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PeakForest version 2.4.2 - - `2022-04-01`

@version: 2.4.2
@notes:
- minor bugs (REST API / edit MS spectra) and add MSMS templates
@new:
- support 2 new LC-MSMS spectra templates for PFEM
@bugs fixed:
- fix bug: error when updating spectra column_name metadata
- fix bug in list-mz query (rest/v1)
- fix bug in import one compound by its InChIKey - no name mapped
- fix bug in rest/v2 (OpenAPI) - missing columns ID / code on mass spectra entities
- fix bug in XLSM spectra template file - error in 'create new GCMS spectrum' macro

PeakForest version 2.4.1 - - `2022-02-18`

@version: 2.4.1
@notes:
- minor bugs and features
@new:
- add MS spectra curation level: 'RI > 5%'
@bugs fixed:
- fix export MS2 spectra error (case NULL value for 'ion beam gas pressure' metadata)
- fix LCMS/LCMSMS/ICMS json template data mapping/dumping error
@other:
- update PFEM LCMS "plasma_method1_QTOF" and "urine_QToF_method" methods / delete LCMS "plasma_method2_QTOF" method

PeakForest version 2.4.0 - - `2022-02-16`

@version: 2.4.0
@notes:
- update LogP tools, debug 'add one compound' pipeline
@new:
- support new options for LogP computing (choose tool and its path)
- 'add one compound' pipeline code refactoring from scratch: use PubChem webservice
@bugs fixed:
- fix bug in upload compound image (PNG format)
@other:
- support new option to hide/show peakmatching view

PeakForest version 2.3.6 - - `2022-01-27`

@version: 2.3.6
@notes:
- add/update CEA methods in templates
@new:
- spectra import: add two new methods / templates (API FIA, MS and MSMS, for CEA)
@bugs fixed:
- update tests in externalbanks-api (non-mock version)
- formula display in search view: fix formatting
- spectra import: edit/update two methods / templates (for CEA)

PeakForest version 2.3.5 - - `2021-12-15`

@version: 2.3.5
@notes:
- add MGF and mzML spectra export
@new:
- add MGF mass spectra export (beta)
- add mzML mass spectra export (beta)
@bugs fixed:
- fix bug: std-matrix LCMS/LCMSMS spectra import from XLSM file
- fix bug: Log4j vulnerability
@other:
- update email sender parameters (SMTP config.)
- new URL for "How to create numbered compound"

PeakForest version 2.3.4 - - `2021-11-04`

@version: 2.3.4
@notes:
- add MSP spectra export
@new:
- MSP export for mass spectra
@bugs fixed:
- update CTS webservice client after server update
- improvements NMR coupling constant parsing from string
- update NMR peakmatching webservice URL
- show more than 50 rows in peaklist edition
- fix GCMS peaklist edition (add new peak)
- fix MetExplore SSL certificate error
- fix OChem mapping error
@other:
- customize main search placeholder content for each instances
- minor improvements in OpenAPI clients generation (abstract entities deserialization)

PeakForest version 2.3.3 - - `2021-09-03`

@version: 2.3.3
@notes:
- bugs fix
@bugs fixed:
- fix bug in Curation Messages pruning
- fix bug: links to ICMS / ICMSMS spectra in compound sheet and compounds search results' spectra modal preview
- fix bug: remove "dead end" in WebApp's modals (add link to sheets from modals)
- fix bug: impossible to save updates on a NMR spectra's peaklist
- fix bug: CSS z-index for NMR numbered compound viewer (modal / header / footer)
@known bugs:
- all services based on CTS are down - this webservice has been updated; an update of the client is required

PeakForest version 2.3.2 - - `2021-07-27`

@version: 2.3.2
@notes:
- improve NMR support (search /export) and bugs fixes
@new:
- add NMR spectra nmrML export
- improve NMR spectra search (with AND/OR linkers)
@bugs fixed:
- list last 500 curation messages in lifo mode (instead of last 250 in fifo mode)
- fix GCMS spectra data dumping from template
@other:
- improve scoring matching results

