Release 2.1.0 #32
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Release 2.1.0 #32
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Member
ericenns
commented
Feb 10, 2023
•
ericenns
commented
- Added in support for importing IRIDA files that are not available locally (i.e. in the cloud)
- Switched from travisCI tests to Github Actions
- Switched integration tests to launch irida via gradle
* Create ci-tests.yml * just unit tests for now * install pytest * make pytest command use python -m pytest * more python libraries, add testing maxtrix * switch py.test to python -m pytest * specify python 3 * specify pip3 * add setuptools * Use conda incubator for management * init bash for activate * default activate __irida_importer_py3.6.7 * now this is advance building * Add postgresql * add check for current conda env * Try using postgres service instead of action * do it via ubuntu service * unit tests * install pytest * irida running locally, galaxy tbd * get basic int test flow working w/o galaxy, trying for github actions * code restructure, galaxy not starting * galaxy, conda, and selenium running locally * galaxy running and stopping * switch to gunicorn for galaxy host, improve irida/galaxy up check tests, tests passing locally * add galaxy configuration post setup * reorder some things to ensure irida/galaxy are killed after tests pass/fail * tool import test working locally * fake files working, galaxy->irida talking, oauth broken * authentication working on final importer test * reset postgres setup, add CONDA_PREFIX environment variable * switch to using ChromeDriverManager for selenium * force chromedriver to run headlesss and without gpu * cleanup now that test runners are all working (YAY) * fix selenium tests for IRIDA release 22.05 * swap dataset data output order
* switch integration tests to launch irida via gradle * update readme and changelog * pin selenium so tests stop breaking every update
Fix tests again
* Added function to download temp file and upload it to galaxy. * Updated to download file if not locally found * Updated logic to decide when to upload file vs link * Fixed incorrect header format. Added exception error message * Refactored logic * Added missing href to samplefile object instantiation * Added print statements * Added print statements to help debug * Added print statements to help debug * Moved setting of library dataset id for a sample file into the if/else statements * Refactored logic * Changed variable iniiialization to None from boolean * Reverted refactoring * Removed variable initialization not required * Added break to for loop once href is found for sample file * Added function to check if sha256 of downloaded file matches the expected sha256 * Updated get_file function to add upload sha 256 to sample file * Updated to get the actual hash * Added missing parameter * Updated logic to still upload a file to galaxy is there was no upload sha set in IRIDA * Updated logic to get file size from response if it exists * Converted bytes to non si unit * Refactored logic * Removed print statement * Updated parameter type comment * Changed param type, removed sha256 hash when creating a new SampleFile * Added comment to clarify that fastq and fast5 files are downloaded using the accept header for fastq files * Updated to explicitly name every argument, formatted for readability, updated param description for size, updated to comparing to None to use is instead of ==, fixed param names in function comments * Updated sample_file to contain content type of file * Added missing accept header * Moved getting content type into sample_file instead of passing content type in and updated to detect file type from file href and returning the content type based on this * Added success tests for checking if correct sample_file object is created and the content type is set correctly using detection of type from href * Removed variable * Fixed path for fast5 file * Added try/except for if an invalid content type is set for a file. Added test for invalid content type * Updated called to assertRaises) * Fixed assert statement for href * Updated to make test class a subclass of unittest so we could inherit assertRaises * Removed inheritance from unittest since it breaks the current setup of the tests. Updated to use a try/catch and assert if the content type threw and error * Attempting to get error message using get * Another attempt to get the error message from valueerror * Yet another attempt to get the error message from the valueerror exception
* Updated version number * Updated wording of changelog entry * Updated branch names from master to main
JeffreyThiessen
requested changes
Feb 10, 2023
JeffreyThiessen
approved these changes
Feb 13, 2023
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