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PeakForest events

• May 2023: FoodPhyt European project annual meeting - Clermont-Ferrand (France) - pres. "MSMS Data in PhytoHUB"
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Join PeakForest team

Two opportunity available for the moment to join the PeakForest dev or data manager team !

• [OPENED] Java developer position (14 months contract): [More information - ENG] - Key words: Java, OpenAPI, Web component, type-script, vue.js, metabolomics

• [CLOSED] Microservices developer position (16 months contract): [INRAE jobs] - Key words: Cloud, OpenAPI, Kubernetes, Python, Java, metabolomics

   

• [CLOSED] internship position (Master level): Spectral data visualisation web-component building. [More information - FR] - Key words: Web component, type-script, vue.js, metabolomics - Célian Barbe was recruted
• [CLOSED] internship position (Master level): Construction and deployment of metabolomics microservices on the CLOUD infrastructure of the Clermont Auvergne Mesocentre. [More information - FR] - Key words: Kubernetes, cloud, Java, python, microservices, OpenAPI, metabolomics - Faustine Souc was recruted

PeakForest version 2.6.0 - - 2023-03-14

• @version: 2.6.0
• @notes:
  • support spectra import using OpenAPI endpoint.
• @new:
  • Add new OpenAPI method POST /spectrum
  • Support new Agromix template
• @bugs fixed:
  • pforest#dev - fix entites mapping in WebServices clients
• @other:
  • pforest#dev - switch CI/CD docker runner on sauron

PeakForest version 2.5.0 - - 2022-06-13

• @version: 2.5.0
• @notes:
  • replace OpenBabel toolbox by CDK
• @new:
  • remove OpenBabel / replace it by CDK

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!