Release notes

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Available versions
VersionDescription
GnpIS 19.2
GnpIS 19.1
GnpIS 18.3
GnpIS 18.2
GnpIS 18.1
GnpIS 17.3
GnpIS 17.2
GnpIS 17.1
GnpIS 16.3
GnpIS 16.2
GnpIS 16.1
GnpIS 15.3
GnpIS 15.2
GnpIS 15.1.1
GnpIS 15.1
GnpIS 14.3.1
GnpIS 14.3
GnpIS 14.2.2Manage private data in ElasticSearch index, add publications on transcriptomic project card
GnpIS 14.2.1
GnpIS 14.2
GnpIS 14.1.1
GnpIS 14.1
GnpIS 13.3.2
GnpIS 13.3.1
GnpIS 13.3
GnpIS 13.2
GnpIS 13.1
GnpIS 12.4.1
GnpIS 12.4Species group restriction, bug fixes, interface improvements, new features.
GnpIS 12.3Rationalize and unify version system, bug fixes, interface improvements, new features.

Version 19.2 (2019/11/05)

Bug

  • [GNP-5156] - Debug GnpIS tests.
  • [GNP-5486] - Bad format of transplant_mapped_markers.csv file
  • [GNP-5515] - KnetMiner link back keyword update
  • [GNP-5572] - Links with accentuaded character doesn't work
  • [GNP-5613] - Missing country in Siregal passport form.
  • [GNP-5614] - Siregal : Geographic drop down don't include "France"
  • [GNP-5630] - Genotyping matrix export failure
  • [GNP-5678] - FAIDARE public version is unable to access ES indices
  • [GNP-5679] - Search studies by trialDbId doesn't work.

Story

  • [GNP-4956] - Remove all non-ascii characters from trial_number
  • [GNP-5183] - Ontologies Elixir: Maize Traits, Drops, Environmental Traits
  • [GNP-5192] - Complete already inserted maize data from Drops project
  • [GNP-5285] - Insert Walnut genetic resources, phenotyping, SSR markers data from BRC (ODS).
  • [GNP-5570] - Insert missing datasets into WheatMine
  • [GNP-5571] - TEST Display VCF & BigWig files from BreedWheat project on the RefSeq v1.0 browser
  • [GNP-5605] - Add IWGSC RefSeq mRNA into the Data Discovery Search
  • [GNP-5639] - ODS Insert F. Balfourier genetic resources
  • [GNP-5640] - Release 19.1

New Feature

  • [GNP-5442] - Deploy RARe portal in production
  • [GNP-5636] - Add IWGSC Assembly v2.0 to download and BLAST

Task

  • [GNP-4123] - Create Trees4Future -> GnpIS data flow
  • [GNP-4913] - Merge maize traits from carto with the maize ontology
  • [GNP-5254] - Remove column language_id from the unique constraint in table accession_synonym_t
  • [GNP-5389] - Remove dataset constraint for accession (SQL, Talend).
  • [GNP-5449] - PHIS to FAIDARE: indexation prototype
  • [GNP-5476] - Manage TaBW280K
  • [GNP-5511] - Add BW SNP positions on the IWGSC RefSeq v1.0
  • [GNP-5519] - Put FAIDARE in production (fully replace old gnpis-core)
  • [GNP-5532] - Add "SELF" as parent type in GermplasmPedigree indexation
  • [GNP-5581] - Extract and reindex data from the new KNetMiner RDF files
  • [GNP-5635] - Add Akhunov diversity data to download and in JBrowse
  • [GNP-5637] - JBrowse config in "Select track mode" for IWGSC RefSeq v1.0
  • [GNP-5666] - Add TFBS data in Arabido POC
  • [GNP-5667] - Gene Card: Implement a Wordle or a word counts to ease the querying

Version 19.1 (2019/06/07)

Bug

  • [GNP-5326] - Can't display sample card
  • [GNP-5429] - Remove Taxon from GermplasmName
  • [GNP-5456] - Confidential data are visible on GPDS (Maize).
  • [GNP-5469] - Memory overflow on PGSQL JSON observation unit document generation
  • [GNP-5527] - RC: Ephesis is too slow
  • [GNP-5538] - Bug on text overflow for Firefox
  • [GNP-5544] - Brapi study/id/germplasm call seems too slow with big page number
  • [GNP-5556] - BrAPI calls is empty on RC

Story

  • [GNP-4441] - Update Vitis accessions from BRC - 2017.
  • [GNP-5228] - New Maize B73 v4 public JBrowse including Mutator track and mailto Biogemma
  • [GNP-5477] - MIAPPE data set for popyomics MIAPPE paper
  • [GNP-5478] - Dataset for MIAPPE paper wheat
  • [GNP-5498] - Release 18.3
  • [GNP-5509] - Add a new track on IWGSC JBrowse with the GOMAP file / Add also remapped genes (TGAC v1 + Survey Sequence)
  • [GNP-5510] - Link IWGSC genes from the IWGSC JBrowse to other tools (Persephone, Ensembl Plant, WheatMine)
  • [GNP-5521] - Add the new durum wheat reference sequence to URGI blast
  • [GNP-5567] - GPDS provide data sources in spring properties rather than backend resources

New Feature

  • [GNP-5431] - Implement continuous delivery with GitLab for GPDS
  • [GNP-5436] - Insert MAAF convention RG + pheno + geno from Pierroton
  • [GNP-5482] - GPDS Xrefs

Task

  • [GNP-4772] - Clean accessions primary descriptors to match an ontology (TDv5).
  • [GNP-5096] - Display Taxon external sources on accession card
  • [GNP-5108] - Insert Populus nigra genotyping in GnpIS
  • [GNP-5363] - Inform every user from GnpIS for RGPD.
  • [GNP-5408] - Solr to ES migration for data-discovery beta version
  • [GNP-5490] - Uniformize GPDS pages and reduce cyclomatic complexity
  • [GNP-5493] - Deduplication of Pea datasets
  • [GNP-5560] - Evaluate Nextflow for ET/L (POC Elixir/URGI)
  • [GNP-5562] - Implement indexing component into FAIDARE
  • [GNP-5566] - Manage fields displayed in germplasm card

Improvement

  • [GNP-5604] - Use common link menu item in Ephesis

Version 18.3 (2019/03/18)

Bug

  • [GNP-5359] - Link to marker card in genotyping result failed
  • [GNP-5393] - Open GPDS data result link to same page (no target _blank)
  • [GNP-5399] - Remove Siregal simple search form redirection towards GPDS when a BRC is selected
  • [GNP-5413] - Remove old "https://gpi.versailles.inra.fr/GnpSeq"
  • [GNP-5440] - GPDS facets don't update systematically the results.
  • [GNP-5444] - Update deduplicate_table_data.pl
  • [GNP-5458] - Ephesis: Selecting Miscanthus in genus does not restrict variable ontology correctly

Story

  • [GNP-4669] - Update DOI talend to handle new API and complete talend metadata
  • [GNP-4712] - Insert INRA Pierroton accessions + phenotypes data for GenTree
  • [GNP-4713] - Insert INRA Orléans accessions + phenotypes data for GenTree
  • [GNP-4715] - Insert CNR accessions + phenotypes data for GenTree
  • [GNP-4716] - Insert AUTH accessions + phenotypes data for GenTree
  • [GNP-4725] - New Maize Genomes : 5 new Public Jbrowse
  • [GNP-4766] - Insert CEH accessions + phenotypes data for GenTree
  • [GNP-4769] - Insert IPAE RAS accessions + phenotypes data for GenTree
  • [GNP-4823] - Data harvester for Solr To Elasticsearch caching
  • [GNP-5000] - Insert Whealbi VCF file + tRNA into RefSeq v1.0 JBrowse
  • [GNP-5107] - Restructure Maven modules in UI
  • [GNP-5224] - Update WIPO with Pauline LASSERRE-ZUBER modifications
  • [GNP-5253] - Update Ephesis & GPDS indexing for Elasticsearch 6
  • [GNP-5284] - Deduplicate contact_t AND add unique constraint
  • [GNP-5372] - Release 18.2
  • [GNP-5385] - Insert BreedWheat Pheno AB-QTL 2018
  • [GNP-5410] - Insert BreedWheat WP3 Association 2017
  • [GNP-5411] - Migrate Ephesis to Elasticsearch 6
  • [GNP-5412] - Migrate GPDS to Elasticsearch 6
  • [GNP-5424] - Minimal Study & Germplasm card to Angular
  • [GNP-5427] - GPDS Advanced Germplasm card
  • [GNP-5481] - Improve Siregal home page text and update mail for Siregal order.

New Feature

  • [GNP-4983] - Create configuration file for indexation for Jbrowse OAK PM1N and OakMine_PM1N
  • [GNP-5421] - Add synonyms for Gentree Avignon accessions
  • [GNP-5433] - GPDS Site card
  • [GNP-5434] - Curate GenTree GPS locations and add missing data

Task

  • [GNP-4228] - Update FAO VIEWS institution names and addresses.
  • [GNP-4924] - Extract JBrowse wheat data for search indexing
  • [GNP-5063] - Integrate BFF Miscantus Data MONS Orleans (ODS data)
  • [GNP-5099] - Improve ontology widget search (add new fields) (Cyril part)
  • [GNP-5131] - MàJ notebook pour préparation des données RepetDB
  • [GNP-5155] - BW WP2 phéno sécherresse et asso
  • [GNP-5315] - Insert Melon private genetic resources from Network.
  • [GNP-5361] - Integrate botanic families into SyntenyViewer
  • [GNP-5390] - Update extraction scripts by removing dataset.
  • [GNP-5416] - Update links to GnpIS modules directly to query form.
  • [GNP-5441] - Make available whealbi wheat accession data in a downloadable file
  • [GNP-5445] - Index Agrold & knet miner in production
  • [GNP-5468] - Move AMS population genotyping experiment to WP2-WP3 restricted group
  • [GNP-5480] - Merge the 2 genotyping talend jobs

Improvement

  • [GNP-5073] - Check language in open street map
  • [GNP-5467] - Improve extract Siregal data Talend.
  • [GNP-5470] - RepetDB Publication Review Feedback
  • [GNP-5491] - Isolate Siregal from GPDS.

