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[SCHEMATIC-192] V24.12.1 into Main (#1562) #1563
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* add new tests * add unit tests * ran black * Update schematic/models/validate_attribute.py Co-authored-by: BryanFauble <[email protected]> * added tests * Update README.md * Update README.md * add unit tests * run black * Update README.md * temp commit * remove old tests * [FDS-2386] Synapse entity tracking and code concurrency updates (#1505) * [FDS-2386] Synapse entity tracking and code concurrency updates * ran black * Update CODEOWNERS * updated data model type rules to include error param * fix validate type attribute to use msg level param * added error handling * run black * create Node class * sat up Node class so that nodes with no displayName fields cause an error on creation * ran black * ran mypy * added new configs for CLI tests * added new manifests for testing CLI commands * automate manual CLI tests * ran black * Update CODEOWNERS * Update scan_repo.yml * Update .github/CODEOWNERS * Update .github/workflows/scan_repo.yml * Attach additional telemetry data to OTEL traces (#1519) * Attach additional telemetry data to OTEL traces * feat: added tracing for cross manifest validation and file name validation (#1509) * add tracing for GX validation * temp commit * Updating contribution doc to expect squash and merge (#1534) * [FDS-2491] Integration tests for Schematic API Test plan (#1512) Integration tests for Schematic API Test plan * [FDS-2500] Add Integration Tests for: Manifest Validation (#1516) * Add Integration Tests for: Manifest Validation * [FDS-2449] Lock `sphinx` version and update `poetry.lock` (#1530) Also install `typing-extensions` in the build * manual test files now being saved in manifests folder * manual test files now being saved in manifests folder * remove lines to delete json files that were under git control * ran black * add try finally blocks to remove created files * ran black * add lines to remove created json files * Update file annotation store process to require filename be present in order to annotate file * add lines to remove created json files * Revert "Update file annotation store process to require filename be present in order to annotate file" This reverts commit f57c718. * Don't attempt to annotate the table * add code in finally blocks to reset config to default values, when tests change them * complete submit manifest command test * ran black * add test for bug case * update test for table tidyness * remove unused import * remove etag column if already present when building temp file view * catch all exceptions to switch to sequential mode * update test for updated data * Revert "update test for updated data" This reverts commit 255e3c0. * Revert "catch all exceptions to switch to sequential mode" This reverts commit 68b0b24. * catch ValueErrors as well * Updates for integration test failures (#1537) * Updates for integration test failures, Config file reset and scope changes * add todos for removing config resets * [FDS-2525] Authenticated export of telemetry data (#1527) * Authenticated export of telemetry data, updating to HTTP otel library * temp reduce tests * restore tests * uncomment tests * redid how files are deleted, manual tests values are set * ran black * [SCHEMATIC-157] Make some dependencies required to avoid `schematic CLI` commands from potentially erroring when doing a pip install (#1540) * Make otel flash non-optional * Add dependencies as non-optional * Include schematic_api for now (#1547) * update toml version to 24.11.1 (#1548) * [SCHEMATIC-193] Support exporting telemetry data from GH integration test runs (#1550) * Support exporting telemetry data from GH run via access token retrieved via oauth2 * [SCHEMATIC-30, SCHEMATIC-200] Add version to click cli / use pathlib.Path module for checking cache size (#1542) * Add version to click cli * Add version * Run black * Reformat * Fix * Update schematic/schemas/data_model_parser.py * Add test for check_synapse_cache_size * Reformat * Fix tests * Remove unused parameter * Install all-extras for now * Make otel flash non-optional * Update dockerfile * Add dependencies as non-optional * Update pyproject toml * Fix trivy issue * Add service version * Run black * Move all utils.general tests into separate folder * Use pre-commit * Add updates to contribution doc * Fix * Add service version to log provider --------- Co-authored-by: BryanFauble <[email protected]> * [SCHEMATIC-212] Prevent traces from being combined (#1552) * Set instance id in github CI run, uninstrument flask auto during integration test run * [SCHEMATIC-163] Catch error when manifest is generated and