Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / OpenBEL/openbel-api issues and pull requests

#142 - Components API is replacing terms in BEL statements

Issue - State: closed - Opened by maestroe over 7 years ago - 6 comments

#141 - PUT /api/nanopubs error

Issue - State: closed - Opened by wshayes over 7 years ago

#140 - How to set the "BEL Nanopub Metadata" through the API?

Issue - State: closed - Opened by maestroe over 7 years ago - 1 comment

#139 - Please provide examples for which the auto-completion is working with semantics

Issue - State: closed - Opened by maestroe over 7 years ago - 3 comments

#138 - Components API is returning a wrong argument.

Issue - State: closed - Opened by maestroe over 7 years ago - 1 comment

#137 - Adding nanopub validation

Issue - State: open - Opened by wshayes over 7 years ago

#136 - Improve documentation for the API method POST:/api/datasets for JSON datasets

Issue - State: closed - Opened by maestroe over 7 years ago - 4 comments

#135 - Wrong function.return_type for rnaAbundance

Issue - State: closed - Opened by maestroe over 7 years ago - 2 comments

#134 - Validation of BEL 2.0 expression (rxn) fails

Issue - State: closed - Opened by maestroe over 7 years ago - 2 comments

#133 - Validation of BEL 2.0 expression (activity and tloc) fails

Issue - State: closed - Opened by maestroe over 7 years ago - 7 comments

#132 - Validation of BEL 2.0 expression (fusion) fails

Issue - State: closed - Opened by maestroe over 7 years ago - 2 comments

#131 - BEL 2 variant modifier syntax parsing issue

Issue - State: closed - Opened by wshayes over 7 years ago - 2 comments

#130 - Confusion regarding Datasets API

Issue - State: closed - Opened by wshayes over 7 years ago - 1 comment

#129 - 404 error GET /api/nanopubs

Issue - State: closed - Opened by wshayes over 7 years ago - 1 comment

#128 - Add gem push submodule to Makefile

Issue - State: open - Opened by wshayes over 7 years ago - 1 comment

#127 - Validation of Nanopub when creating/updating nanopubs

Issue - State: closed - Opened by abargnesi over 7 years ago
Labels: enhancement

#126 - Equivalents and Orthologs <targets>

Issue - State: open - Opened by wshayes over 7 years ago
Labels: enhancement

#125 - Semantic autocompleting of BEL expressions using parsed AST

Issue - State: closed - Opened by abargnesi over 7 years ago - 2 comments
Labels: enhancement, api

#124 - Update nanopub_resource serialization

Issue - State: closed - Opened by wshayes almost 8 years ago - 1 comment
Labels: bug

#123 - use /data as mounted volume for RDF data

Pull Request - State: closed - Opened by abargnesi almost 8 years ago - 2 comments

#122 - use /data as mounted volume; updated dev doc

Pull Request - State: closed - Opened by abargnesi almost 8 years ago - 1 comment

#120 - Uploading non utf-8 encoded datasets

Issue - State: closed - Opened by nbargnesi about 8 years ago
Labels: bug

#119 - Missing namespace definitions in dataset nanopub GET

Issue - State: closed - Opened by nbargnesi about 8 years ago - 1 comment
Labels: bug

#118 - Cannot list datasets; reports 404.

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: high priority

#117 - HTTP 500 in datasets POST (BEL Script) - invalid function

Issue - State: closed - Opened by nbargnesi over 8 years ago

#116 - Add version for OpenBEL API.

Issue - State: open - Opened by abargnesi over 8 years ago
Labels: in progress

#115 - HTTP 400 in /api/datasets POST (xbel)

Issue - State: closed - Opened by nbargnesi over 8 years ago - 1 comment

#114 - HTTP 500 in /api/datasets POST (BEL Script)

Issue - State: closed - Opened by nbargnesi over 8 years ago
Labels: bug

#113 - Authentication enabled for /api/expressions

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: high priority

#112 - JSON response for Expression validation

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: api, low priority

#111 - File lock exception when processing URL namespaces.

Issue - State: closed - Opened by abargnesi over 8 years ago - 3 comments
Labels: bug, high priority

#110 - Fix generator of resource links for Annotations and Namespaces.

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: bug, api

#109 - Download link error

Issue - State: closed - Opened by wshayes over 8 years ago - 1 comment
Labels: bug

#108 - look for tokens as parameters as well

Pull Request - State: closed - Opened by nbargnesi over 8 years ago - 2 comments

#107 - Update OpenBEL API documentation to reflect 0.6.0 enhancements.

