MSMetaEnhancer - v0.4.1

What's Changed

• WIP:Upgraded some libraries - specifically matchms by @acquayefrank in https://github.com/RECETOX/MSMetaEnhancer/pull/157
• updated version and changelog by @hechth in https://github.com/RECETOX/MSMetaEnhancer/pull/159

New Contributors

• @acquayefrank made their first contribution in https://github.com/RECETOX/MSMetaEnhancer/pull/157

Full Changelog: https://github.com/RECETOX/MSMetaEnhancer/compare/v0.4.0...v0.4.1

Scientific Software - Peer-reviewed - Python
Published by hechth about 1 year ago

MSMetaEnhancer - v0.4.0

What's Changed

• Update IDSM SPARQL queries to achieve better performance by @galgonek in https://github.com/RECETOX/MSMetaEnhancer/pull/152
• Switched to poetry and added additional converters by @hechth in https://github.com/RECETOX/MSMetaEnhancer/pull/155

New Contributors

• @galgonek made their first contribution in https://github.com/RECETOX/MSMetaEnhancer/pull/152

Full Changelog: https://github.com/RECETOX/MSMetaEnhancer/compare/v0.3.0...v0.4.0

Scientific Software - Peer-reviewed - Python
Published by hechth over 2 years ago

MSMetaEnhancer - v0.3.0

[0.3.0] - 2023-05-12

Added

• general class Data for input handling #141
• DataFrame class to read and handle tabular metadata input #141
• implementation of blocking time in PubChem #145 ### Changed
• Spectra class is an instantiation of Data class #141
• fix throttling freezing the app #144 ### Removed
• retired NLM (ChemIDplus) service #140

Scientific Software - Peer-reviewed - Python
Published by xtrojak about 3 years ago

MSMetaEnhancer - v0.2.5

What's Changed

• Fix Circuit Breaker pattern in python 3.9; fix skipping async tests by @maximskorik in https://github.com/RECETOX/MSMetaEnhancer/pull/124
• Fix Publish to PyPi action by @maximskorik in https://github.com/RECETOX/MSMetaEnhancer/pull/125
• Update package version by @maximskorik in https://github.com/RECETOX/MSMetaEnhancer/pull/127
• Minor fixes to bibliography by @csoneson in https://github.com/RECETOX/MSMetaEnhancer/pull/128
• Release 025 by @hechth in https://github.com/RECETOX/MSMetaEnhancer/pull/130

New Contributors

• @csoneson made their first contribution in https://github.com/RECETOX/MSMetaEnhancer/pull/128

Full Changelog: https://github.com/RECETOX/MSMetaEnhancer/compare/v0.2.4...v0.2.5

Scientific Software - Peer-reviewed - Python
Published by hechth almost 4 years ago

MSMetaEnhancer - v0.2.4

[0.2.4] - 2022-08-30

Changed

• escaping of single quotes in IDSM arguments #102
• unified environment and packaging management #115
• apply circuit breaker pattern in WebConverter #113 ### Removed
• removed test case from curator which fails in matchms > 0.14 [#112](https://github.com/RECETOX/MSMetaEnhancer/issues/112

Scientific Software - Peer-reviewed - Python
Published by xtrojak almost 4 years ago

MSMetaEnhancer - v0.2.3

[0.2.3] - 2022-05-12

Added

• KEGG ID conversions support to BridgeDB service #101 ### Changed
• double quotes to single quotes in IDSM #102

Scientific Software - Peer-reviewed - Python
Published by xtrojak about 4 years ago

MSMetaEnhancer - v0.2.2

[0.2.2] - 2022-04-27

Added

• introduced error level into logging #95
• logging of unknown errors in Annotator #90 ### Changed
• the log file is now written continuously during annotation and the metrics added at the end of the file #92

What's Changed

• Log unknown errors by @xtrojak in https://github.com/RECETOX/MSMetaEnhancer/pull/91
• Enabled CI for all platforms by @hechth in https://github.com/RECETOX/MSMetaEnhancer/pull/97
• Store logs during annotation by @xtrojak in https://github.com/RECETOX/MSMetaEnhancer/pull/96
• Create publish_pypi.yaml by @hechth in https://github.com/RECETOX/MSMetaEnhancer/pull/98
• Update to version 0.2.2 by @hechth in https://github.com/RECETOX/MSMetaEnhancer/pull/100

Full Changelog: https://github.com/RECETOX/MSMetaEnhancer/compare/v0.2.1...v0.2.2

Scientific Software - Peer-reviewed - Python
Published by hechth about 4 years ago

MSMetaEnhancer - v0.2.1

[0.2.1] - 2022-04-05

Added

• try-finally block to ensure the Monitor thread is always terminated #86 ### Changed
• improved parsing of PubChem responses #84

Scientific Software - Peer-reviewed - Python
Published by xtrojak over 4 years ago

MSMetaEnhancer - v0.2.0

[0.2.0] - 2022-03-19

Added

• BridgeDB supporting conversion of several database IDs #76
• ComputeConverter class for conversions based on computation instead of querying #75
• ConverterBuilder which validates and initialises converters #75
• reintroduced PubChem service using direct REST web interface #76 ### Changed
• reorganised Converter class to support computation approach #75
• renamed PubChem service to IDSM to avoid confusion #73

Scientific Software - Peer-reviewed - Python
Published by xtrojak over 4 years ago

MSMetaEnhancer - v0.1.3

[0.1.3] - 2022-02-15

Added

• multidict package requirement
• tracking of attributes validation in log #68
• CIR: Inchi -> SMILES conversion #66 ### Changed
• passed multidict instead of frozendict to aiohttp.ClientSession.post (required by package)
• take only first result when there are multiple hits in CIR conversions #69
• support ISOMERIC_SMILES and CANONICAL_SMILES in PubChem instead of generic SMILES #67

Scientific Software - Peer-reviewed - Python
Published by xtrojak over 4 years ago

MSMetaEnhancer - v0.1.2

[0.1.2] - 2022-01-06

Added

• generate_options() function in Galaxy submodule to create all possible conversions supported by the tool in a format suitable for the galaxy tool form #58
• monitoring of services status during annotation process #56
• validation of obtained metadata #59 ### Changed
• structure and contents of documentation #51 ### Removed
• tests checking contents and consistency of individual services #54

Scientific Software - Peer-reviewed - Python
Published by xtrojak over 4 years ago

MSMetaEnhancer - v0.1.1

[0.1.1] - 2021-12-07

Added

• get_conversion_functions on the level of Converter ### Changed
• computation of all available jobs in Application ### Removed
• get_all_conversions on the level of Annotator

Scientific Software - Peer-reviewed - Python
Published by xtrojak over 4 years ago

MSMetaEnhancer - v0.1.0

The first release of MSMetaEnhancer. The tool is used for massspectra files annotation (.msp format supported). In this version, it supports four services: CIR, CTS, NLM, and PubChem. The app uses asynchronous implementation of annotation process, benefiting from non-trivial amount of time spent by waiting for a web query response.

The main features of this version are asynchronous requests (#15), generalised requests to obtain multiple values at once (#20), logging and quantitative success summary of annotation process (#22), usage of IDSM SPARQL for PubChem service (#25), and available conda environment files (#35).

Scientific Software - Peer-reviewed - Python
Published by xtrojak over 4 years ago