existing one doesn't have `entityId` (#1551) * adds error handling * adds unit tests for _get_file_entityIds * updates error message * adds entityid check to parent func * updates docstring * [SCHEMATIC-183] Use paths from file view for manifest generation (#1529) source manifest file paths from synapse fileviews at generation * [SCHEMATIC-214] Wrap pandas functions to support not including `None` with the NA values argument (#1553) * Wrap pandas functions to support not including `None` with the NA values argument * Ignore types * pylint issues * ordering of ignore * Add to integration test to cover none in a manifest * Add additional test for manifest * [SCHEMATIC-210] Add attribute to nones data model (#1555) Update example_test_nones.model.csv component and add new invalid manifest with nones * first commit * ran black * add test for validateModelManifest * [SCHEMATIC-214] change data model and component (#1556) * add valid values to Patient attributes * update data model * add test manifests * update test for new model * update test for new valid value * change test to use new manifests * remove uneeded test file * revert file * revert file * change tests to use new manifests * remove uneeded manifests * ran black * add tests back in * ran black * revert manifest * Split up valid and errored test as separate testing functions * Remove unused import --------- Co-authored-by: Gianna Jordan <[email protected]> Co-authored-by: Andrew Lamb <[email protected]> Co-authored-by: Thomas Yu <[email protected]> * incremented packge version number * Update publish.yml * Update test.yml * Update api_test.yml * Update pdoc.yml * Update version.py * updates publish.yml (#1558) (#1561) Co-authored-by: Brad Macdonald <[email protected]> --------- Co-authored-by: BryanFauble <[email protected]> Co-authored-by: Jenny V Medina <[email protected]> Co-authored-by: Thomas Yu <[email protected]> Co-authored-by: Lingling <[email protected]> Co-authored-by: GiaJordan <[email protected]> Co-authored-by: Brad Macdonald <[email protected]> Co-authored-by: Gianna Jordan <[email protected]>
thomasyu888
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Dec 16, 2024
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@andrewelamb I merged via git cli
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add new tests
add unit tests
ran black
Update schematic/models/validate_attribute.py
added tests
Update README.md
Update README.md
add unit tests
run black
Update README.md
temp commit
remove old tests
[FDS-2386] Synapse entity tracking and code concurrency updates ([FDS-2386] Synapse entity tracking and code concurrency updates #1505)
[FDS-2386] Synapse entity tracking and code concurrency updates
ran black
Update CODEOWNERS
updated data model type rules to include error param
fix validate type attribute to use msg level param
added error handling
run black
create Node class
sat up Node class so that nodes with no displayName fields cause an error on creation
ran black
ran mypy
added new configs for CLI tests
added new manifests for testing CLI commands
automate manual CLI tests
ran black
Update CODEOWNERS
Update scan_repo.yml
Update .github/CODEOWNERS
Update .github/workflows/scan_repo.yml
Attach additional telemetry data to OTEL traces (Attach additional telemetry data to OTEL traces #1519)
Attach additional telemetry data to OTEL traces
feat: added tracing for cross manifest validation and file name validation (feat: added tracing for cross manifest validation and file name validation #1509)
add tracing for GX validation
temp commit
Updating contribution doc to expect squash and merge (Updating contribution doc to expect squash and merge #1534)
[FDS-2491] Integration tests for Schematic API Test plan ([FDS-2491] Integration tests for Schematic API Test plan #1512)
Integration tests for Schematic API Test plan
[FDS-2500] Add Integration Tests for: Manifest Validation ([FDS-2500] Add Integration Tests for: Manifest Validation #1516)
Add Integration Tests for: Manifest Validation
[FDS-2449] Lock
sphinx
version and updatepoetry.lock
([FDS-2449] Locksphinx
version and updatepoetry.lock
#1530)Also install
typing-extensions
in the buildmanual test files now being saved in manifests folder
manual test files now being saved in manifests folder
remove lines to delete json files that were under git control
ran black
add try finally blocks to remove created files
ran black
add lines to remove created json files
Update file annotation store process to require filename be present in order to annotate file
add lines to remove created json files
Revert "Update file annotation store process to require filename be present in order to annotate file"
This reverts commit f57c718.