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: documentation

#106 - fixes #105

Pull Request - State: closed - Opened by nbargnesi over 8 years ago - 1 comment

#105 - Missing authorization header reported when header is malformed

Issue - State: closed - Opened by nbargnesi over 8 years ago - 1 comment

#104 - API route to retrieve supported translators

Issue - State: open - Opened by abargnesi over 8 years ago
Labels: api

#103 - Run syntax/semantic validation for exported BEL Nanopubs.

Issue - State: open - Opened by abargnesi over 8 years ago

#102 - Dataset URIs are used as resource URLs; prohibitive

Issue - State: open - Opened by abargnesi over 8 years ago
Labels: bug, api

#101 - Issue100

Pull Request - State: closed - Opened by nbargnesi over 8 years ago - 2 comments

#100 - Simplify authentication mechanics

Issue - State: closed - Opened by nbargnesi over 8 years ago - 4 comments

#99 - Support translation of dataset evidence to all available BEL translators

Issue - State: open - Opened by abargnesi over 8 years ago
Labels: enhancement

#98 - Update required version of MongoDB to 3.2.

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: documentation

#97 - Evidence facets not computed on first search after importing dataset

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: bug

#96 - Full-text search on evidence results in Mongo error

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: bug

#95 - Dataset's evidence collection has malformed annotation/namespace URIs

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: bug, api

#94 - Incorrect total when filtering evidence collection

Issue - State: open - Opened by abargnesi over 8 years ago
Labels: bug, api

#93 - Fix evidence facet filtering when user authentication is enabled

Issue - State: closed - Opened by abargnesi almost 9 years ago
Labels: bug

#92 - Support configured MongoDB user for authentication

Issue - State: closed - Opened by abargnesi almost 9 years ago

#91 - Report semantic version of OpenBEL API

Issue - State: closed - Opened by abargnesi almost 9 years ago - 1 comment

#90 - Namespace/Annotation field and autocomplete workflow requirements

Issue - State: closed - Opened by abargnesi almost 9 years ago - 12 comments
Labels: enhancement

#89 - Store evidence documents as a VoID dataset

Issue - State: closed - Opened by abargnesi almost 9 years ago - 1 comment
Labels: api, feature

#88 - Namespace value resources do not convey multiple encoding types

Issue - State: closed - Opened by abargnesi almost 9 years ago - 2 comments
Labels: bug, api

#87 - Collection of resources should return empty array if it the response is ∅

Issue - State: open - Opened by abargnesi almost 9 years ago
Labels: enhancement, api

#86 - include bel and redlander as deps w/ version info

Pull Request - State: closed - Opened by nbargnesi almost 9 years ago

#85 - Arbitrary SwissProt accession identifier returned when record has multiple

Issue - State: open - Opened by abargnesi almost 9 years ago
Labels: bug, data

#84 - expression completions returns incorrect types

Issue - State: closed - Opened by abargnesi almost 9 years ago
Labels: bug, api

#83 - Authentication support

Issue - State: closed - Opened by nbargnesi almost 9 years ago - 2 comments
Labels: feature

#82 - Create BEL Evidence from supported BEL formats

Issue - State: open - Opened by abargnesi almost 9 years ago
Labels: enhancement, api

#81 - search results export as CSV

Issue - State: open - Opened by wshayes about 9 years ago
Labels: enhancement, api

#80 - Add query term match in annotation and namespace results

Issue - State: closed - Opened by wshayes about 9 years ago - 4 comments
Labels: high priority

#79 - Can you add the annotation name to api/annotations/values search results?

Issue - State: closed - Opened by wshayes about 9 years ago - 2 comments

#78 - Creating evidence (POST /api/evidence) may not conform to evidence schema

Issue - State: closed - Opened by abargnesi about 9 years ago - 5 comments
Labels: bug, high priority

#77 - Retrieve components of a BEL expression through decomposition

Issue - State: closed - Opened by abargnesi about 9 years ago - 1 comment
Labels: enhancement, api

#76 - Grouping facets

Issue - State: closed - Opened by wshayes about 9 years ago - 5 comments

#75 - /api/evidence GET statistics

Issue - State: closed - Opened by wshayes about 9 years ago - 3 comments

#74 - experiment_context filters will not match evidence resources

Issue - State: closed - Opened by abargnesi over 9 years ago
Labels: bug

#73 - Show max facet values for context/name pairs

Issue - State: closed - Opened by abargnesi over 9 years ago
Labels: enhancement, api

#72 - Add relationship vocabulary listing to API

Issue - State: open - Opened by wshayes over 9 years ago - 1 comment

#71 - Evidence metadata may be supported by a well-defined vocabulary.

