ghga-de / datahub-file-service
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coverage: 81.782% (+81.8%) from 0.0%
21486105188

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web-flow 
DFHS Initial implementation (GSI-1993) (#2)

* Add port definition and model for file upload

* Push everything in case disaster strikes

* Still need to resolve config problems and add tests

* Add S3Cleaner entrypoint

* Add class comparison script

* Update config to use single private key and clean up class def diffs

* Change caching retry config so we don't spam retries on 500 responses

* Add cached and computed encrypted_part_count property to FileUpload model

* Add connection error translation to http module

* Fix encrypted secret encoding

* Replace direct obj storage use in S3Cleaner with S3Client

* Add error handling and further logic to S3Client class

* Rename CentralClient's storage alias param to inbox_storage_alias

* Update interrogator to use renamed s3client methods

* Update injection module

* Include 206 as a success code when downloading content range

* Add first slew of tests...

* Fix mypy errors

* Bas64-encode part md5 when generating url

* Fix crypt4gh and jwk config

* Place reencrypted chunks in upload buffer until part size is reached

* Add interrogation storage alias to CentralClient setup

* Fix offset and part range calculation on FileUpload model

* Update tests and add happy path integration test

* Fix S3 tests and md5 handling

* Refactor S3 error handling and update doc strings

* Add S3Client to comparison script

* Rework Interrogator error handling and update doc strings

* Rewrite part ranges function to adapt part size to segment size

* Download normal part sizes and examine those in 64k chunks

* Grab template updates

* Add download URL caching and a test

* Replace own constant with identical one from crypt4gh

* Add tests for FileUpload model

* Abort interrogation if FIS API is unreachable

* Add test for file not in inbox

* Add tests for decryption and checksum errors

* Fix httpx should mock

* Expand logging/error handling in S3Cleaner with some tests

* Fix empty bucket test

* Fix api unre... (continued)

615 of 735 new or added lines in 16 files covered. (83.67%)

624 of 763 relevant lines covered (81.78%)

0.82 hits per line

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763 RELEVANT LINES 624 COVERED LINES
0.82 HITS PER LINE
Source Files on main

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
21486105188 main DFHS Initial implementation (GSI-1993) (#2) * Add port definition and model for file upload * Push everything in case disaster strikes * Still need to resolve config problems and add tests * Add S3Cleaner entrypoint * Add class comparison scr... push web-flow github
81.78
21485647721 feature/implement_GSI-1993 Make sure url life constants are in seconds, no milliseconds Pull #2 TheByronHimes github
81.78
21485558986 feature/implement_GSI-1993 Calculate segments_per_part consistently Pull #2 TheByronHimes github
81.78
21470889321 feature/implement_GSI-1993 Fix loop sleep time Pull #2 TheByronHimes github
81.78
21443211833 feature/implement_GSI-1993 Change name to include 'seconds' Pull #2 TheByronHimes github
81.78
21443153316 feature/implement_GSI-1993 Add looping mode for interrogator with min wait interval Pull #2 TheByronHimes github
81.78
21442339458 feature/implement_GSI-1993 Get inbox bucket ID from FileUpload instead of configuration and include bucket ID on interrogation report Pull #2 TheByronHimes github
82.74
21437500997 feature/implement_GSI-1993 Remove data_hub and go back to using only storage_alias Pull #2 TheByronHimes github
82.74
21436653977 feature/implement_GSI-1993 Add default= to make type checker accept defaults Pull #2 TheByronHimes github
82.76
21436529996 feature/implement_GSI-1993 Add descriptions to InterrogationReport fields Pull #2 TheByronHimes github
82.76
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