PeakForest version 2.3.1 - - `2021-07-01`

@version: 2.3.1
@notes:
- SDF export and GUI to edit GCMS/ICMS spectra
@new:
- add compounds SDF export
- add GUI to edit GCMS spectra
- add GUI to edit ICMS spectra
@bugs fixed:
- update CF_PFEM_plasma_method1_TIMSTOF method
- fix some URL still in inra.fr (instead of inraE.fr) - db server, ontologies framework, metexplore, ...
- fix NMR raw spectra viewer (based on NMRPro)
- fix 1D-NMR peakmatching error
- fix 'flush sessions' feature
@other:
- add documentation about cart for compounds
- update webapp link to REST API and REST API Doc (v1 → v2)

PeakForest version 2.3.0 - - `2021-06-09`

@version: 2.3.0
@notes:
- add Ion Chromatography support
@new:
- add annotation in MassBank record sheets (mass spectra)
- support ICMS spectra (import/export from/to XLSM files; search; view)
- add new LCMS sample prep. solvent - H20+0.1% FA / ACN+0.1% FA (50/50, V/V)
- display top 3 peaks labels on LCMS/LCMSMS spectra viewers
@bugs fixed:
- Fix bug prevention 2D-NMR spectra deletion
- display compound first name in search windows instead of showing the main one
- allow a curator to edit MS2 spectra fragmentation energy
- add missing CAS number on compounds sheets
- add missing GCMS spectra in compounds info modal view
- fix derived compound image display / recompute
- fix documentation file hosting
- fix REST/V2 webservice on getSpectra method - ionization_method filter
- fix Monoisotopic Mass search (with ± proton mass)
@other:
- Remove LCMS method CF_UBP_PLASMA_TOF, add CF_PFEM_plasma_method1_TIMSTOF

PeakForest version 2.2.6 - - `2021-04-12`

@version: 2.2.6
@notes:
- small bug fixes
@new:
- New MTBLS studies list formatting
- Add LC/GC chromatography method name in spectra listing (search/peakmatching)
@bugs fixed:
- Fix values in LCMS method CF_PFEM_plasma_method1_QTOF
- Update MassBank record doc. URL
- Fix search by HMDB ID direct input
- List / add ontologies and std matrix in backoffice
- New MetExplore biosources coverage/mapping
- Fix issues with compound curation lvl update / filtering via rest/v2
- Increase tomcat session timeout from 30 minutes to 2 hours
- Fix nightly database reset on re-deploy
@known bugs:
- Cannot delete some NMR spectra
- Cannot update a parameter in MS2 (Frag. Energy)

PeakForest version 2.2.2 - - `2021-03-12`

@version: 2.2.2
@notes:
- fix small bugs
@new:
- N/A
@bugs fixed:
- Fix expected JSON response from citations service
- Fix PForest generated link with HTTP protocol instead of HTTPS
- Fix PForest REST/V1 LazyInitializationException error on /get-range-clean/ path
- Remove ALogPS webservice (down) replace it with OChem one
- Fix compounds formula formating
- Restart peakforest instances with a cron daily (cmd docker restart)
@other:
- Add reference for Discovery tool in about page

PeakForest version 2.2.1 - - `2021-02-24`

@version: 2.2.1
@notes:
- add new small features and fix minor bugs
@new:
- New search option: search compounds by LogP value
- New search regex: search compounds by SMILES
- New naive peakmatching REST webservices (v2 - OpenAPI)
- Add PeakPattern for 1D NMR spectra in REST webservices (v2 - OpenAPI)
- Add 'metabolights pub. using websementic tech' section in compounds sheets
- Support compounds external IDs
@bugs fixed:
- Fix 302 error on MetExplore WebServices
- Update mapping from objects returned by EBI REST WS (for citations)
- Fix link to my pforest page
- Allow web browser CORS requests in REST webservices (v2 - OpenAPI; HTTP header auth.)

PeakForest version 2.2.0 - - `2020-11-26`

@version: 2.2.0
@notes:
- Epic GCMS
- Update MexExplore webservices
- Add and impl. OpenAPI webservices
@new:
- Add backoffice method to recompute LC chromatography columns codes
@bug fixed:
- Fix infos / links for "derivated compounds" in GCMS spectra sheets
- Fix "update peakforest stat." mechanism: compute stat. on-the-fly
- Improve GCMS "derivated type" data management (display, query)
- Fix tests after remove webservice database update - peakforest-api@4f15ad33
- Fix CI docker image build
@other:
- Improve CI and releases pipelines
- Improve CI and Dockerfile files
- Add OpenAPI projects in nightly CI
- Add OpenAPI projects in release manager