Issue - State: open - Opened by abargnesi over 9 years ago
Labels: question, ready, future

#70 - Represent evidence biological context annotations as URIs

Issue - State: closed - Opened by nbargnesi over 9 years ago - 4 comments
Labels: enhancement

#69 - Evidence facets with null values are not filtered.

Issue - State: closed - Opened by abargnesi over 9 years ago

#68 - Summary Text enhancements

Issue - State: open - Opened by ncatlett over 9 years ago
Labels: enhancement, ready

#67 - 400 if evidence bel_statement is syntactically invalid

Issue - State: open - Opened by abargnesi over 9 years ago
Labels: api, high priority

#66 - Smarter autocomplete using BEL sematic information

Issue - State: closed - Opened by ncatlett over 9 years ago - 1 comment

#65 - support autocomplete for values that include spaces

Issue - State: closed - Opened by ncatlett over 9 years ago - 2 comments

#64 - Expression equivalence

Issue - State: open - Opened by abargnesi over 9 years ago
Labels: enhancement, api, ready

#63 - Expression orthology

Issue - State: open - Opened by abargnesi over 9 years ago - 1 comment
Labels: enhancement, api, ready

#62 - Migrating mongodb data

Issue - State: closed - Opened by abargnesi over 9 years ago - 1 comment

#61 - Evidence resource collection can return 404 after an evidence deletion

Issue - State: closed - Opened by abargnesi over 9 years ago - 2 comments

#60 - Support document-level properties on evidence

Issue - State: closed - Opened by nbargnesi over 9 years ago - 2 comments

#59 - Collection filter design

Issue - State: open - Opened by abargnesi over 9 years ago - 1 comment
Labels: api, future

#58 - Evidence query for biological_context is flawed

Issue - State: closed - Opened by abargnesi over 9 years ago
Labels: bug

#51 - Rename biological_context to experiment_context within evidence schema.

Issue - State: closed - Opened by nbargnesi over 9 years ago - 4 comments
Labels: enhancement

#48 - Provide match context for annotation / namespace value search

Issue - State: closed - Opened by abargnesi over 9 years ago - 1 comment

#44 - Retrieve evidence resource collection (/api/evidence) using BEL translators

Issue - State: open - Opened by abargnesi over 9 years ago
Labels: ready

#39 - Syntax validation of expressions.

Issue - State: open - Opened by abargnesi over 9 years ago
Labels: enhancement, api

#38 - Access annotation prefix from an annotation_value resource.

Issue - State: closed - Opened by abargnesi over 9 years ago - 1 comment
Labels: enhancement, api, high priority

#34 - Consistent JSON error response handling

Issue - State: open - Opened by abargnesi over 9 years ago

#30 - Namespace and Annotation cannot return more than one encoding type

Issue - State: closed - Opened by abargnesi over 9 years ago - 1 comment
Labels: api

#20 - Resources should convey uri property for application/json media type

Issue - State: closed - Opened by abargnesi over 9 years ago
Labels: api

#18 - Serve API schemas from /api/schemas

Issue - State: open - Opened by abargnesi over 9 years ago - 2 comments
Labels: enhancement, api

#17 - Expressions API

Issue - State: closed - Opened by abargnesi over 9 years ago - 1 comment
Labels: api, feature, ready

#15 - Namespaces API

Issue - State: closed - Opened by abargnesi over 9 years ago - 1 comment
Labels: api, feature, ready, mostly-done

#13 - Resource objects should have plural type names and always be arrays

Issue - State: closed - Opened by abargnesi over 9 years ago - 2 comments
Labels: enhancement, api

#11 - Integrate yaks to provide hypermedia html formatter

Issue - State: closed - Opened by abargnesi over 9 years ago
Labels: enhancement, prototype, api

#6 - Experiement with guidomb/app_configuration

Issue - State: closed - Opened by abargnesi about 10 years ago
Labels: prototype

#1 - Sinatra router issue using paths containing forward slashes in value

Issue - State: closed - Opened by abargnesi over 10 years ago - 1 comment