.

This accepts dcicutils 4.0.
Minor change to .gitignore to add .python-cmd.
Constrains boto3, botocore, boto3-stubs, and botocore-stubs.

5.7.0

PR 222 Invalidation Scope Fix (C4-854)

Repairs several important cases in invalidation scope by revising the core algorithm, which is now described in the filter_invalidation_scope docstring.
Should work correctly for object fields, links beyond depth 1 and *.
Other small changes include repairing the test script and allowing indexer worker runs to re-use testapp for 100 iterations (thus preserving cache, probably speeding up indexing and reducing DB load)

5.6.2

PR 221 Remove embeds of unmappable properties

Here, we remove embeds of properties that cannot be mapped within our system, namely those that fall under additionalProperties or patternProperties in our schema.
As far as I understand things, since these fields cannot be mapped, adding them to an item's embedding list will not work regardless of the changes here, specifically the explicit removal of the properties from the default embeds in find_default_embeds_for_schema. Thus, no properties in the schema defined under additionalProperties or patternProperties can be embedded or used for invalidation scope with our current set-up, and significant refactoring would be required to make these work.

5.6.1

PR 220 Further upgrader version fix

The recent upgrader fix (in v.5.6.0) added the default version of 1 for upgrader calls, but not all calls to the upgrader were included in the fix. Specifically, the upgrader call within resources.py is still resulting in errors. We fix that here, as well as the call within the possibly defunct batchupgrade.py for good measure. (Grepping snovault for upgrader.upgrade didn't reveal any other instances of calls to the upgrader to fix.)

5.6.0

PR 218 Lock 3.8, Repair Upgraders

Locks Python 3.8, which appears stable with no changes
Default current_version in upgraders to 1 instead of '', so items that do not have a default schema_version will default to a sane value that should hit an upgrade target.

5.5.1

PR 217 Repair mirror health resolution

Resolve IDENTITY so authenticated requests can be made with credentials

5.5.0

5.4.0

PR 215 Fix Serializer

Undo JSON serializer override, falling back to the pyramid default which appears to be ~10x more performant with waitress

5.3.0

PR 214 Type Specific Index Setting

Implements type specific index settings, documenting the important settings
Configurable by overriding the Collection.index_settings method to return a custom snovault.util.IndexSettings object

5.2.0

PR 213 Make pillow, wheel, and pyyaml be dev dependencies. If the portals wa...

Make pillow, wheel, and pyyaml be dev dependencies. If the portals want them, they can make them be regular dependencies.

5.1.1

PR 212 Fix some dependencies to be a bit more flexible

Various adjustments in pyproject.toml.

5.1.0

PR 211 Python 3.7 compatibility changes (C4-753)

This change intends to let Snovault work in Python 3.7.

Update psycopg2 to use psycopg2-binary.
Use matrix format testing and adjust the way indices are built in so they include Python version number. Needed to assure proper cleanup, but also to avoid these different processes colliding with one another.
Adjusted GA testing to use 250 timeout instead of 200.