PeakForest version 2.1.1 - - `2020-08-24`

@version: 2.1.1
@notes:
- Epic GCMS
@new:
- Add buttons to zoom in, out and reset zoom for nmrpro
- Basic GCMS spectra search
@bug fixed:
- Fix nmrpro zoom for 1D and 2D spectra
- Fix GCMS spectra viewer zoom
- Fix images generation

PeakForest version 2.1.0 - - 2020-07-22 - -

PeakForest version 2.1.0 features:

@notes:

Epic GCMS

@new:

Improve "import spectra from XLSM template" panel

@bug fixed:

Fix "MassBank doc." link in spectra viewer
Fix "NMRPRo" link in "about page"

@other:

Improve code quality
Fix stats web-gui reporting

PeakForest version 2.0.4 - - 2020-05-11 - -

PeakForest version 2.0.4 features:

@notes:

release for bugfix

@bug fixed:

Fix bug in 3D mol. viewer
Update KeGG webservice expected results in unit tests
Fix bug in delete LC-MSMS spectra
Fix bug in spectra annotation edition
Fix bug in REST GET COMPOUND(s) json output
Fix OpenBabel depiction error
CTS webserice is down (could not add compound using web GUI)

@other:

Force MySQL database engine in InnoDB
Update this patchnote file
Release validation (KO-GO)

@known bugs:

Some MetExplore's webservies are down
CTS webserice is down (could not add compound using web GUI)

PeakForest version 2.0.3 - - 2019-12-02 - -

PeakForest version 2.0.3 features:

@notes:

minor update of PeakForest, update architecture
fix bug, add gitlab CI and project management
update old webservice clients' methods

@bug fixed:

Update Webservices used to add a single compound
Fix error on quick search with mz=165
Fix error in LCMS spectra viewer
Fix errors in metabo cards' spectra listing
Fix error in InChIKey regexp for search
Fix errors in mass search filering / sorting
Fix errors in mass search filering / sorting
Fix errors in compounds' formula search
Fix errors in compounds' name search
Fix errors in MetExplore webservice quering
Fix error in PForest version tracking IDs / info on GUI
Fix error in PeakMatching
Fix error in "update compound" modal
Update ALogPS webservice call

@other:

Global update on project (hibernate, third part tools, external resources, ...)
Update XLSM template file - set it as maven dependency
Update docker image for CI tests / add CI tests.
Update 3D mol. viewer (optional loading)
Update search using external / internal database identifiers
Class refactoring: new Maven Dep.
Fix error on XLSM spectra file export - bug fixed in post-release

@known bugs:

Some MetExplore's webservies are down
Bug in 3D mol. viewer

PeakForest version 2.0.1 - - 2018-03-07 - -

PeakForest version 2.0.1 features:

@notes:

minor update of PeakForest

@new:

support compound Networks IDs - d9551e5b
add button to upload your own MOL and SVG files for compounds - b9af7621 (issue #138)

@bug fixed:

add missing MSMS data in spectra sheet - 4a99f333 ec0f5b6a
solve bad redirect bug - 8a8ca4fb
solve issue with compound images display - 4e514577
solve NMR peakmaching issue - 7be22ac1

@other:

compute number of relevant query for a search - 3744dc06 (issue #135)
change home page default message - 3d3b43b0 (issue #137)

PeakForest version 2.0 - - 2017.09.27 - -

PeakForest version 2.0 features:

@notes:

fourth WebApp release!

@new:

MSMS spectra management / peakmatching - 24d32633
edit 2D NMR spectra data - 6edb286e
Analytical Matrix management - eaa1c179
Analytical Matrix spectra management - eaa1c179

@bug fixed:

bug fixed in search - a9f26997 / b6721a4a
bug fixed in NMR spectra edit - 1de6aa55

@other:

cleanup and performance improvement.
improve numbered compound loading.

PeakForest version 1.8 - - 2017.03.16 - -

PeakForest version 1.8 features:

@notes:

third WebApp release!

@new:

token management system for webservices - branch token-mgmt
2D NMR spectra management services - branch release_1.8
MetExplore Viz - 48e8eb93
BioSM and compound chemical properties - 479e6786 / 41610f50
LCMS spectra splash ID - de5f1fff

@bug fixed:

login: return to last visited page - 797c1e4e
analytics: set code as a customizable value for admins - 81aabb3e
compounds search and score management - #93 #94 #95

@other:

SEO, JS debug, ...

PeakForest version 1.5 - - 2016.07.12 - -

PeakForest version 1.5 features:

@notes:

third WebApp release!

@new:

add NMR 13 carbon spectra
add user setting "main technology" - 8c0e5821
implement new PeakForest IDs for compounds and spectra - 47484506
export LCMS spectra in MassBank format - e0cd166a
implement NMRPro viewer for 13C spectra - 99ece4f4

@bug fixed:

spectra viewer in compound modal (if only NMR spectrum, bug on CSS property select) - 4212bc0b
jsMOL viewer on Firefox - c0ce2450
missmatch real generic compounds / chemical compound without chiral center - 1e33c61e
NMR spectra peak-pattern H annotations - io-spectrafile-api@46f08b16
spectra ZIP file import process progress - 3b35aec6
NMR "light" "real" viewer: display correct name - 4884e85e

PeakForest version 1.1 - - 2016.02.18 - -

PeakForest version 1.1 features:

@notes:

second WebApp release!

@new:

NMR viewer: impl. NMR viewer (dev. by PMB) - 278c70b5
NMR spectrum processing data: impl. NMRreader (dev. by PMB) - 278c70b5
LCMS PeakMatching: impl. LCMSMatching (dev. by CEA) - 4b2134be
License manager - feb545d1

@bug fixed:

LDAP login: open LDAP login for all INRA users - ae9e233a
space character in compounds InChIKey - (PeakForest - DataModel)
avoid MetExplore Web-Service multi-requesting via CRON functions - 003515de
add missing "how to" for numbered compounds - 80846468
several other bug (special character in numbered compounds, logs rotation, close spectra modal if compound modal open after, ...)

PeakForest version 1.0 - - 2015.12.15 - -

PeakForest version 1.0 features:

@notes:

first WebApp release!

Join PeakForest team

PeakForest version 2.4.2 - - 2022-04-01

PeakForest version 2.4.1 - - 2022-02-18

PeakForest version 2.4.0 - - 2022-02-16

PeakForest version 2.3.6 - - 2022-01-27

PeakForest version 2.3.5 - - 2021-12-15

PeakForest version 2.3.4 - - 2021-11-04

PeakForest version 2.3.3 - - 2021-09-03

PeakForest version 2.3.2 - - 2021-07-27

PeakForest version 2.3.1 - - 2021-07-01

PeakForest version 2.3.0 - - 2021-06-09

PeakForest version 2.2.6 - - 2021-04-12

PeakForest version 2.2.2 - - 2021-03-12

PeakForest version 2.2.1 - - 2021-02-24

PeakForest version 2.2.0 - - 2020-11-26

PeakForest version 2.1.1 - - 2020-08-24

PeakForest version 2.1.0 - - 2020-07-22 - -

PeakForest version 2.0.4 - - 2020-05-11 - -

PeakForest version 2.0.3 - - 2019-12-02 - -

PeakForest version 2.0.1 - - 2018-03-07 - -

PeakForest version 2.0 - - 2017.09.27 - -

PeakForest version 1.8 - - 2017.03.16 - -

PeakForest version 1.5 - - 2016.07.12 - -

PeakForest version 1.1 - - 2016.02.18 - -

PeakForest version 1.0 - - 2015.12.15 - -

PeakForest version 2.4.2 - - `2022-04-01`

PeakForest version 2.4.1 - - `2022-02-18`

PeakForest version 2.4.0 - - `2022-02-16`

PeakForest version 2.3.6 - - `2022-01-27`

PeakForest version 2.3.5 - - `2021-12-15`

PeakForest version 2.3.4 - - `2021-11-04`

PeakForest version 2.3.3 - - `2021-09-03`

PeakForest version 2.3.2 - - `2021-07-27`

PeakForest version 2.3.1 - - `2021-07-01`

PeakForest version 2.3.0 - - `2021-06-09`

PeakForest version 2.2.6 - - `2021-04-12`

PeakForest version 2.2.2 - - `2021-03-12`

PeakForest version 2.2.1 - - `2021-02-24`

PeakForest version 2.2.0 - - `2020-11-26`

PeakForest version 2.1.1 - - `2020-08-24`