Don't attempt to annotate the table
add code in finally blocks to reset config to default values, when tests change them
complete submit manifest command test
ran black
add test for bug case
update test for table tidyness
remove unused import
remove etag column if already present when building temp file view
catch all exceptions to switch to sequential mode
update test for updated data
Revert "update test for updated data"
This reverts commit 255e3c0.
This reverts commit 68b0b24.
catch ValueErrors as well
Updates for integration test failures (Update for integration test failures #1537)
Updates for integration test failures, Config file reset and scope changes
add todos for removing config resets
[FDS-2525] Authenticated export of telemetry data ([FDS-2525] Authenticated export of telemetry data #1527)
Authenticated export of telemetry data, updating to HTTP otel library
temp reduce tests
restore tests
uncomment tests
redid how files are deleted, manual tests values are set
ran black
[SCHEMATIC-157] Make some dependencies required to avoid
schematic CLI
commands from potentially erroring when doing a pip install ([SCHEMATIC-157] Make some dependencies required to avoidschematic CLI
commands from potentially erroring when doing a pip install #1540)Make otel flash non-optional
Add dependencies as non-optional
Include schematic_api for now ([SCHEMATIC-136] Include schematic_api to resolve dependency issue #1547)
update toml version to 24.11.1 (update toml version to 24.11.2 #1548)
[SCHEMATIC-193] Support exporting telemetry data from GH integration test runs ([SCHEMATIC-193] Support exporting telemetry data from GH integration test runs #1550)
Support exporting telemetry data from GH run via access token retrieved via oauth2
[SCHEMATIC-30, SCHEMATIC-200] Add version to click cli / use pathlib.Path module for checking cache size ([SCHEMATIC-30, SCHEMATIC-200] Add version to click cli / use pathlib.Path module for checking cache size #1542)
Add version to click cli
Add version
Run black
Reformat
Fix
Update schematic/schemas/data_model_parser.py
Add test for check_synapse_cache_size
Reformat
Fix tests
Remove unused parameter
Install all-extras for now
Make otel flash non-optional
Update dockerfile
Add dependencies as non-optional
Update pyproject toml
Fix trivy issue
Add service version
Run black
Move all utils.general tests into separate folder
Use pre-commit
Add updates to contribution doc
Fix
Add service version to log provider
[SCHEMATIC-212] Prevent traces from being combined ([SCHEMATIC-212] Prevent traces from being combined #1552)
Set instance id in github CI run, uninstrument flask auto during integration test run
[SCHEMATIC-163] Catch error when manifest is generated and existing one doesn't have
entityId
([SCHEMATIC-163] Catch error when manifest is generated and existing one doesn't haveentityId
#1551)adds error handling
adds unit tests for _get_file_entityIds
updates error message
adds entityid check to parent func
updates docstring
[SCHEMATIC-183] Use paths from file view for manifest generation ([SCHEMATIC-183] Use paths from file view for manifest generation #1529)
source manifest file paths from synapse fileviews at generation
[SCHEMATIC-214] Wrap pandas functions to support not including
None
with the NA values argument ([SCHEMATIC-214] Wrap pandas functions to support not includingNone
with the NA values argument #1553)Wrap pandas functions to support not including
None
with the NA values argumentIgnore types
pylint issues
ordering of ignore
Add to integration test to cover none in a manifest
Add additional test for manifest
[SCHEMATIC-210] Add attribute to nones data model ([SCHEMATIC-210] Add attribute to nones data model #1555)
Update example_test_nones.model.csv component and add new invalid manifest with nones
first commit
ran black
add test for validateModelManifest
[SCHEMATIC-214] change data model and component ([SCHEMATIC-214] change data model and component #1556)
add valid values to Patient attributes
update data model
add test manifests
update test for new model
update test for new valid value
change test to use new manifests
remove uneeded test file
revert file
revert file
change tests to use new manifests
remove uneeded manifests
ran black
add tests back in
ran black
revert manifest
Split up valid and errored test as separate testing functions
Remove unused import
incremented packge version number
Update publish.yml
Update test.yml
Update api_test.yml
Update pdoc.yml
Update version.py
updates publish.yml ([SCHEMATIC-192] Patches publish.yml #1558) (updates publish.yml (#1558) #1561)