Deprecate drug, pharmacogenomics, targetEngine, and knownDrug steps#405
Merged
Deprecate drug, pharmacogenomics, targetEngine, and knownDrug steps#405
Conversation
76 tasks
- Remove drug, pharmacogenomics, targetEngine, and knownDrug step registrations from Main.scala - Remove drug, pharmacogenomics, targetEngine, and knownDrug configurations from Configuration.scala Steps case class - Remove unused configuration case classes (DrugSection, InputExtension, PharmacogenomicsSection, TargetEngineSection, KnownDrugSection) - Update reference.conf: remove deprecated step configurations and update drug references to direct paths - search, openfda, literature steps now reference external drug datasets - drug references updated to use paths: drug_molecule, drug_indication, drug_mechanism_of_action - Remove target-based computation from openFDA step (keep only chembl_id dimension) - Remove fda_targets_unfiltered, fda_targets_results, and sampling_targets outputs from openfda - Delete all drug, pharmacogenomics, targetEngine, and knownDrug implementation files - Delete DrugUtils utility (no longer used) - Delete related test files for deprecated modules Configuration test passes - validates configuration structure integrity
DSuveges
force-pushed
the
4247_drug_adjustments
branch
from
1fc0bde to
94970db
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Related to opentargets/issues#4247
Configuration test passes - validates configuration structure integrity