Ruslan

Java bingo-elastic substructure search cannot use QueryMolecule as target

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**Steps to Reproduce** ``` var indigoObject = indigo.loadQueryMolecule(smiles); var target = new IndigoRecordMolecule.IndigoRecordBuilder() .withIndigoObject(indigoObject).build(); ``` **Expected behavior** We're expecting, that target will be loaded and used by SubstructureSearch **Actual behavior**...

Add resource for basic and acid PKA calculations

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This PR fixes Issue https://github.com/epam/Indigo/issues/709 Added new resource "/indigo/pka", Currently for correct pka calculation user is required to pass `pka_model_build` object: ``` { sdf: string, max_level: int, threshold: float }...

WIP: fix timeout error when running .layout

1

This PR fixes https://github.com/epam/Indigo/issues/724

Terminating with uncaught exception of type std::bad_cast: std::bad_cast

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OS: **MacOS** Indigo Version: **1.4.0-beta.r0-ga8773211 mac10.7** How to reproduce: Using `rxnfiles/legio-amides.rdf` from indigo tests: ```python for mol in session.iterateRDFile("rxnfiles/legio-amides.rdf"): print(mol) exact_matcher = bingo_conn.searchExact(mol, "") ``` Result: ``` 2020-09-29 14:54:46 [INFO]...

Add sorting and pagination to bingo-elastic

3

**Background** Currently, users can only access a limited count of compounds (up to 10,000 by default) from ElasticSearch. We need to incorporate sorting and pagination functionality into the bingo-elastic driver....

BadgerDoc should allow users to send file revisions back to the pipeline engine to enhance ML models following manual checks or annotations. After an annotation is committed, each file has...

Currently, some microservices use minio or boto3 as libraries to connect with S3. We need to replace these with aioboto3 and make all S3 queries asynchronous. Additionally, it is reasonable...

Currently, BadgerDoc supports only one pipeline manager. However, after the `1.8.0` release, it will become necessary to allow users to configure multiple pipeline managers in a single BadgerDoc installation. Post-release,...

We need to restore unit-tests and add them into GitHub actions. Badgerdoc is going to use pytest as library to test, so all tests must be migrated to pytest. All...