Ecosyste.ms: Issues

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GitHub / OpenBEL/bel_parser issues and pull requests

#75 - NoMethodError - undefined method 'string_literal' for #<String:0x...>:

Issue - State: closed - Opened by nbargnesi over 8 years ago - 1 comment
Labels: bug, critical

#74 - Uninitialized ValueEcodiing constants

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

#73 - Reinitialized constant warnings when running BEL commands.

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

#72 - Can't upload BEL Script in BELMgr

Issue - State: closed - Opened by wshayes over 8 years ago - 2 comments

#71 - BELMgr import/export formats

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

#70 - Allow multi-line strings (common in SET records).

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

#69 - Refactor syntax/signature checks due to missing value AST in parameter.

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

#68 - Relationship parser is incorrect and does not yield.

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: ragel, test

#67 - Statement comment ragel never yields.

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: ragel, test

#66 - String does not yield incomplete AST if starting with non-quote.

Issue - State: closed - Opened by abargnesi over 8 years ago - 1 comment
Labels: ragel, test

#65 - Identifier does not yield incomplete AST on invalid char.

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: ragel, test

#64 - Function ragel FSM is not used

Issue - State: closed - Opened by abargnesi over 8 years ago - 3 comments
Labels: question, ragel, test

#63 - Incomplete string in parameter will not yield of EOF.

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: ragel, test

#62 - added ragel FSM tracer; refs #61

Pull Request - State: closed - Opened by abargnesi over 8 years ago

#61 - Trace execution of ragel FSMs

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

#60 - Parameter parser does not work by itself.

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

#59 - Fix comment_line parsing

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

#58 - Issue3 rebase

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

#57 - Test reference combination from multiple files.

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

#56 - Test translation for nanopub equivalence

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

#55 - Test topics

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

#54 - Fix OpenBEL API query param authentication token bug

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

#53 - Capture errors/warnings from NanopubMapper.

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

#52 - BEL Nanopub model within bel.rb

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

#51 - Add BEL Version to an API endpoint for exposure in BELMgr

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

#50 - Normalize Demo, Dev and Production servers

Issue - State: closed - Opened by wshayes over 8 years ago - 5 comments

#49 - Update OpenBEL API RAML documentation.

Issue - State: open - Opened by abargnesi over 8 years ago - 1 comment
Labels: in progress

#48 - return_type in bel_parsers for relationships

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

#47 - Errors retrieving annotations/namespace from OpenBEL API.

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

#46 - Update BELMgr to use /api/relationships

Issue - State: closed - Opened by wshayes over 8 years ago - 3 comments

#45 - Update Autocomplete API to use BEL specifications

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

#44 - Implement expression validation in API

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

#43 - Implement a BEL Translator plugin within bel_parser.

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

#42 - BEL Script validator

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

#41 - Set character range for AST nodes.

Issue - State: open - Opened by abargnesi over 8 years ago - 1 comment

#40 - Add syntax validation for incomplete AST.

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

#39 - Convert BEL 2.0 to RDF (bel.rb)

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

#38 - Provide autocomplete API with language specification.

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

#37 - Fix descriptions of BEL 1 / 2 functions and relationships.

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

#36 - Expression parsers do not forgive whitespace.

Issue - State: open - Opened by abargnesi over 8 years ago
Labels: ragel, test

#35 - Develop migration tool for BEL 1->2

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

#34 - Update BELMgr and OpenBEL API terminology

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

#33 - Add BEL relationships for BEL 1.0 / BEL 2.0.

Issue - State: closed - Opened by abargnesi over 8 years ago - 2 comments

#32 - Review BEL specifications for 1.0 and 2.0

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

#31 - Update OpenBEL Wiki

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

#30 - Migration plan for upgrading BEL content from 1.0 to 2.0.

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

#29 - HGVS syntax check / recognizer

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

#28 - Enhance Input AST with namespace and encoding properties.

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

#27 - Add ragel machine for SET DOCUMENT record.

Issue - State: closed - Opened by abargnesi over 8 years ago
Labels: enhancement, ragel

#26 - Improve naming and documentation for return types (e.g. Any).

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

#23 - Most nodes heuristic when resulting in incomplete ASTs.

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

#22 - Apply semantic AST comparison to complete expression.

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

#21 - Define functional semantic AST in language specifications.

Issue - State: closed - Opened by abargnesi over 8 years ago - 2 comments

#20 - Add encoding type hierarchy to language specification.

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

#19 - Add function return type hierarchy to language specification.

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

#18 - Access children from type-specific AST nodes.

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

#17 - Apply properties to AST nodes

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

#16 - Factor out behavior in specification hierarchy.

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

#15 - Move bel_expression to expression; Drop bel_

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

#14 - Simple statement parse failure for identifier AST in error condition

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

#13 - BEL RDF 2.0: Design RDF schema for BEL, version 2.0.

Issue - State: closed - Opened by abargnesi over 8 years ago - 2 comments

#12 - BEL JGF 3.0: Alignment of evidence format to support BEL Nanopubs.

Issue - State: closed - Opened by abargnesi over 8 years ago - 3 comments

#11 - XBEL 2.0: Support BEL version 2.0 and document enhancements

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

#10 - Syntax validation for BEL expressions (1.0 / 2.0).

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

#9 - apply style fixes

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

#8 - Expand line continuator in AST generator.

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

#7 - Normalize line terminators in AST generator.

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

#6 - Yield comment lines as AST.

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

#5 - Yield blank lines as AST.

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

#4 - Add complete/incomplete markers to AST nodes.

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

#3 - Allow incomplete AST results.

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

#2 - Add character range to AST nodes.

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

#1 - Prototype a layered approach to parsing using ragel

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