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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!