Exploratory Task

  • [GNP-5064] - Migrate Geno to Elasticsearch 6

Version 18.2 (2018/10/29)

Bug

  • [GNP-4752] - WheatIS shard ping mechanism opens too many file descriptors (Raphaël part)
  • [GNP-4969] - The script manage_release.sh does not work properly for maven projects (Erik part)
  • [GNP-5005] - The script manage_release.sh does not work properly for maven projects (Dorothée's part)
  • [GNP-5007] - Make unified interface more robust against groups webservice status
  • [GNP-5173] - Url to Ephesis with variableId doesn't work
  • [GNP-5177] - RepetDB minor fixes for publication
  • [GNP-5180] - Deduplicate Apache accession
  • [GNP-5181] - Errors in genotyping form, tab 'Accessions'
  • [GNP-5278] - Unecessary error message on Ephesis
  • [GNP-5312] - Can't deselect trait class and ontology on unified interface
  • [GNP-5331] - The related objects are not displayed on sequence taxon card.
  • [GNP-5344] - Add species and variable enrichment to generic indexation

Story

  • [GNP-3842] - Semantic data discovery V1
  • [GNP-4233] - Extract RG data for Eurisco (part 2: Légumes, Avoine).
  • [GNP-4553] - Manage Ontologies Language
  • [GNP-4673] - Amaizing T3.2, List of 58 candidate Structural Variants (SVs)
  • [GNP-4748] - Semantic data discovery interface displaying semantic enrichment (Facet)
  • [GNP-5092] - Update Rice Ontology for CIRAD
  • [GNP-5168] - Update BW phenotyping AND association results
  • [GNP-5198] - Insert Whealbi Barley phenotyping data
  • [GNP-5210] - Release 18.1
  • [GNP-5244] - Index AgroLD
  • [GNP-5247] - Feedback fixes to the UI datadiscovery interface
  • [GNP-5250] - Implement data discovery facets
  • [GNP-5252] - Add URI URL parameter to accession card
  • [GNP-5259] - Co-develop Brapi endpoint for Tropgene
  • [GNP-5305] - Hotfix 18.1.1

New Feature

  • [GNP-4519] - Create data discovery portal indexing Jenkins job

Task

  • [GNP-4869] - Isolate & Document the generic ES query engine in gnpis core
  • [GNP-4973] - Install & deploy dataverse in production
  • [GNP-4984] - Manage new xrefs in the unified interface
  • [GNP-5113] - Déploiement automatique de Jbrowse dans la VRE
  • [GNP-5140] - Improve ontology widget search (add new fields) (Mélanie's part)
  • [GNP-5157] - Migrate Nexus to VM
  • [GNP-5236] - List tables with a PK containing a nullable column
  • [GNP-5237] - Implement continuous integration on data discovery indexing tool (Erik's part)
  • [GNP-5241] - Develop RARe ETL tool for transforming remote data in generic JSON file
  • [GNP-5242] - Get URGI infrastructure ready to deploy RARe developments
  • [GNP-5243] - Migrate GnpIS git repositories towards MIA forge (Raphaël's part)
  • [GNP-5256] - Deduplicate site_t
  • [GNP-5257] - Evaluate GraphQL GrandStack
  • [GNP-5268] - Implement continuous integration on data discovery indexing tool (Célia's part)
  • [GNP-5319] - Migrate GnpIS git repositories towards MIA forge (Erik's part)

Improvement

  • [GNP-5291] - Link GenTree sites description file to each GenTree trial

Exploratory Task

  • [GNP-5136] - Evaluate KNetMiner data integration into WheatIS search tool

Version 18.1 (2018/07/03)

Epic

  • [GNP-3647] - UO4: GnpMap V2 including Marker Pivot

Bug

  • [GNP-4864] - Rename column in observation_variable
  • [GNP-5006] - Fix Load-CI-Data 17.3

Story

  • [GNP-3940] - Test: add the average pval on Manhattan plot on regions
  • [GNP-3945] - Display the filtered markers on an Asso Manhattan plot.
  • [GNP-4745] - Improve ontology versionning & workflow
  • [GNP-4749] - Script RepetDB installation
  • [GNP-4867] - Improve unified interface form autocompletion (Dorothée part)
  • [GNP-4899] - Feed taxonIds from NCBI
  • [GNP-4902] - Add trial set link to virtuoso on data result page
  • [GNP-4949] - Data insertions & corrections for RepetDB publication
  • [GNP-4965] - Improve unified interface form autocompletion (Erik part)

Task

  • [GNP-4799] - Upgrade Solr 4 to Solr 6 on Gimli first then on production server (Raphaël part)
  • [GNP-4829] - Update configurations files and code to use the unified interface redirection (Erik part)

Improvement

  • [GNP-4851] - Improve Poplar Jbrowse V2
  • [GNP-4904] - Vitis 12X.2 Jbrowse: add the COST V3 annotation

Version 17.3 (2018/03/12)

Bug

  • [GNP-4520] - Features having a delimiter character in their name can not be found in GnpIS portal (Raphaël part)
  • [GNP-4531] - Synteny reloads on suspect reproducible error
  • [GNP-4649] - Update germplasmDbId in WS for Perpheclim to use DOI instead of the accession identifier
  • [GNP-4751] - Fix Load-CI-Data 17.2
  • [GNP-4786] - Fix display bugs in SyntenyViewer
  • [GNP-4838] - Cure bad encoding on accession data in pgsql
  • [GNP-4846] - Correct missing links between accessions and Pea collections in RG ES indices (AMS collection and RILS/NILS )
  • [GNP-4873] - Tab Association Region of association result view doesn't update on filter change
  • [GNP-4950] - Insert additional info/ publi on Prod
  • [GNP-4966] - Error on GnpSNP marker export
  • [GNP-4999] - Features having a delimiter character in their name can not be found in GnpIS portal (Erik part)
  • [GNP-5008] - Error when print asso without genotyping
  • [GNP-5012] - Ephesis MIAPPE-ISATAB export button doesn't work
  • [GNP-5013] - The ontology widget is unable to load only one big ontology
  • [GNP-5015] - Count error on association data when extracting them for SolR portal

Story

  • [GNP-4192] - Insert BW Asso Data
  • [GNP-4331] - Peamust WP1 phenotyping data: insert them handling the private status of several accessions
  • [GNP-4374] - Set column holding_institution_id of accession_t table to not null
  • [GNP-4573] - Update interface for small time series (+ indexation improv)
  • [GNP-4578] - Better variable details display on Ephesis (4ODS)
  • [GNP-4602] - Trial data as direct file download
  • [GNP-4709] - Insert UOULU accessions + phenotypes data for GenTree
  • [GNP-4710] - Insert ASU accessions + phenotypes data for GenTree
  • [GNP-4718] - Insert ASP accessions + phenotypes data for GenTree
  • [GNP-4722] - Upgrade GnpIS to MIAPPE v1.1
  • [GNP-4738] - Check BW phenotyping data integrity
  • [GNP-4881] - Add links from GBrowse Physical Maps to RefSeqv1.0 JBrowse
  • [GNP-4897] - Insert public accessions from AKER
  • [GNP-4903] - Publish the "Beet Ontology"
  • [GNP-4934] - Release 17.2
  • [GNP-4987] - Implement RDA Wheat guidelines into FAIRsharing

New Feature

  • [GNP-5027] - Add GrainGenes node to SolR production instance

Task

  • [GNP-3438] - Export genotypes (SNP discovery & arrays) in VCF
  • [GNP-4125] - Create GnpIS -> Evoltree data flow
  • [GNP-4526] - Insert Rapsodyn phenotypes.
  • [GNP-4527] - Insert Rapsodyn association data - Sophie.
  • [GNP-4534] - Insert Rapsodyn genotypage.
  • [GNP-4656] - Maize Ontology
  • [GNP-4759] - Insert Quercus phenotypes (from pierroton portal) in GnpIS
  • [GNP-4763] - Create the "Woody Plant Ontology" version 1.2
  • [GNP-4773] - Implementation of the Site card (Thomas part)
  • [GNP-4774] - Implementation of the Institution card
  • [GNP-4829] - Update configurations files and code to use the unified interface redirection (Erik part)
  • [GNP-4910] - Merge woody traits from carto with the Woody Plant Ontology
  • [GNP-4920] - Export validated markers in VCF
  • [GNP-4963] - Implementation of the Site card (Célia part)
  • [GNP-4989] - Wheat physical map 7DSv2
  • [GNP-4994] - Update configurations files and code to use the unified interface redirection (Raphaël part)
  • [GNP-5009] - Set correct PATH for Jenkins jobs which use PostgreSQL
  • [GNP-5105] - Create Forest BRC
  • [GNP-5109] - Create EUFGIS xrefs file and index it

Improvement

  • [GNP-4542] - Add IWGSC source in indexed data
  • [GNP-4683] - Add a link to Solr tool package in the WheatIS search tool
  • [GNP-4970] - Use two distinct constants for the links toward home and portal home in the left menu (Dorothée part)
  • [GNP-4971] - Use two distinct constants for the links toward home and portal home in the left menu (Erik part)
  • [GNP-4978] - Allow GnpSNP to handle "file download only" data submissions (no integration)

Version 17.2 (2017/11/07)

Release Notes - GnpIS - Version 17.2

Epic

  • [GNP-4741] - Unified interface Germplasm V2

Bug

  • [GNP-4570] - Improve Ephesis GWT size
  • [GNP-4801] - Ephesis multiuser : genotype form down > 12 users
  • [GNP-4821] - Link widget version to GnpIS version
  • [GNP-4834] - Asso boxplot display error
  • [GNP-4839] - Bad URL from left menu in unified interface
  • [GNP-4849] - Title of association result pager
  • [GNP-4850] - Association result: Query that runs all the time
  • [GNP-4870] - Handle principal & group in HTTP session & session scoped bean
  • [GNP-4896] - Accent character in BrAPI WS URL are miss interpreted
  • [GNP-4927] - BrAPI study's germplasm incorrect query
  • [GNP-4964] - Bug in RC: Unable to deserialize interface from JSON

Story

  • [GNP-3658] - Improve GnpMap data model (DDL)
  • [GNP-3843] - Integrate Pheno Data as RDF in URGI Virtuoso (RDA)
  • [GNP-4080] - Index SouthGreen Data in IFB node
  • [GNP-4248] - Phenotype data file
  • [GNP-4451] - Export trait carto in CropOntology TV5
  • [GNP-4498] - Insert AMS population RG in production
  • [GNP-4499] - Insert AMS population's SNP discovery batch in production
  • [GNP-4503] - Update Brassica genetic resources (december 2016).
  • [GNP-4554] - Migrate Asso to ontology TDV5
  • [GNP-4592] - IFB portal in production
  • [GNP-4608] - Choose RDFENO Domaine Ontology
  • [GNP-4629] - Integrate Bouchet 2016 Accession & Pheno data
  • [GNP-4633] - Release 17.1
  • [GNP-4655] - Maize dataset in MIAPPE V1,1 Bouchet 2013/2016
  • [GNP-4672] - Amaizing Jbrowse V4 B73
  • [GNP-4685] - Improve germplasm form and accession card
  • [GNP-4691] - Add download button for association experiment
  • [GNP-4692] - Insertion of BW SNP positions
  • [GNP-4721] - Write a procedure to explain dataset management.
  • [GNP-4724] - Amaizing New Maize Genomes : Blast
  • [GNP-4729] - Update marker_set_id in matrix_wheat_axiom
  • [GNP-4744] - Implement OpenMinTeD indexing workflow
  • [GNP-4747] - Semantic data discovery ontology generator
  • [GNP-4760] - OpenMinTed: final mapping between WIPO & WTO + Assignments
  • [GNP-4775] - Migrate germplasm JSON generation from Java to SQL
  • [GNP-4779] - Full BrAPI WS @ GnpIS
  • [GNP-4802] - Indexing GnpIS 4 BrAPI Pheno
  • [GNP-4819] - Delete Ephesis Matrix in Asso result
  • [GNP-4827] - Update genetic ressources talend to generate accessions PUID
  • [GNP-4866] - Feed Taxon_t.externalIds
  • [GNP-4872] - Disable boxplot button when no data available
  • [GNP-4880] - Add the SGCNO to the WIPO
  • [GNP-4898] - Add biosampleId in ObservationUnit Index

Task

  • [GNP-4372] - Add the missing wheat genotyping experiments and SNPS
  • [GNP-4440] - IWGSC RefSeq v1.0 JBrowse
  • [GNP-4525] - Insert Rapsodyn genetic resources.
  • [GNP-4548] - Develop a tool to count the number of WheatIS search requests
  • [GNP-4615] - Divide git ETL in 2 new git projects
  • [GNP-4670] - Create Pea Trait Ontology
  • [GNP-4735] - Correct markers indexation problems
  • [GNP-4761] - Publish the "Woody Plant Ontology" in cropontology and agroportal
  • [GNP-4777] - Implement 2 iRODS rules for metadata submission
  • [GNP-4785] - Insert into production QTL/MetaQTL data related to Synteny Wheat dataset
  • [GNP-4795] - Define a list of required metadata that could be used for data submission into Dataverse and create a form for metadata submission.
  • [GNP-4798] - Inject iRODS metadata into Dataverse.
  • [GNP-4808] - Genotyping result page: add genomic positions for validated markers
  • [GNP-4809] - Use IDROP/iRODS cloud browser to see all the iRODS metadata.
  • [GNP-4836] - Update unified interface implementation to match new version of Germplasm index
  • [GNP-4841] - Generate the DOI for Vitis 12X.2 annotation
  • [GNP-4842] - Generate the DOI for Muscares dataset (fastq)
  • [GNP-4892] - Use better ElasticSearch suggester for unified interface
  • [GNP-4988] - Insert Peamust users in their restricted groups

Improvement

  • [GNP-4569] - Complete the missing legacy data
  • [GNP-4789] - Evaluate and upgrade Solr indexing package to Solr 6.x version with up-to-date configuration files.
  • [GNP-4822] - Identify the variety of accessions.
  • [GNP-4918] - Genotyping result page: remove export buttons in marker tabs when empty table
  • [GNP-4947] - Commit the new genotyping/snpdisco talend job
  • [GNP-4948] - Clean genotyping development ES indices

Exploratory Task

  • [GNP-4793] - Evaluate NDS Labs environment as a data management PaaS (Raphael part)
  • [GNP-4804] - Evaluate NDS Labs environment as a data managment PaaS (Laura part)

Version 17.1 (2017/07/03)

Release Notes - GnpIS - Version 17.1

Sub-task

  • [GNP-3998] - Replace the context of group_id by 0 : Genotype

Technical task

Epic

  • [GNP-2039] - UO1: Unified interface Germplasm V1
  • [GNP-2381] - Continuous data integration
  • [GNP-2383] - Continuous bug fix
  • [GNP-2431] - EO1: Integrate PlantaComp data (phenotypes and genetic ressources) in GnpIS
  • [GNP-2758] - RG05: Export Siregal data to international biodiversity databases.
  • [GNP-2880] - PO2: Export Phenotyping data in IsaTab
  • [GNP-3044] - EO4: Integrate Salicaceae data (from Salicaceae Portal) in GnpIS
  • [GNP-3114] - PO6: Phenomic distributed IS for Phenome and query improvement
  • [GNP-3116] - SO6: Integrate and Query SNP discovery and genotyping data in the NoSQL Document index system
  • [GNP-3263] - WO14: DSpace linked to iRODS
  • [GNP-3362] - TO17: SyntenyViewer displays QTL and TE
  • [GNP-3428] - TO18: Releases management
  • [GNP-3443] - GeO2: Transposable Elements management in GnpIS
  • [GNP-3549] - PO7: Implement long time series
  • [GNP-3550] - PO8: Integrate phenotyping data files (NIRS/microdensitometrie)
  • [GNP-3647] - UO4: GnpMap V2 including Marker Pivot
  • [GNP-3682] - TO21: Distributed search portal
  • [GNP-3788] - RG06 : Update genetic resources data in 2016
  • [GNP-3790] - Peamust Data in GnpIS
  • [GNP-3834] - RG15: Improve Taxon and Varieties Management
  • [GNP-4030] - WO17: Wheat IWGSC reference sequence data management
  • [GNP-4047] - TO28: Geolocation tool
  • [GNP-4076] - TO27: URGI Triple Store (Geno, Pheno, RG)
  • [GNP-4121] - EO5: Create data flow between GnpIS and other EFPA SI
  • [GNP-4247] - TO29: Dataset archive management and user interface
  • [GNP-4264] - TO30: Distributed semantic search portal
  • [GNP-4290] - EO6: Create a "Woody Plant Ontology"
  • [GNP-4434] - PO11: Pheno Ontology Management
  • [GNP-4488] - VRE epigenetic
  • [GNP-4517] - WO18 : BreedWheat and Whealbi data management 2017
  • [GNP-4605] - UO6 Unified interface for data discovery V1
  • [GNP-4626] - Datamanager internship 2017

Bug

  • [GNP-4158] - remplace I205_usa accession by I205_inra
  • [GNP-4394] - Bad mRNA indexation on 3B annotation JBrowse configuration
  • [GNP-4410] - Error on MarkerSet listbox on Asso form for Wheat data
  • [GNP-4479] - Error when display lot number in genotyping result table
  • [GNP-4486] - Form Asso: update request when search by marker
  • [GNP-4533] - Improve SolR performances for GnpIS and WheatIS
  • [GNP-4598] - Improve SolR performances for GnpIS and WheatIS (Erik part)
  • [GNP-4645] - Minor fixes on variable ontology widget
  • [GNP-4648] - Wheat accession don't appear in Ephesis previsualization tab
  • [GNP-4652] - White page on refresh Ephesis result page
  • [GNP-4653] - Fix update of ontology list in WS
  • [GNP-4660] - Change Solr node queried by PlantSyntenyViewer by transPLANT@URGI
  • [GNP-4676] - Correct accession_population.population_id FK and recreate site unicity constraint
  • [GNP-4681] - Validated markers' tab is not displayed when we use an URL token (experimentIds=<expid>)
  • [GNP-4684] - Ephesis panel selection does not work on trial list

Story

  • [GNP-3597] - POC Portal semantic : Solr Skos analyser version
  • [GNP-3868] - Navigation GnpMap
  • [GNP-3939] - Add Accession number to the genotyping export
  • [GNP-4056] - GEstion de GnpIS avec une seule webAPP privée + publique.
  • [GNP-4069] - Perpheclim Web Service finalisation
  • [GNP-4072] - Simple submission interface using iRODS + DSpace
  • [GNP-4099] - Implementation of the accession card
  • [GNP-4200] - RepetDB: add data set list in data source tab
  • [GNP-4209] - Update transplant registry WS and add new ones
  • [GNP-4231] - Update order of level in ephesis result table
  • [GNP-4280] - Index Pheno data with ontologies from portal
  • [GNP-4287] - Configure GnpIS Dspace environment (VM, Git, Tomcat, etc.)
  • [GNP-4426] - Implementation of the accession card (Célia part)
  • [GNP-4431] - Update genome version for each synteny dataset.
  • [GNP-4442] - RepetDB Brassicaceae dataset insertion
  • [GNP-4457] - Assign DOI to BRC accessions.
  • [GNP-4459] - Insert M. graminicola SNP discovery experiments
  • [GNP-4460] - Release 16.3
  • [GNP-4491] - Install RepetDB on VRE VM
  • [GNP-4560] - Improve GnpMap data model (Erik part)
  • [GNP-4584] - Display MetaQTL on SyntenyViewer interface.
  • [GNP-4586] - Add missing fields in the search form
  • [GNP-4591] - Add missing fields in the search form (Cyril part)
  • [GNP-4601] - Release brapi germplasm & pheno WS for Excelerate
  • [GNP-4606] - Perpheclim Web Service finalisation (Guillaume Part)
  • [GNP-4610] - Pheno indexing without downtime
  • [GNP-4620] - Don't display link to phytozome if no data is found
  • [GNP-4624] - Simple submission interface using iRODS + DSpace (Laura part)
  • [GNP-4651] - Map SCNO ontology on WTO ontology
  • [GNP-4657] - Add accessions dans biosample
  • [GNP-4689] - Finalize Exelerate BRAPI search POC
  • [GNP-4698] - Tomcat on gimli run with jdk 1.6
  • [GNP-4723] - Delete obsolete BW association experiments
  • [GNP-4728] - Deduplicate BW panel
  • [GNP-4755] - Prepare unified interface v1 for production

New Feature

  • [GNP-4207] - Dynamic XRef of unified interface
  • [GNP-4483] - WIPO update in GnpIS
  • [GNP-4518] - Update queries from the new portal
  • [GNP-4607] - Dynamic XRef of unified interface (Cyril Part, WS)
  • [GNP-4659] - Insert Markers & QTL from Quercus_composite_2015 map (GenOak)

Task

  • [GNP-4292] - Create the "Woody Plant Ontology" version 1
  • [GNP-4362] - Add legacy SSR markers and genotypes in the new GnpSNP interface (ES)
  • [GNP-4363] - Correct genomic assignments of CnvMaize project (chromosome_ids and genome_ids)
  • [GNP-4378] - Add a License form in WheatIS DSpace
  • [GNP-4492] - Insert Quercus and Pinus genetic resources (from pierroton portals) in GnpIS
  • [GNP-4506] - Insert Data for SxG, T. Flutre ODS dataIntegration Doligez et al
  • [GNP-4558] - Update 2 Allium accessions.
  • [GNP-4564] - Update forest tree accession's holding institutions and generate DOI
  • [GNP-4566] - Update PlantaExp Pinus pinea origin sites
  • [GNP-4567] - Improve Variables export in Adonis and Json BRAPI format
  • [GNP-4571] - Update Genetic resources web service for ARCAD-Florilège.
  • [GNP-4594] - Generate DOI for Wheat CBR
  • [GNP-4646] - Map SmallGrainCereal Ontology on Wheat Trait Ontology
  • [GNP-4693] - Create a DOI for Vitis 12X.2 genetic maps

Improvement

  • [GNP-4496] - Replace the TPS gene family track with the corrected version
  • [GNP-4589] - Insert TE for SyntenyViewer in production
  • [GNP-4618] - Provide the tokens in GnpSNP to build Xrefs from JBrowses/Gbrowses (to GnpSNP)
  • [GNP-4663] - Update Avignon CRB email.
  • [GNP-4743] - Improve the tokens in GnpSNP to build Xrefs from JBrowses/Gbrowses handling genome names

Exploratory Task

  • [GNP-4427] - Evaluate multi indices aggregations and performances on markers indexation
  • [GNP-4521] - Evaluate multi indices aggregations and performances on markers indexation (Erik part)

Version 16.3 (2017/03/06)

Release Notes - GnpIS - Version 16.3

Epic

  • [GNP-2772] - PO5: Ontologies, Deliverables for Phenome 2014

Bug

  • [GNP-4108] - GnpIS GWT portal launches too many HTTP requests when facets have been used
  • [GNP-4215] - Genotyping results: the "Genotyping Experiments/Result count/View" link duplicates tables when 1 experiment matches the query
  • [GNP-4313] - Change link to public banks
  • [GNP-4383] - Some sites have a bad geographical location
  • [GNP-4384] - Trouble with URL generated for bofut4edit conf after extraction
  • [GNP-4416] - Feed column lots_count in dn_association table
  • [GNP-4418] - Link on association result table to Ephesis doesn't work
  • [GNP-4419] - Duplicate treatments on the filter panel of asso result
  • [GNP-4424] - Indexed iRODS files are not visible in portal
  • [GNP-4433] - No semi-private data for Genotype form in Ephesis
  • [GNP-4453] - Ephesis : Too many trials displayed in results page when selecting a variable
  • [GNP-4477] - Wrong links from Maize GBrowse toward GNPIS (gpi instead of urgi)
  • [GNP-4480] - HTTPD configuration jenkins job is broken
  • [GNP-4481] - Genotyping form: bugs on release 16.2 with contigs/scaffolds genomes
  • [GNP-4485] - Safari compatibilité Ephesis
  • [GNP-4494] - Trial count not updating on campaign selection
  • [GNP-4508] - Update SMTP for Siregal, JIRA, Jenkins.

Story

  • [GNP-3119] - Migrate polymorphic loci in ES: data
  • [GNP-3303] - Integrate Recital/Apache resequencing data as a Breedwheat SNP track into Gbrowse survey (Jbrowse ?)
  • [GNP-3721] - Migration of GnpSNP Talend job to use ES
  • [GNP-3858] - Display TE density on SyntenyViewer interface
  • [GNP-4017] - Export Variables in Adonis Format
  • [GNP-4034] - Update 4AL physical map GBrowse
  • [GNP-4060] - WebServices for Maize accesions on private server (War ws @ private)
  • [GNP-4079] - RDF model for Pheno
  • [GNP-4199] - Ontology widget on Breeding API WebService
  • [GNP-4273] - Ontology update workflow
  • [GNP-4284] - GnpIS - PHIS connection WS
  • [GNP-4296] - V1 : Genomic data insertion in iRods
  • [GNP-4318] - Release 16.2
  • [GNP-4332] - Pisum sativum JBrowse
  • [GNP-4347] - Correct STS_CHS and TPS tracks in Vitis JBrowse
  • [GNP-4360] - Update Wheat Network with technical data 2014
  • [GNP-4399] - Update Observation Variable BrAPI WebService
  • [GNP-4402] - Manage observation variables annotation
  • [GNP-4403] - Deduplicate forest tree Accessions
  • [GNP-4417] - Script migrating variable ontologies to CropOntology
  • [GNP-4422] - Update Ephesis observation variable ES indexing
  • [GNP-4429] - Update Observation Variable BrAPI WebService (Erik part)
  • [GNP-4430] - Create a Jenkins job for the unified interface CI
  • [GNP-4432] - Design carto interface prototype V2: Mockflow
  • [GNP-4435] - Clean Taxon - Dorothée
  • [GNP-4437] - Clean Taxon - Thomas
  • [GNP-4443] - Rename AMAIZING to Amaizing
  • [GNP-4445] - Prepare production for first release
  • [GNP-4446] - Prepare production for first release (Raphaël part)
  • [GNP-4454] - Insert AMS population RG for the Peamust 2016 annual meeting
  • [GNP-4455] - Insert AMS population's SNP discovery batch for the Peamust 2016 annual meeting

New Feature

  • [GNP-3569] - Insert PlantaExp Pinus pinea data (phenotypes + rg)
  • [GNP-3860] - Display Genome Zipper Data in WSS GBrowse (Michael Abrouk)
  • [GNP-4191] - WIPO in Trait Template on GitLab

Task

  • [GNP-4368] - Add links from Trait card (mapping data) to Phenotyping results (ephesis)
  • [GNP-4398] - Add a new track on the Amazing JBrowse
  • [GNP-4439] - IWGSC-WGA v1.0 JBrowse with annotation data
  • [GNP-4452] - Add a search by gene for Wheat_version_2
  • [GNP-4487] - Vitis Data Thimothée Flutre
  • [GNP-4497] - Map WIPO on Wheat Trait Ontology
  • [GNP-4516] - IWGSC-WGA v0.4 JBrowse with annotation data

Improvement

  • [GNP-4545] - Genotyping form: add a start/end label in genome range filter (marker tab)

Exploratory Task

  • [GNP-3196] - Index iRODS metadata in SolR transPLANT data model

Version 16.2 (2016/11/11)

Release Notes - GnpIS - Version 16.2

Technical task

  • [GNP-4421] - Deploy swagger in production

Bug

  • [GNP-4179] - Improve css to fit with graphical charter
  • [GNP-4334] - Upgrade CI tomcat to production version
  • [GNP-4337] - Binary tools does not work anymore
  • [GNP-4338] - Load tree paths does not work anymore
  • [GNP-4340] - WS /brapi/v1/variables does not work anymore
  • [GNP-4342] - Accession card: the map legend is displayed even if there are no associated sites
  • [GNP-4349] - Indexing of phenotyping data is broken
  • [GNP-4350] - Fix WS deployment on beta server
  • [GNP-4382] - Fix Synteny unit tests.

Story

  • [GNP-2448] - Update Mapping Talend to meet the standards established for the submit format
  • [GNP-3303] - Integrate Recital/Apache resequencing data as a Breedwheat SNP track into Gbrowse survey (Jbrowse ?)
  • [GNP-3583] - Phenome ontology publicly available
  • [GNP-3671] - Implement configurable species restriction mechanism in WheatIS GWT portal
  • [GNP-3829] - Update RG to AEGIS collection.
  • [GNP-3918] - Insert wheat RNA-seq data and link it to the browser
  • [GNP-4027] - New version of GnpIS_counting
  • [GNP-4177] - SolR Data from Jbrowse in Production
  • [GNP-4336] - Add observation variable term identifier to /phenotype/optionids output

New Feature

  • [GNP-4178] - Display Genome Zipper Data in survey sequence GBrowse for 3DS (Jan Bartos)

Task

  • [GNP-3662] - Interop between Monocot and Dicot synteny datasets (Angiosperm version)
  • [GNP-3761] - URL GnpIS vers PHIS
  • [GNP-3953] - Improve the genome range widget
  • [GNP-4390] - Veille sur nouvelle version de JBrowse

Improvement

  • [GNP-4391] - Remove code duplication in web services tests
  • [GNP-4407] - Upgrade Jenkins to version 2.X

Version 16.1 (2016/06/27)

Technical task

  • [GNP-3786] - geno
  • [GNP-3871] - Release GnpIS 15.3 modules for release candidate
  • [GNP-3872] - Release GnpIS 15.3 portal for release candidate
  • [GNP-3873] - Deployment of GnpIS 15.3 on release candidate server
  • [GNP-3874] - Release candidate: functional validation for GnpIS 15.3
  • [GNP-3875] - Deploy all submission formats
  • [GNP-3876] - Release GnpIS 15.3 modules for production
  • [GNP-3877] - Release GnpIS 15.3 portal for production
  • [GNP-3878] - Deployment of GnpIS 15.3 on production servers
  • [GNP-3879] - Dump gpprod and restore all GnpIS development database schemas
  • [GNP-3880] - Post production: functional validation for GnpIS 15.3
  • [GNP-3881] - Add news on URGI and Wheat-URGI home pages.

Epic

  • [GNP-1947] - TO13: Continuous integration chain improvement
  • [GNP-2039] - UO1: Unified interface, first release
  • [GNP-2166] - SO1: Create genotyping interface
  • [GNP-2168] - EO2: Implement Plantacomp needs in GnpIS
  • [GNP-2373] - TO13: GnpIS technical/hidden improvements 2014
  • [GNP-2375] - AO1: Association for GnpAsso
  • [GNP-2379] - WO5: Wheat 3B reference sequence and survey sequence data management
  • [GNP-2381] - Continuous data integration
  • [GNP-2383] - Continuous bug fix
  • [GNP-2384] - TO1: Consolidate germplasm pivot
  • [GNP-2496] - AO2: Association data for GnpAsso
  • [GNP-2572] - WO6: Wheat physical maps data management
  • [GNP-2772] - PO5: Ontologies, Deliverables for Phenome 2014
  • [GNP-3044] - EO4: Integrate Salicaceae data in GnpIS
  • [GNP-3114] - PO6: Phenomic distributed IS for Phenome and query improvement
  • [GNP-3117] - VO2: Integrate all genomic data mapped on Vitis 12X in a genome browser
  • [GNP-3321] - ExO1: RNASeq transcriptomic experiments management
  • [GNP-3362] - TO17: SyntenyViewer displays QTL, TE and RNA-seq data
  • [GNP-3443] - GeO2: Transposable Elements management in GnpIS
  • [GNP-4047] - TO28: Geolocation tool
  • [GNP-4057] - TO26: Distributed Authentification with renater
  • [GNP-4121] - EO5: Create data flow between GnpIS and other EFPA SI

Bug

  • [GNP-3981] - Improve & Merge Talend RG.
  • [GNP-4105] - Fix Perpheclim web services which are in error state
  • [GNP-4107] - Set same coloration to related lines and theirs reference genes.
  • [GNP-4172] - X and Y columns are not displayed in ephesis result page
  • [GNP-4176] - Bad link on Run card
  • [GNP-4182] - Ephesis date display offset by one day
  • [GNP-4184] - Improve SolR packaging according to last configuration updates
  • [GNP-4193] - Quick search link toward Synteny genes is broken
  • [GNP-4198] - Error in Ensembl Plant urls in SolR for rice genes.
  • [GNP-4203] - Update issue on geolocation map in Ephesis result page
  • [GNP-4206] - Phenotyping data accessions not indexed
  • [GNP-4238] - Delete duplicate ancestral homeologues genes in ancestral gene popup.

Story

  • [GNP-2043] - Data Model + ETL RG/Json/Elasticsearch
  • [GNP-2809] - Insert Wheat association data
  • [GNP-2891] - Ensure perenity of our URL's through an URI dereferencement system
  • [GNP-3551] - Bird eye view documentation of data submission process for biologists
  • [GNP-3592] - Handle Phenotype datasets (avoid pheno duplication)
  • [GNP-3601] - Create minimal dev database: Update Copy tool
  • [GNP-3617] - Migration to VM: GBrowse
  • [GNP-3621] - Gather maize QTL data of SyntenyViewer's genes
  • [GNP-3625] - Technological watch on data confidentiality for elasticsearch
  • [GNP-3630] - Improve Synteny gene popup, gathering data from Phytozome and transPLANT SolR
  • [GNP-3665] - Whealbi panel: genetic resources (hordeum data)
  • [GNP-3673] - Create an iRODS instance to share big files
  • [GNP-3755] - DOI for Pheno Network / Study card from trial sets
  • [GNP-3759] - Highlight genes linked to a selected QTL
  • [GNP-3776] - Update Talend to replace the context of group_id by 0 (static data)
  • [GNP-3821] - integrate missing Collections and panels
  • [GNP-3833] - Clean taxon_t table
  • [GNP-3836] - Integration of the remaining 9 matrix of Axiom
  • [GNP-3839] - Tech Watch BioSolR
  • [GNP-3845] - Insert WP2 Snp discovery in GnpIS
  • [GNP-3855] - BRAPI Compliant version of Ephesis: Full data in elasticSearch
  • [GNP-3870] - Release 15.3
  • [GNP-3901] - Improve RG submission format.
  • [GNP-3902] - Update BreedWheat Trials (2012)
  • [GNP-3923] - Ephesis ES indexing full process in standalone ant task
  • [GNP-3931] - Update nomenclature on BW pheno data
  • [GNP-3938] - SNP discovery sets: add short description
  • [GNP-3949] - Add brothers and sisters in genealogy.
  • [GNP-3960] - Add links from GBrowses toward CNRGV resources
  • [GNP-3989] - Handle dataset version in SyntenyViewer
  • [GNP-3992] - Set up GBrowse for improved survey sequence (David Konkin)
  • [GNP-4002] - Update Wheat RG - january 2016.
  • [GNP-4018] - Trial card: Add back to form when possible
  • [GNP-4031] - SolR Data from Jbrowse/Intermine in Production
  • [GNP-4033] - Landing Page DOI in GnpIS
  • [GNP-4035] - Insert BreedWheat Septoriose-Fusariose Phenotyping Data
  • [GNP-4048] - Add simple map on accession and site cards
  • [GNP-4050] - Add simple map on trial card
  • [GNP-4058] - LDAP authentication: Web services validation
  • [GNP-4062] - Insert a Wheat Genetic Map into GnpIS to check data consistency
  • [GNP-4077] - Include Variables and Genetic ressources in Experiments (Pheno/Asso)
  • [GNP-4084] - Add geographical map on phenotyping results page
  • [GNP-4086] - Add link towards phenotyping trials on geographical map popups
  • [GNP-4090] - Edit BreedWheat ontology file to load it into Ontology widget
  • [GNP-4094] - Simple submission interface using iRods (Raphael part)
  • [GNP-4095] - Share IFB/WheatIS Portal developments (Florian part)
  • [GNP-4096] - SolR Data from Jbrowse/Intermine in Production (Raphaël part)
  • [GNP-4109] - Display a human readable error message when genotyping application connection to ES Server fails
  • [GNP-4110] - Add databases and nodes lists in WheatIS search
  • [GNP-4115] - Update BW pheno variables
  • [GNP-4128] - Rework on autocompletion and suggestion displayed on GWT portal
  • [GNP-4131] - Setup code infrastructure for unified interface (server+GWT client)
  • [GNP-4134] - Add new GBrowse Physical Map : 3AL
  • [GNP-4141] - Insert a Wheat Genetic Map into GnpIS to check data consistency (Dorothee part)
  • [GNP-4142] - Add taxonomic fields to /accession/phenotyped WS
  • [GNP-4146] - Rewrite /phenotype/optionids WS output
  • [GNP-4148] - Update /phenotype/lastchange output
  • [GNP-4155] - Read trait ontologies from online JSON files and implement Brapi /variables/* WS
  • [GNP-4156] - Add new GBrowse Physical Map : 3DSv2
  • [GNP-4157] - Create generic Jenkins job to index phenotyping data
  • [GNP-4162] - Insert Avena genetic resources.
  • [GNP-4163] - Insert Barley genetic resources.
  • [GNP-4164] - Insert Triticale genetic resources.
  • [GNP-4165] - Update Wheat genetic resources from Clermont.
  • [GNP-4169] - Rename traitId parameter and output field to observationVariableId in /phenotype/optionids WS
  • [GNP-4170] - Change /site/trialNumber/{trialNumber} to /site/trial/number/{trialNumber}
  • [GNP-4173] - Add right click on referent gene to show homologs genes.
  • [GNP-4174] - Use ant filter to set tab names in navigators
  • [GNP-4175] - Use maven property to set mine names on GnpIS portal
  • [GNP-4183] - Implement Brapi phenotypes dataset specifications
  • [GNP-4185] - Update description of BreedWheat phenotyping variables
  • [GNP-4190] - Create observation unit Brapi data type in phenotyping index
  • [GNP-4195] - Externalize GnpIS portal home examples in dedicated maven profile
  • [GNP-4197] - Add new GBrowse Physical Map : 3ASv2
  • [GNP-4212] - Manage indexing of phenotyping data by trial
  • [GNP-4274] - Add link towards web services documentation page in GnpIS portal menu

Task

  • [GNP-2985] - Integrate Poplar TE on database poplarV2
  • [GNP-3112] - Add post-filters on genotyping results and manage index updates
  • [GNP-3767] - LDAP authentication: Identify required Apache/Java libraries/modules
  • [GNP-3768] - LDAP authentication: GnpIS Validation
  • [GNP-3994] - Insert new markers from VVBX-A and MRBX
  • [GNP-4112] - Insertion of Wheat V2 synteny dataset in production
  • [GNP-4129] - Export to JSON snp markers from GnpSNP
  • [GNP-4181] - Make public beet Accession data
  • [GNP-4194] - Create AKER collection
  • [GNP-4208] - Create merge requests on GnpIS and database for feature-GNP-4183

Improvement

  • [GNP-3863] - Upgrade genotyping queries to be Elasticsearch 2.3 compliant
  • [GNP-4085] - Update locus_name in *_assignment_t tables
  • [GNP-4087] - Insert missing proximal and distal locus
  • [GNP-4116] - Migrate phenotyping Elasticsearch queries to ElasticSearch API QueryBuilders
  • [GNP-4130] - Upgrade phenotyping queries to be Elasticsearch 2.3 compliant

Exploratory Task

  • [GNP-2932] - Apache login/out, single URL for public & private
  • [GNP-3153] - Veille techno outils recherche distribuée + sémantique
  • [GNP-3853] - Unified interface: architecture

Version 15.3 (2016/02/29)

Sub-task

  • [GNP-3999] - Replace the context of group_id by 0 : Siregal
  • [GNP-4000] - Replace the context of group_id by 0 : Project

Technical task

  • [GNP-3599] - Service Layer And model Updates
  • [GNP-3882] - Optionally: make a deposit to APP (french software protecting agency)
  • [GNP-3885] - Insert in production
  • [GNP-3909] - Test Cases
  • [GNP-3916] - Update grapevine accessions.

Bug

  • [GNP-837] - Handle timeout for long queries in search by loci.
  • [GNP-3604] - Bug WS correction Ephesis
  • [GNP-3676] - Indexed traits are not linked to their species
  • [GNP-3717] - Add mapping_method as mandatory field in QTL submission format
  • [GNP-3817] - Bad marker_name in range_assignment_t and interval_assignment table
  • [GNP-3848] - SyntenyViewer seems broken when using Safari web browser
  • [GNP-3862] - Marker sequences are not displayed in GnpMap
  • [GNP-3886] - GnpMap Talend does not insert assignment abs_distance correctly
  • [GNP-3888] - Species group filter does not work in production (Siregal)
  • [GNP-4015] - Common JSP does not work under tomcat 7.0.60X
  • [GNP-4020] - The selgen icon is not displayed on its home page
  • [GNP-4139] - Bad link to phenotyping results on taxon result page

Epic

  • [GNP-2380] - TO14: Integrate GnpIS as a TransplantDb element
  • [GNP-2880] - PO2: Export Phenotyping data in IsaTab
  • [GNP-3260] - WO11: BreedWheat and Whealbi data management 2015
  • [GNP-3368] - TO11: Oracle to PostgreSQL migration
  • [GNP-3429] - TO19: Feed indices (ES/SolR) from heterogenous data

Improvement

  • [GNP-2539] - Display theme name around trait name in QTL query form
  • [GNP-2548] - Display a generic "No Result" message when no result is available else hide export button
  • [GNP-2968] - The 'Home' link in the left menu must send user to the portal
  • [GNP-3012] - Improve sample display in experiment card
  • [GNP-3634] - Improve GnpArray (layout, data, form).
  • [GNP-4022] - Upgrade Jenkins with the lastest version

New Feature

  • [GNP-3784] - Link Wheat3BMine to Ephesis
  • [GNP-3887] - Reinsert salicaceae genetic mapping for Monclus2012

Story

  • [GNP-2357] - Deduplicate MARKER_T data
  • [GNP-2853] - Temporal series in GnpIS.Ephesis
  • [GNP-3160] - Update Grapevine genetic resource from T. Lacombe (GBIF).
  • [GNP-3291] - Add publication form on all modules
  • [GNP-3314] - Add a genomic chromosome location filter tab (asso/geno)
  • [GNP-3335] - Externalize GBrowse passwords in a dbconnect file
  • [GNP-3344] - Manage ITK in Ephesis
  • [GNP-3450] - GBrowse wheat physical maps add : (Bayer) 2B, 2D, 4B, 5BL, 5DL, (Elena Salina) : 5BS, (Hikmet) :5DS, 146v2 (Zeev)
  • [GNP-3462] - Add a page in the sequence repository with all genetic maps and download of marker sequences and positions
  • [GNP-3463] - Technology watch on raw data from EnsemblPlant
  • [GNP-3610] - Integration of 1 matrix of genotyping axiom data V2
  • [GNP-3624] - Migration to VM: GnpIS production instance
  • [GNP-3645] - Heavy memory usage in Talend for Association Data
  • [GNP-3650] - Migration to VM: GnpIS development instance
  • [GNP-3661] - BreedWheat pheno 2013
  • [GNP-3681] - Ontology : template & widget CropOntology For Ontology Portal
  • [GNP-3688] - Release 15.2
  • [GNP-3700] - PhenomeDistributed IS prototype
  • [GNP-3703] - Insert phenotypes from BioMareau project
  • [GNP-3711] - Veille Biomart v0.9
  • [GNP-3720] - Migration of GnpSNP data in an ES index
  • [GNP-3749] - Solr Data in production for Public Transplant and URGI portal
  • [GNP-3772] - Add a link to the publication in the Map card
  • [GNP-3780] - Migrate script deduplicate_table_data.pl
  • [GNP-3791] - Insert WP1 data in GnpIS
  • [GNP-3798] - Make DSpace storing items into iRODS using the same directory tree than in DSpace
  • [GNP-3800] - Insert Wheat data into iRODS
  • [GNP-3811] - Consistent Trial Levels Handling
  • [GNP-3813] - Add minor changes in Plant Synteny Viewer
  • [GNP-3814] - Full Elastic Search version of GnpIS.Ephesis
  • [GNP-3818] - Display Wheat QTL in 3B JBrowse
  • [GNP-3819] - Set cross ref from marker card to Browsers correctly
  • [GNP-3824] - RNAseq Results: improve performances
  • [GNP-3825] - RNAseq Form: input gene list by paste or file
  • [GNP-3832] - Integrate Vitis Phenology Data (Vassal, Perpheclim)
  • [GNP-3837] - Minor refactor from Ephesis dojo feedbacks
  • [GNP-3838] - Finish and production for data discovery portal
  • [GNP-3846] - RepetDB insertion of new data set
  • [GNP-3849] - Association - benchmark heavy datasets
  • [GNP-3856] - Ontology : widget CropOntology in GnpIS
  • [GNP-3859] - Write tomcat instance creation tool
  • [GNP-3861] - Prepare the matrix indexes to be ready when the 15.2 release will be put in production
  • [GNP-3913] - Set public the Populus nigra sanger batches
  • [GNP-3928] - Migration to VM: SolR

Task

  • [GNP-1701] - Marker card: display junction type for ISBP
  • [GNP-2524] - Submit the wheat survey sequence into GnpIS (GnpSeqNGS)
  • [GNP-2607] - Insert ISBP capture sequence
  • [GNP-2632] - Insert data from sugar beet accessions
  • [GNP-3010] - Create Jenkins job for Continuous Integration over GPRC during RC period
  • [GNP-3080] - Update annotation tomato Jbrowse (ITAG2.4 corresponds to build 2.5)
  • [GNP-3663] - Developments to Integrate Wheat V2 synteny dataset
  • [GNP-3775] - Add list box containing ancestral chromosomes for a selected gene
  • [GNP-3831] - Add PlantMaterial Talend call in Ephesis Talend
  • [GNP-3835] - Improve Dspace forms and behaviour related to iRods
  • [GNP-3867] - Improve Genotyping Talend
  • [GNP-3990] - Insert QTL of robur composite map
  • [GNP-4008] - Update unique constraint in Talend

Version 15.2 (2015/10/12)

Release Notes - GnpIS - Version 15.2

Technical task

Bug

  • [GNP-3536] - GWT applications may be desynchronized between cached client and server upon deployments
  • [GNP-3635] - The AssertJ API iterates on all pages of Iterator<T> instances
  • [GNP-3676] - Indexed traits are not linked to their species

Epic

  • [GNP-2166] - SO1: Create genotyping interface
  • [GNP-2168] - EO2: Integrate Plantacomp data in GnpIS
  • [GNP-2170] - TO6: Merge GnpSeq with GnpSeqNGS
  • [GNP-2372] - PO1: Phenotyping Interface V3
  • [GNP-2375] - AO1: Association for GnpAsso
  • [GNP-2379] - WO5: Wheat 3B reference sequence and survey sequence data management
  • [GNP-2380] - TO14: Integrate GnpIS as a TransplantDb element
  • [GNP-2381] - Continuous data integration
  • [GNP-2383] - Continuous bug fix
  • [GNP-2384] - TO1: Consolidate germplasm pivot
  • [GNP-2496] - AO2: Association data for GnpAsso
  • [GNP-2572] - WO6: Wheat physical maps data management
  • [GNP-2772] - PO5: Ontologies, Deliverables for Phenome 2014
  • [GNP-2789] - SGO1: SelGen Interface
  • [GNP-2880] - PO2: Export Phenotyping data in IsaTab
  • [GNP-3044] - EO4: Integrate Salicaceae data in GnpIS
  • [GNP-3117] - VO2: Integrate all genomic data mapped on Vitis 12X in a genome browser
  • [GNP-3260] - WO11: BreedWheat and Whealbi data management 2015
  • [GNP-3321] - ExO1: RNASeq transcriptomic experiments management
  • [GNP-3362] - TO17: SyntenyViewer displays QTL, TE and RNA-seq data
  • [GNP-3368] - TO11: Oracle to PostgreSQL migration
  • [GNP-3429] - TO19: Feed indices (ES/SolR) from heterogenous data
  • [GNP-3443] - GeO2: Transposable Elements management in GnpIS

Exploratory Task

  • [GNP-3196] - Check how iRODs can be indexed with SolR transPLANT data model

Improvement

  • [GNP-3012] - Improve sample display in experiment card
  • [GNP-3041] - Add Synteny app in GnpIS flower
  • [GNP-3460] - Add export feature to WheatIS portal

New Feature

  • [GNP-2426] - Implement site ecology informations
  • [GNP-2599] - Insert PlantaExp Pinus pinea and Abies alba data (phenotypes + rg).
  • [GNP-3719] - add graphs on result rna-seq page

Story

  • [GNP-2301] - Create static data extraction tool
  • [GNP-2353] - Deduplicate ASSIGNMENT_T data
  • [GNP-2357] - Deduplicate MARKER_T data
  • [GNP-2358] - Deduplicate CONTACT_T data
  • [GNP-2389] - Deduplicate INSTITUTION_T data.
  • [GNP-2527] - Remove GnpSeq specific tables from GnpIS database.
  • [GNP-2587] - Index InterMine data in GnpIS SolR
  • [GNP-2689] - Integrate Wheat Historic data 1999 -> 2014
  • [GNP-3097] - GWT version for URGI, WheatIS and IFB portal
  • [GNP-3118] - Create the Vitis JBrowse
  • [GNP-3119] - Migrate polymorphic loci in ES: data
  • [GNP-3148] - Insert Pea selgen data set publication
  • [GNP-3194] - Insert Maize Dent private genotyping data
  • [GNP-3265] - SNP discovery ISBP file
  • [GNP-3267] - Migrate Pheno on ES and Select multiple phenotyping campaign
  • [GNP-3268] - Insert salicaceae phenotypes for population POP2
  • [GNP-3269] - Insert salicaceae genotypes for Monclus2012
  • [GNP-3270] - Insert salicaceae genetic mapping for Monclus2012
  • [GNP-3271] - Insert salicaceae polymorphism
  • [GNP-3312] - Implement interoperability for data export between Asso and Pheno & Geno
  • [GNP-3314] - Add a genomic/genetic chromosome location filter tab
  • [GNP-3412] - Migrate Talend jobs to use PostgreSQL: SNP
  • [GNP-3414] - Migrate Talend jobs to use PostgreSQL: VCF
  • [GNP-3421] - Migrate polymorphism perl scripts to postgresql
  • [GNP-3448] - RepetDB annotations sharing server (TrackHubs)
  • [GNP-3454] - Insert grapevine phenotypes: phenology for Perpheclim
  • [GNP-3456] - Phenotyping API WS @ GnpIS: draft
  • [GNP-3465] - Improve genotyping index management in ES
  • [GNP-3468] - Release 15.1
  • [GNP-3552] - Clean database git repository
  • [GNP-3559] - Manage populations in GnpIS
  • [GNP-3582] - GBrowse wheat physical maps : add 146D (LTC)
  • [GNP-3589] - Finish Insert grapevine phenotypes: phenology for Perpheclim
  • [GNP-3596] - Add new addresses in Siregal static data
  • [GNP-3597] - Use SolR/Elastic Search analyzer with Ontologies
  • [GNP-3610] - Integration of genotyping axiom data V2
  • [GNP-3613] - Insertion Data RG, Pheno & Geno Amaizing
  • [GNP-3615] - Add all URGI web service to transPLANT registry
  • [GNP-3617] - Migration to VM: GBrowse
  • [GNP-3621] - Gather QTL data of SyntenyViewer's genes
  • [GNP-3623] - Migration to VM: JIRA
  • [GNP-3624] - Migration to VM: GnpIS production instance
  • [GNP-3631] - RepetDB corrections
  • [GNP-3637] - Remove deprecated MapComparator source code
  • [GNP-3641] - Use scan&scroll for genotyping result export
  • [GNP-3642] - Improve genotyping result page and exports
  • [GNP-3643] - RNAseq Form/result table: Gene criteria tab End
  • [GNP-3649] - RepetDB in production
  • [GNP-3650] - Migration to VM: GnpIS development instance
  • [GNP-3651] - Data Integration and Validation in SolR
  • [GNP-3661] - BreedWheat pheno 2013
  • [GNP-3671] - Implement configurable species restriction mechanism in WheatIS GWT portal
  • [GNP-3675] - Improve association regions
  • [GNP-3685] - Add automatic tests for Talend insertion.
  • [GNP-3703] - Insert phenotypes from BioMareau project
  • [GNP-3718] - Display genome and annotation versions on synteny viewer

Task

  • [GNP-2062] - Implementation of testing Talend data insertion.
  • [GNP-2440] - Refactor SyntenyViewer using MVP pattern
  • [GNP-2485] - Convert GBrowse 3B annotation into JBrowse 3B annotation
  • [GNP-2788] - Add sample type and library name search criterias in sequence form.
  • [GNP-3080] - Update annotation tomato Jbrowse (ITAG2.4 corresponds to build 2.5)
  • [GNP-3096] - Customize DSpace and link it to iRODS
  • [GNP-3197] - Update vitis 18k markers by adding synonyms
  • [GNP-3198] - Add GBrowse physical maps and survey sequence annotation to GnpIS quicksearch
  • [GNP-3539] - Integrate new version of Cereal synteny relationships
  • [GNP-3616] - Error detection in Synteny data coherence for file Submit_Synteny_14.1_Cereals_V2.xlsx.
  • [GNP-3660] - Update talend job submit_synteny with new database schema.
  • [GNP-3663] - Integrate Wheat V2 synteny dataset
  • [GNP-3669] - Integrate genome version/annotation for existing Synteny data

Version 15.1.1 (2015/09/03)

Bug

  • [GNP-3701] - Phenotyping Campaign Filter badly applied
  • [GNP-3704] - Pheno campain bad Display
  • [GNP-3710] - Climatik data download freezed
  • [GNP-3713] - ISATAB export not working on some trials
  • [GNP-3727] - Ephesis : bad handling of phenocampaign on result page

Version 15.1 (2015/07/06)

Sub-task

  • [GNP-3512] - Add news in google doc transPLANT

Technical task

Bug

  • [GNP-3457] - Asso to Jbrowse : auto zoom and display tracks
  • [GNP-3560] - Accession order form: update zip code validation rules
  • [GNP-3571] - Encoding Problem with CSV download
  • [GNP-3638] - Siregal and portal link to ephesis broken
  • [GNP-3639] - Remove all links from portal to deprecated GnpSeq application
  • [GNP-3640] - Interop with Ephesis trials is broken

Improvement

  • [GNP-3040] - Complete Wheat Synteny dataset's SNP data in order to query it via GnpSNP form
  • [GNP-3309] - Add accession name column on Genotype > Build your own varietal list

New Feature

  • [GNP-2427] - Implement trial installation and composition informations
  • [GNP-2512] - Right click on a gene should display a popup with descriptive information and link to QuickSearch
  • [GNP-3045] - Insert salicaceae factorial genetic resources (NxN, TxT, DxT)
  • [GNP-3546] - Insert salicaceae population genetic resources (pop1, pop3a, pop3b)

Story

  • [GNP-1648] - Migrate GnpIS database administration tools to use PostgreSQL
  • [GNP-2214] - Create association boxPlot
  • [GNP-2502] - Create Synteny configuration for indexing in portal and allow linking to given feature
  • [GNP-2799] - Migrate all datamarts to use PostgreSQL instance
  • [GNP-2807] - Rename class fr.inra.transcriptome.model.Array to fr.inra.transcriptome.model.TransArray
  • [GNP-3086] - Integration of genotyping axiom data part 1 (dev + prod)
  • [GNP-3167] - RNAseq Form/result table: Gene criteria tab
  • [GNP-3208] - Use common genotype widget in Ephesis
  • [GNP-3276] - Integration of genotyping axiom data (prod)
  • [GNP-3307] - Add possibility to paste accessions (names)
  • [GNP-3308] - Update Breedwheat phenotyping campaign names
  • [GNP-3310] - Rename Breedwheat trial names according to nomenclature defined at annual meeting
  • [GNP-3313] - Allow to search regions having high association between adjacent markers
  • [GNP-3343] - Manage trials without data
  • [GNP-3361] - Insert Whealbi barley pheno data from Luigi: Beta
  • [GNP-3365] - GBrowse wheat physical maps : add 1D, 4D, 6D, 3A, 7A, 5A
  • [GNP-3373] - Initial data migration
  • [GNP-3374] - Migrate GnpIS database copy tools
  • [GNP-3375] - Migrate GnpIS public data flag tools
  • [GNP-3378] - Migrate all GnpIS configuration files to use PostgreSQL instance
  • [GNP-3379] - Migrate web applications to use PostgreSQL
  • [GNP-3383] - Migrate GnpIS portal indexing components to PostgreSQL instance
  • [GNP-3384] - Create IC chain for PostgreSQL
  • [GNP-3385] - SolR indexation
  • [GNP-3386] - Migrate GBrowse to use PG database
  • [GNP-3387] - Migrate JBrowse to use PG database
  • [GNP-3388] - Migrate Talend jobs to use PostgreSQL: Ephesis
  • [GNP-3389] - Migrate Talend jobs to use PostgreSQL: Genotypage
  • [GNP-3390] - Migrate Talend jobs to use PostgreSQL: Association
  • [GNP-3393] - Migrate Talend jobs to use PostgreSQL: Carto
  • [GNP-3394] - Migrate Talend jobs to use PostgreSQL: Sequence
  • [GNP-3395] - Migrate Talend jobs to use PostgreSQL: Synteny
  • [GNP-3409] - Final data migration
  • [GNP-3410] - Migrate Talend jobs to use PostgreSQL: Ontologies
  • [GNP-3411] - Migrate Talend jobs to use PostgreSQL: SelGen
  • [GNP-3413] - Migrate Talend jobs to use PostgreSQL: Genetic ressources
  • [GNP-3417] - Gather Breedwheat and TraitQTL in the same ontology
  • [GNP-3432] - DataModel based on transPLANT schema as Mediator
  • [GNP-3433] - ETL tools & procedure for all plateformes : indices loader
  • [GNP-3437] - Genotyping form: restrict panels, markers and markerSets by taxon
  • [GNP-3444] - RepetDB: Mock-up and architecture choice
  • [GNP-3451] - Insert Whealbi genetic resources data from Audrey Didier
  • [GNP-3461] - Add feedback link on survey GBrowse conf and check others
  • [GNP-3530] - RepetDB data model & data integration
  • [GNP-3532] - RepetDB consensus TE browser
  • [GNP-3533] - RepetDB consensus TE form & card
  • [GNP-3538] - Migrate GnpIS orchestration tools
  • [GNP-3562] - Sustain genome browser links and genome version in Association core schema
  • [GNP-3567] - Publish synteny dicotyledons dataset
  • [GNP-3578] - Migrate Talend jobs to use PostgreSQL: Plant Material
  • [GNP-3636] - Create RC job

Task

  • [GNP-2986] - GBrowse Malus TE on database malus
  • [GNP-3227] - Add a data coherence check in Synteny talend job
  • [GNP-3228] - Create a script allowing to delete all data linked to a synteny dataset
  • [GNP-3423] - RNAseq: Mockflow validation and DataModel
  • [GNP-3425] - Indexation JBrowse data into SolR
  • [GNP-3435] - Export genotyping matrix
  • [GNP-3659] - Add transplantdb URL in configuration files

Version 14.3.1 (2015/03/03)

Bug

  • [GNP-2959] - Hardcoded context path in autocompletion tool
  • [GNP-3486] - GnpMap textual interface: bug on download buttons (floppy icon)
  • [GNP-3487] - Undisplayed number when filtered by results per page
  • [GNP-3500] - The number of associated information is not displayed in the taxon card
  • [GNP-3515] - Ln values instead of log10 values for maize associations
  • [GNP-3521] - Bad management of intermine links display
  • [GNP-3523] - Add a distinct restriction on marker id in SNP results table
  • [GNP-3525] - The accession descriptor WS seems to return only one value
  • [GNP-3526] - Configure all Jenkins job to use JAVA 1.7.x
  • [GNP-3529] - Quick search indices are not copied to the correct location

Improvement

  • [GNP-3528] - Improve genetic resources web services

Story

Version 14.3 (2015/02/04)

Technical task

  • [GNP-2979] - Create Families WS for ARCAD PORTAL
  • [GNP-3068] - Dedicated tomcat instance for web services
  • [GNP-3089] - Create Talend job to insert Taxon
  • [GNP-3090] - Create Talend job to insert Accession
  • [GNP-3091] - Update Talend jobs to insert Site and Genealogy
  • [GNP-3092] - Create Talend job to insert Collection
  • [GNP-3093] - Create Talend jobs to insert Grc, Network and Photo
  • [GNP-3143] - Add accessions in panel card
  • [GNP-3144] - Link panels and association experiments to genotyping and phenotyping results
  • [GNP-3164] - Add phenotypes pivot in panel card and association experiment card
  • [GNP-3165] - Display LD and Kinship as matrix and add export
  • [GNP-3195] - Update tools to validate Genetic Resources submision file.
  • [GNP-3203] - export genotyping table
  • [GNP-3215] - README
  • [GNP-3224] - Mise à jour des talends Pheno , Asso et Selgen
  • [GNP-3247] - Update comment protocol for breedwheat data
  • [GNP-3272] - Update Dn Handling and migrate text code to shortName
  • [GNP-3315] - UML TODO
  • [GNP-3342] - UML TODO
  • [GNP-3345] - UML TODO 2
  • [GNP-3346] - Clean UML after impl
  • [GNP-3351] - Validation

Bug

  • [GNP-2947] - Evaluate GnpIS Prod stress capacity
  • [GNP-2954] - Problem with NGS_sample data : wrong accession link.
  • [GNP-2974] - The transcriptomic protocols are visible even if wheat species group is chosen
  • [GNP-3025] - Error when getting Ephesis results on a specific trait
  • [GNP-3031] - IGV & GV buttons disappear in chrome under mac os
  • [GNP-3038] - Bad counting in the taxonomy tree
  • [GNP-3043] - Species group problem with gnpmap markers
  • [GNP-3050] - Internal server error from genelist to geneCard
  • [GNP-3051] - Loci exported file contains mislabeled and shifted columns
  • [GNP-3072] - Existing link to GnpIS public cards from the private/rc application
  • [GNP-3128] - Wrong geographical localisation for experimental sites.
  • [GNP-3141] - Vitis 12X Gbrowse back link to GnpIS is broken
  • [GNP-3154] - Accession card linked to an Ephesis trial displays an error
  • [GNP-3180] - No tab in asso form under IE
  • [GNP-3181] - MarkerSet field is too small in asso form
  • [GNP-3182] - Some cross references betweeen GnpSNP and Wheat Gbrowses are broken
  • [GNP-3193] - Populus' gbrowse is miconfigured
  • [GNP-3200] - update cmap links in private GnpMap
  • [GNP-3206] - Ephesis form Accession name instead of accession number in DAO
  • [GNP-3210] - Ephesis : choose Quercus only trigger no results
  • [GNP-3211] - Ephesis Trial result : Remove "get data" button when data are not accessible.
  • [GNP-3212] - Ephesis Result page : autoload first page of result
  • [GNP-3223] - Link to site does not take private context into account for Ephesis trials
  • [GNP-3225] - Back Button from Panel card triggers error (on MAC ?)
  • [GNP-3274] - Fixes in asso form
  • [GNP-3325] - Bad informations displayed and bad link for genotyping experiments
  • [GNP-3326] - Popup not available on several dots for Maize Manhattan Plot
  • [GNP-3332] - Check token interception for gnpAsso
  • [GNP-3376] - Handle genus export
  • [GNP-3399] - Wrong encoding for distributor section on Accession card
  • [GNP-3400] - Ephesis plant material export does not work
  • [GNP-3401] - Ephesis form tabs are not linked anymore
  • [GNP-3402] - The number of associated information is not displayed in the taxon card
  • [GNP-3404] - WheatIS portal is too slow...
  • [GNP-3405] - BioMercator does not work with generated XML files
  • [GNP-3406] - Display variables in the table for Ephesis Application
  • [GNP-3408] - Loci results export does not work anymore
  • [GNP-3415] - Ephesis ontology portal links and deployment
  • [GNP-3418] - Indexing process failed to execute
  • [GNP-3420] - No data available in RC.
  • [GNP-3449] - Ephesis exports corrections

Epic

  • [GNP-1947] - TO13: Continuous integration chain improvement
  • [GNP-2056] - TO8: Data submission for GnpIS (interface and submission files)
  • [GNP-2071] - TO12: GnpIS packaging
  • [GNP-2166] - SO1: Create genotyping interface
  • [GNP-2168] - EO2: Implement forest trial descriptors in GnpIS
  • [GNP-2170] - TO6: Merge GnpSeq with GnpSeqNGS
  • [GNP-2244] - VO3: Enrich vitis integrable data
  • [GNP-2359] - TO13: Deduplicate tables data in database
  • [GNP-2372] - P01: Improve Phenotype user interface
  • [GNP-2373] - TO13: GnpIS technical/hidden improvements 2014
  • [GNP-2374] - Integrates work unrelated to clear objectives
  • [GNP-2375] - AO1: Association
  • [GNP-2379] - WO5: Sequence and annotation data management of 3B ref and survey sequence (3BSEQ, IWGSC)
  • [GNP-2380] - TO14: Integrate GnpIS as a TransplantDb element
  • [GNP-2381] - Continuous data integration
  • [GNP-2383] - Continuous bug fix
  • [GNP-2384] - TO1: Consolidate germplasm pivot
  • [GNP-2463] - WO10: Gene center view
  • [GNP-2496] - AO2: Association data
  • [GNP-2522] - WO4: BreedWheat data and related data management 2014
  • [GNP-2572] - WO6: Physical maps data management (IWGSC)
  • [GNP-2573] - WO8: Distributed index search engine for WheatIS and transPLANT
  • [GNP-2670] - Improve insertion/update tool for genetic resources.
  • [GNP-2772] - P05: Ontologies, Deliverables for Phenome 2014
  • [GNP-2779] - Integrate amaizing data (RNA-seq, polymorphisms, accessions)
  • [GNP-2789] - SGO1: SelGen Interface
  • [GNP-2880] - PO2: Export and interoperability (Pheno/O2)
  • [GNP-3044] - EO4: Create Salicaceae GnpIS (genomic and genetic data)
  • [GNP-3116] - SO6: Integrate SNP discovery and genotyping data in the same distributed index system
  • [GNP-3117] - VO2: Integrate all genomic data mapped on Vitis 12X in a genome browser
  • [GNP-3428] - TO18: Releases management

Improvement

  • [GNP-3075] - UI improvements
  • [GNP-3145] - "BioMart INRA URGI GnpIS" >"Grapevine 12x" means "12x.2" or "12x.0"
  • [GNP-3178] - Manage private data in ElasticSearch index
  • [GNP-3348] - Handle the 400 ES error code in genotyping talend job.

New Feature

  • [GNP-3046] - Create Jbrowse for Populus v3
  • [GNP-3084] - Finalize complete talend for genetic resources (CRB) insertion.
  • [GNP-3347] - Account request for 'Amaizing - D Steinbach' by Delphine Hourcade

Story

  • [GNP-1663] - Create lot card.
  • [GNP-2339] - Export varietal list from Accession Search (Aimazing, Ephesis,, Perpheclim, ...)
  • [GNP-2361] - Deduplicate ADDRESS_T data
  • [GNP-2474] - Set up a virtual machine based on pearson for the Checker/Mapper
  • [GNP-2519] - Update indexation of URGI Data for TransplantDB.
  • [GNP-2686] - Update Grapevine genetic resources
  • [GNP-2773] - Wheat trait Ontology/Thesaurus
  • [GNP-2774] - Pea trait ontology for Phenome
  • [GNP-2775] - Environment Ontology/Thesaurus
  • [GNP-2776] - Improve Ontology handling in GnpIS
  • [GNP-2781] - Jbrowse skill transmission, Evaluate efpBrowser, IGV and JBrowse for RNA-seq
  • [GNP-2808] - Insert Maize association data (S1P9 - 1 trait)
  • [GNP-2818] - SelGen interface: cards
  • [GNP-2828] - Improve WheatIS portal design using CSS of Wheat URGI website
  • [GNP-2854] - Link to agroclim datasets
  • [GNP-2862] - Selgen Interface: filters
  • [GNP-2939] - Add Wheat3BMine in GnpIS portal
  • [GNP-2976] - Create web services for ARCAD portal
  • [GNP-3009] - Create a "Contributors" link on GnpIS portal toward urgi tool page
  • [GNP-3013] - Accession simple form : add wildcard for taxon field
  • [GNP-3030] - Improve Genotyping interface
  • [GNP-3052] - Insert Vitis 18K Genotyping data
  • [GNP-3062] - Partage de compétences avec Loïc
  • [GNP-3064] - Isatab export improvements
  • [GNP-3113] - Add a second source to WheatIS SolR
  • [GNP-3130] - Release 14.3
  • [GNP-3140] - Handle TE and Gene Update requested by F. Maumus
  • [GNP-3142] - Integrate 2A Wheat physical map
  • [GNP-3147] - Beet test data set insertion
  • [GNP-3152] - Insert Tomato Flomediv association data
  • [GNP-3163] - Complete Panel Card / experiment card pivot (asso - geno - pheno)
  • [GNP-3170] - Update submission file
  • [GNP-3174] - Insert BcVEL1-BcLAE1 transcriptome data
  • [GNP-3216] - DataLift technology watch
  • [GNP-3221] - Upgrade GnpIS to Java 1.7.x, Tomcat 7.0.x and dependencies
  • [GNP-3231] - Add publications on transcriptomic project card
  • [GNP-3278] - GnpIS 14.2.1 external delivery
  • [GNP-3280] - Hotfix 14.2.2
  • [GNP-3292] - Update DB schema & Talend jobs to match new submission file
  • [GNP-3302] - Gbrowse/Jbrowse annotation 1Bv1
  • [GNP-3333] - Update contacts/institutions for Pea in Siregal
  • [GNP-3339] - Insert Pea genetic ressources
  • [GNP-3349] - Update script deduplicate_table_data.pl

Task

  • [GNP-2493] - Update all xref from GnpSeq to match the new GnpSeqNGS URL
  • [GNP-2622] - BreedWheat SNP discovery 8 files
  • [GNP-2643] - Insert tomato markers in GnpIS
  • [GNP-2802] - Continuous ignored/failing tests correction
  • [GNP-2835] - Deploy a first version of the WheatIS portal in production
  • [GNP-2996] - Create SolR Git repository for versionning our configuration changes
  • [GNP-3014] - Manage notators in Ephesis
  • [GNP-3054] - Jumboree for functional tests
  • [GNP-3095] - Use Gitlab for versionning all GnpIS configuration files
  • [GNP-3110] - Export genotyping results (table) + display matrix
  • [GNP-3111] - Sort Genotyping results by several criteria and add xrefs
  • [GNP-3151] - Create Siregal specific property for character encoding: ISO-8859-1 instead of UTF-8
  • [GNP-3229] - Improve Genotyping talend job to handle very very big data
  • [GNP-3273] - Request by Genus instead of taxon in Asso/Selgen/geno forms
  • [GNP-3290] - Switch the ES genotyping production cluster (and data) to the dedicated VM
  • [GNP-3295] - Add the vitis 12x markers in the list of indexed features

Version 14.2.2 (2014/12/23)

Technical task

  • [GNP-3298] - Genotyping/association hotfix 14.2.2

Bug

  • [GNP-3184] - Species restriction is not applied on genotyping data

Improvement

  • [GNP-3178] - Manage private data in ElasticSearch index

Story

  • [GNP-3231] - Add publications on transcriptomic project card

Version 14.2.1 (2014/10/13)

Bug

  • [GNP-3154] - Accession card linked to an Ephesis trial displays an error
  • [GNP-3159] - No restriction by experiment/markerset/panel in genotyping results
  • [GNP-3172] - Polym. loci export: can not load taxons in "Genomes with contigs/scaffolds" pane

Task

Version 14.2 (2014/10/01)

Sub-task

  • [GNP-2817] - Create new data submission file

Technical task

  • [GNP-2812] - Update code generator to use PostgreSQL query for the species group filter
  • [GNP-2814] - Fix all remaining failing queries
  • [GNP-2815] - Update build.properties.sample file
  • [GNP-2816] - Final functional validation
  • [GNP-2830] - Filter WheatIS portal results on wheat data only.
  • [GNP-2833] - Implement facets in WheatIS to count and display results for data types, data sources
  • [GNP-2876] - Update Private Genetic and phenotype resources datamarts
  • [GNP-2877] - Update Private Genetics maps and NGS Variants datamarts
  • [GNP-2878] - Update Private wheat and Zea Mays annotation datamarts
  • [GNP-2879] - Update Private TAIR V10 and create Tomato annotation datamarts
  • [GNP-2997] - Packaging of the WheatIS portal
  • [GNP-3000] - Create REST endpoint to expose species groups

Bug

  • [GNP-2261] - GnpArray data : Duplicate operator name in selecti...
  • [GNP-2855] - Sequence results times out when querying EST
  • [GNP-2896] - Association flag tool configuration is not up to date
  • [GNP-2904] - Update Wheat RG data.
  • [GNP-2938] - Fix Tomato Gbrowse (link, xyplots)
  • [GNP-2940] - Oracle database indices are ignored in explain plan
  • [GNP-2941] - Trial result pager is too slow
  • [GNP-2943] - Missing Accessions from Taxon Card
  • [GNP-2944] - Pager display "no result found" in some case on Siregal
  • [GNP-2972] - Fix Dygraph incompatibility with Internet Explorer (9)
  • [GNP-3008] - Gene order inside a modern chromosome is inconsistent
  • [GNP-3011] - The database connection pool does not support more than 50 concurrent users
  • [GNP-3032] - Modern chromosome size is wrong
  • [GNP-3035] - Server error when download a result file in analysis
  • [GNP-3036] - No result on several taxons in Genome Variant Bulk Download
  • [GNP-3047] - Miss style for buttons
  • [GNP-3073] - Silent error when loading data
  • [GNP-3074] - some markers display no results using the "search by marker" form
  • [GNP-3076] - Truncated panel in genotyping form
  • [GNP-3094] - Bad links beetween association manhattan plots and gbrowse for tomato

Improvement

  • [GNP-2827] - Use SolR Transplant schema for the WheatIS
  • [GNP-2881] - Improve WheatIS portal (data, facets)
  • [GNP-2966] - Mockito jumboree

New Feature

  • [GNP-2864] - Create talend to insert Accession with a minimal submission format.

Story

  • [GNP-2167] - Genot-interface Scenario 1: Genotyping form and export result file.
  • [GNP-2452] - Update genetic resources Talend to meet the standards established for the submit format
  • [GNP-2683] - Update grapevine accessions.
  • [GNP-2693] - Evaluate GrinGlobal scalability
  • [GNP-2780] - Add link to Jbrowse in analysis card for RNA-seq experiments
  • [GNP-2782] - Insert amaizing RNA-seq and polymorphysm data in JBrowse
  • [GNP-2786] - Allow ISA-Tab export on Ephesis
  • [GNP-2787] - Migrate all unit tests to JUnit 4 and create test suites.
  • [GNP-2794] - Update Database Schema for SelGen
  • [GNP-2795] - Create Talend jobs for SelGen data sets insertions
  • [GNP-2797] - Migrate GnpIS Oracle database under PostgreSQL development instance
  • [GNP-2798] - Migrate web applications to use PostgreSQL
  • [GNP-2801] - Migrate all GnpIS configuration files to use PostreSQL instance
  • [GNP-2803] - Migrate GnpIS portal indexing components to PostgreSQL instance
  • [GNP-2829] - Deploy SolR frontend/backend architecture in production
  • [GNP-2837] - Talend to insert distributors.
  • [GNP-2841] - Design Genotyping data architecture and process
  • [GNP-2849] - New COSfinder in SyntenyViewer
  • [GNP-2852] - Wheat3BMine in production
  • [GNP-2861] - Selgen interface : search form, results, export
  • [GNP-2865] - Update Private datamarts
  • [GNP-2866] - Release 14.2
  • [GNP-2882] - Display X/Y coordinates positionning an individual in a trial.
  • [GNP-2884] - Insert amaizing Rna-Seq Metadata in GnpSeQNGS
  • [GNP-2885] - Create GnpIS development instance under PostgreSQL
  • [GNP-2889] - Update Tomato association data
  • [GNP-2893] - Install a private tomcat instance on morgoth
  • [GNP-2925] - Taxon card fails to display on Tomcat 7
  • [GNP-2928] - Create IC chain for PostgreSQL migration
  • [GNP-2929] - Disable MapComparator button on restricted selection form
  • [GNP-2936] - Add support for postgreSQL to species_group flag tool
  • [GNP-2988] - Insert UE Arboricole, INRA Bordeaux
  • [GNP-2989] - Update Avignon GRCs.
  • [GNP-2990] - Update Dijon BRC.
  • [GNP-2991] - Update Allium BRC.
  • [GNP-2993] - Set Wheat accessions from FAO collection to MLS distribution status.

Task

  • [GNP-2057] - Thinking about the implementation of a tool for testing submission format.
  • [GNP-2532] - Update BreedWheat wp2 phenotyping data
  • [GNP-2769] - Update IRODS FileStorage
  • [GNP-2770] - Add metadata schema in Dspace
  • [GNP-2771] - Configure wheat design of Dspace graphical interface
  • [GNP-2858] - Create public Amaizing JBrowse
  • [GNP-2971] - Integrate Tomato TE on database Tomato
  • [GNP-2973] - Add Indexation support of Tomato and Malus databases for quicksearch
  • [GNP-2995] - Update database access for indexing components
  • [GNP-3001] - Migrate genotyping data to new data process
  • [GNP-3006] - Update Biomart's URL of private site
  • [GNP-3049] - Add links to BioMercator tool and documentation pages in GnpMap welcome page
  • [GNP-3053] - Update misconfigured Gbrowses' datasources in production

Version 14.1.1 (2014/07/17)

Bug

  • [GNP-2805] - Genes used for Synteny are also indexed for Transcriptome in GnpIS portal
  • [GNP-2909] - Error 500 with species group
  • [GNP-2910] - Missing instance in search results
  • [GNP-2912] - Links and counts for taxon associated informations are wrong in Taxon card
  • [GNP-2923] - Bad link to laboratory card from contact card
  • [GNP-2924] - Page out of bounds causes an interval server error
  • [GNP-2926] - Some data are not flagged in wheat species group
  • [GNP-2931] - Rename ARRAY_T to TRANS_ARRAY_T in portal
  • [GNP-2935] - Bad Tomato phenotypes in production
  • [GNP-2937] - Dead link to download files on run card

Story

  • [GNP-2927] - Add a 'Query' link in Synteny sidebar and display a redirection to 'synteny-cereal' for Wheat dataset in dedicated drop down
  • [GNP-2946] - Query link are not displayed in genetic resources sidebar

Version 14.1 (2014/06/04)

Sub-task

  • [GNP-2647] - GBrowse wheat physical map: add 7DS
  • [GNP-2648] - GBrowse wheat physical map: 6B. Append anchor marker informations
  • [GNP-2649] - GBrowse wheat physical map: add 4A
  • [GNP-2650] - Manage non-oriented scaffolds in 3B annotation
  • [GNP-2651] - [GBrowse] Remove 3B annotation prototype and delete related links into physical map
  • [GNP-2652] - [GBrowse] Add mailto link to physical maps popup

Technical task

  • [GNP-2434] - Integrate IGV (javaWebStart) in GnpIS
  • [GNP-2435] - Polymorphic loci bulk download
  • [GNP-2529] - Implement a prototype allowing to manage Irods entities (for indexing purpose)
  • [GNP-2533] - Remove wp2 data from production
  • [GNP-2534] - Check wp2 data
  • [GNP-2535] - Send updated file to Frederic Sapet and wait for his updates. Insert dev/int/prod
  • [GNP-2575] - Update Public Genetic and phenotype resources datamarts
  • [GNP-2576] - Update Public Genetics maps and NGS Variants datamarts
  • [GNP-2577] - Update Public wheat and Zea Mays annotation datamarts
  • [GNP-2578] - Update Public TAIR V10 and populus annotation datamarts
  • [GNP-2727] - Deploy all submission formats
  • [GNP-2785] - Explicit RG home page with links to query forms.

Bug

  • [GNP-2309] - Date format is wrong in project card
  • [GNP-2471] - "Back to form" does not keep the values ​​previous...
  • [GNP-2822] - Quicksearch: Feature containing a sharp have a bad Xref generated (sharp is not encoded)
  • [GNP-2842] - Phenotype trials count is missing on taxon card
  • [GNP-2851] - Bugs in RC for polymorphic loci export
  • [GNP-2859] - Wrong ressource for button name
  • [GNP-2886] - Flag species group problem on BW phenotyping data
  • [GNP-2890] - No phenotyping values in Ephesis results (Tomato Association data)
  • [GNP-2899] - Results reinitialized when go back in history in asso results.
  • [GNP-2902] - Download Trial file triggers internal server error
  • [GNP-2903] - Phenotype index are not available on RC server

Epic

  • [GNP-2056] - Data submission for GnpIS (interface and submission files) (Transversal/O8)
  • [GNP-2071] - GnpIS packaging (Transversal/O13)
  • [GNP-2075] - Schemas fusion (Transversal/O6)
  • [GNP-2168] - Implement forest trial descriptors (EFPA/O2)
  • [GNP-2170] - Merge GnpSeq with GnpSeqNGS.
  • [GNP-2185] - Integrate new types of SNP data (O4/SNP)
  • [GNP-2210] - Synteny Reloaded (TrsvO7) - Merge forks and update insertion tools
  • [GNP-2221] - Better manage accession outside BRC.
  • [GNP-2283] - Oracle to PostgreSQL migration evaluation (Transversal/O11)
  • [GNP-2372] - Improve Phenotype user interface (Ephesis/O1)
  • [GNP-2375] - Association (Asso/O1)
  • [GNP-2377] - Update Genetic Resources data in 2014.
  • [GNP-2379] - Wheat O5: Sequence and annotation data management (3BSEQ, IWGSC) (sept 14):
  • [GNP-2380] - Integrate GnpIS as a TransplantDb element (Transversal/O14)
  • [GNP-2381] - Continuous data integration
  • [GNP-2383] - Continuous bug fix
  • [GNP-2446] - Improve GnpSeqNGS
  • [GNP-2447] - Update Talend to insert new submission formats (Transversal/O8)
  • [GNP-2463] - Wheat O10 : Gene center view (may 14)
  • [GNP-2482] - Technology watch to deal with big data
  • [GNP-2496] - Association data
  • [GNP-2522] - Wheat 04: BreedWheat data and related data management 2014 (oct 14)
  • [GNP-2572] - Wheat O6: Physical maps data management (IWGSC) (dec 14)
  • [GNP-2573] - Distributed index search engine for WheatIS and transPLANT (Wheat/O8)
  • [GNP-2671] - Insert Siregal data to GrinGlobal.
  • [GNP-2779] - Integrate amaizing data (RNA-seq, polymorphism, accession ..etcc)

Exploratory Task

  • [GNP-2284] - Indexation of PostgreSQL GnpIS instance
  • [GNP-2285] - Species group filter evaluation
  • [GNP-2286] - Web applications validation
  • [GNP-2287] - Evaluation of Talend jobs migration
  • [GNP-2714] - Evaluation of user confidentiality in PostgreSQL instance

Improvement

  • [GNP-1672] - Link ngs_analysis and genome tables.
  • [GNP-2589] - Use common jsp to download files in GnpSeqNGS.
  • [GNP-2713] - Handle links to specific application state within HTML anchor instead of URL parameter
  • [GNP-2737] - Use properties for home page url and feedback url

New Feature

  • [GNP-2171] - Create a Talend job to generate GnpSeqNGS submission files with GnpSeq data.
  • [GNP-2182] - Display Amaizing polymorphism data in GnpSNP
  • [GNP-2424] - