Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / biocypher/biocypher issues and pull requests
#409 - update github action config:
Pull Request -
State: closed - Opened by slobentanzer 1 day ago
#408 - Add option to load resource download definition from config
Issue -
State: open - Opened by slobentanzer 1 day ago
- 1 comment
Labels: enhancement
#407 - [Bug]: RDF support
Issue -
State: open - Opened by jdreo 2 days ago
- 3 comments
Labels: enhancement
#406 - Add system test for operating system handling of characters (newline problems, quote escapes)
Issue -
State: open - Opened by slobentanzer 3 days ago
#405 - Fix neo4j CSV output not escaping quote character and cause import error
Pull Request -
State: closed - Opened by kpto 15 days ago
- 2 comments
Labels: bug
#404 - Upgrade CI components to Python 3.11 default
Issue -
State: open - Opened by slobentanzer 16 days ago
#403 - Dev-networkx-ruff
Pull Request -
State: closed - Opened by slobentanzer 17 days ago
- 2 comments
#402 - Feature-networkx-output
Pull Request -
State: closed - Opened by slobentanzer 17 days ago
#401 - Feature networkx output
Pull Request -
State: closed - Opened by ryxx0811 18 days ago
- 1 comment
#400 - Umbrella package to unify access to raw biocypher adapters, ontoweaver adapters, and pipeline functions
Issue -
State: open - Opened by slobentanzer 22 days ago
#397 - Upgrade documentation
Issue -
State: open - Opened by slobentanzer 2 months ago
#396 - Developer docs: Ruff process including VSCode configuration
Issue -
State: open - Opened by slobentanzer 2 months ago
#395 - Implement Ruff linting
Issue -
State: closed - Opened by slobentanzer 2 months ago
#394 - Add `merge_nodes` param to the configuration example of ontology hybridisation
Issue -
State: open - Opened by slobentanzer 3 months ago
#393 - Docker compose on Windows: paths / characters failure
Issue -
State: open - Opened by slobentanzer 3 months ago
- 2 comments
#392 - Add volume purge to the docker build script
Issue -
State: open - Opened by slobentanzer 3 months ago
#391 - Update docstring of BioCypherEdge class
Issue -
State: open - Opened by slobentanzer 3 months ago
#389 - Rename `preferred_id` to `namespace`
Issue -
State: open - Opened by slobentanzer 3 months ago
#388 - add specific resource classes to init in order to allow import
Pull Request -
State: closed - Opened by slobentanzer 3 months ago
#386 - DFG project 528753569
Issue -
State: open - Opened by slobentanzer 3 months ago
#385 - Open Targets project OTAR3088
Issue -
State: open - Opened by slobentanzer 3 months ago
#384 - Create central `adapters` repository to collect external adapters and adapter templates for specific formats
Issue -
State: open - Opened by slobentanzer 3 months ago
#383 - Remove Python shebang and copyright comments from the top of modules
Issue -
State: open - Opened by slobentanzer 3 months ago
#382 - Add web page monitoring
Issue -
State: closed - Opened by slobentanzer 3 months ago
- 1 comment
#381 - Cache the ontology files
Issue -
State: open - Opened by slobentanzer 3 months ago
#380 - Adhere to SPEC 0
Issue -
State: open - Opened by slobentanzer 4 months ago
#379 - Folder for drawio diagrams
Pull Request -
State: closed - Opened by ecarrenolozano 4 months ago
- 31 comments
#378 - Folder for diagrams in biocypher/docs
Pull Request -
State: closed - Opened by ecarrenolozano 4 months ago
#376 - use GPT alternative to try and find the error with validations
Pull Request -
State: closed - Opened by slobentanzer 4 months ago
#375 - Create config.yml
Pull Request -
State: closed - Opened by slobentanzer 4 months ago
#374 - Graph nodes Semantic search
Issue -
State: open - Opened by winternewt 5 months ago
- 2 comments
#373 - Properties of duplicate nodes
Issue -
State: closed - Opened by mbaric758 5 months ago
- 5 comments
#372 - update to api request caching and doc
Pull Request -
State: closed - Opened by ryxx0811 5 months ago
#371 - Related to #296:Resource download with parameter
Pull Request -
State: closed - Opened by ryxx0811 5 months ago
- 2 comments
#370 - Mock downloads in _get module tests
Issue -
State: open - Opened by slobentanzer 5 months ago
- 1 comment
#369 - add function for caching API requests and refine the args description
Pull Request -
State: closed - Opened by ryxx0811 6 months ago
- 2 comments
#368 - Boolean sometimes not imported correctly (all 'false')
Issue -
State: open - Opened by slobentanzer 6 months ago
- 1 comment
#367 - Duplicate removal in Open-Targets Data.
Issue -
State: closed - Opened by rahulmaurya1507 6 months ago
- 2 comments
#366 - Update supported Python versions in the Readme
Issue -
State: closed - Opened by nilskre 6 months ago
- 2 comments
Labels: good first issue
#365 - fix(import_call):Database name after import prefix
Pull Request -
State: closed - Opened by mbaric758 6 months ago
- 12 comments
#364 - Files with CHEMBL ID entries from Open Targets not getting processed.
Issue -
State: closed - Opened by rahulmaurya1507 7 months ago
- 2 comments
#363 - Error importing csv files with Neo4j v.5.21.2
Issue -
State: closed - Opened by mbaric758 7 months ago
- 3 comments
#362 - How to add new database like i want to add "Human Phenotype Ontology" using open-target.
Issue -
State: closed - Opened by shaileshchaudhary11 7 months ago
- 2 comments
#361 - Streamline output api
Pull Request -
State: closed - Opened by nilskre 7 months ago
- 26 comments
#360 - Allow for time stamped directories as used in some of the examples
Pull Request -
State: closed - Opened by Mjvolk3 7 months ago
- 9 comments
#359 - Fixed tests and continuous integration for adapters (template?)
Issue -
State: open - Opened by slobentanzer 7 months ago
#358 - Directly get in memory networkx graph from BioCypher
Issue -
State: open - Opened by nilskre 8 months ago
- 5 comments
#357 - Close component issues
Issue -
State: open - Opened by slobentanzer 8 months ago
- 1 comment
#356 - The BioCypher meta-graph link in the documentation appears to be down
Issue -
State: open - Opened by tskir 8 months ago
- 1 comment
#355 - Discuss possible solutions and define a target architecture to tackle the reusability of adapters
Issue -
State: open - Opened by nilskre 8 months ago
- 3 comments
#354 - Automatically ensure that docstrings are up to date
Issue -
State: open - Opened by nilskre 8 months ago
- 4 comments
Labels: good first issue
#353 - Not existing method start_ontology are called from core methods
Issue -
State: open - Opened by nilskre 8 months ago
- 1 comment
#352 - Networkx and csv output adapter
Pull Request -
State: closed - Opened by nilskre 8 months ago
#351 - Neo4j version specification via config
Issue -
State: open - Opened by slobentanzer 8 months ago
#350 - Neo4j v5: incremental admin import
Issue -
State: open - Opened by slobentanzer 8 months ago
#349 - Enable multiple output formats within one BioCypher run
Issue -
State: open - Opened by nilskre 8 months ago
#348 - Pandas/CSV
Issue -
State: closed - Opened by nilskre 8 months ago
#347 - networkx
Issue -
State: closed - Opened by nilskre 8 months ago
#346 - End-to-end tutorial, how to run Graph Machine Learning models on a BioCypher KG
Issue -
State: open - Opened by nilskre 8 months ago
- 2 comments
#345 - PyG HeteroData
Issue -
State: open - Opened by nilskre 8 months ago
#344 - iRefIndex - new adapter
Issue -
State: open - Opened by abotzki 8 months ago
- 1 comment
#343 - Add `legacy-style-quoting` to BioCypher core for use with Neo4j admin-import
Issue -
State: open - Opened by slobentanzer 9 months ago
- 5 comments
#342 - CI: Python 3.9 not on MacOS latest any more, but 3.12 also fails
Issue -
State: open - Opened by slobentanzer 9 months ago
- 3 comments
#341 - Create full ETL for RDF type output
Issue -
State: open - Opened by LoesvdBiggelaar 9 months ago
Labels: enhancement
#340 - #339: adapt pr cicd config to limit number of runs for neo4j v4 and v5
Pull Request -
State: closed - Opened by nilskre 9 months ago
#339 - Run Neo4j v4 test action only on Linux (legacy)
Issue -
State: closed - Opened by slobentanzer 10 months ago
#338 - Rdf output adapter
Pull Request -
State: closed - Opened by slobentanzer 10 months ago
- 6 comments
#337 - first version of RDF conversion
Pull Request -
State: closed - Opened by LoesvdBiggelaar 10 months ago
- 13 comments
#336 - #321: fix cicd pipeline
Pull Request -
State: closed - Opened by nilskre 10 months ago
- 1 comment
#335 - [Feature request] Support for long neo4j-admin database import
Issue -
State: open - Opened by JPonsa 10 months ago
- 3 comments
#334 - Relational constraints to SQLLITE output
Issue -
State: open - Opened by dbdimitrov 10 months ago
#333 - Refactoring: split up large files into different files within one folder (like `write`)
Issue -
State: open - Opened by nilskre 11 months ago
#332 - Refactoring: include neo4j-utils in BioCypher core
Issue -
State: open - Opened by nilskre 11 months ago
#331 - error occurred when use poetry add biocypher
Issue -
State: open - Opened by willy20040711 11 months ago
- 1 comment
#329 - refactor(write): return the path of the import call file
Pull Request -
State: closed - Opened by jdreo 11 months ago
- 1 comment
#328 - doc(error messages): more detailled errors
Pull Request -
State: closed - Opened by jdreo 11 months ago
- 1 comment
#327 - Ontology reverse id label yaml config
Pull Request -
State: closed - Opened by nilskre 11 months ago
- 1 comment
#326 - Add unit tests to template repo
Issue -
State: open - Opened by nilskre 11 months ago
#325 - #273: add unit test for duplicated tail ontologies
Pull Request -
State: closed - Opened by nilskre 11 months ago
#324 - Log real path of the `schema_config.yaml` on startup
Issue -
State: closed - Opened by nilskre 11 months ago
#323 - Sqlite output adapter
Pull Request -
State: closed - Opened by nilskre 11 months ago
#322 - Refactoring: split _write.py in mutliple files for better readability
Issue -
State: closed - Opened by nilskre 11 months ago
#321 - Neo4j version 5 patch
Pull Request -
State: closed - Opened by mbaric758 11 months ago
- 15 comments
#320 - Head join node not found in head ontology
Issue -
State: closed - Opened by clairelaudy 11 months ago
- 7 comments
#319 - Multiple copies of NetworkX graph in memory: problem for larger ontologies?
Issue -
State: closed - Opened by slobentanzer 11 months ago
- 1 comment
#318 - RDF parsing leads to `none` type nodes
Issue -
State: open - Opened by slobentanzer 11 months ago
#317 - Add a document for building Pole standalone Docker image
Pull Request -
State: closed - Opened by fengsh27 11 months ago
#316 - Ontology parsing can not handle Snomed CT pre/post coordinated expressions
Issue -
State: closed - Opened by nilskre 11 months ago
#315 - bin/neo4j-admin import not working in latest DBMS 5.15
Issue -
State: closed - Opened by JPonsa 11 months ago
- 2 comments
#314 - SQLite
Issue -
State: closed - Opened by nilskre 11 months ago
- 3 comments
#313 - Ontology: Make reverse_labels configurable via biocypher_config.yaml
Issue -
State: closed - Opened by nilskre 12 months ago
- 1 comment
#312 - Neo4j parsing: replace dots with underscores categorically
Issue -
State: open - Opened by nilskre 12 months ago
#311 - #310: improve runtime of rdflib to networkx transformation
Pull Request -
State: closed - Opened by nilskre 12 months ago
- 3 comments
#310 - Ontology: Improve performance of rdflib -> networkx graph
Issue -
State: closed - Opened by nilskre 12 months ago
#309 - Brackets in ontology names
Pull Request -
State: closed - Opened by nilskre almost 1 year ago
- 5 comments
#308 - Bugfix ontology multiple parents
Pull Request -
State: closed - Opened by nilskre about 1 year ago
- 11 comments
#307 - OWL/TTL ontology containing child nodes with multiple parent nodes defined via `owl:intersectionOf` are not working
Issue -
State: closed - Opened by nilskre about 1 year ago
- 5 comments
#306 - Brackets in ontology names result in improper Neo4j file names
Issue -
State: closed - Opened by nilskre about 1 year ago
- 8 comments
#305 - Resource class and downloader: cache API requests
Issue -
State: closed - Opened by slobentanzer about 1 year ago
Labels: good first issue
#304 - create CICD template repo
Issue -
State: open - Opened by nilskre about 1 year ago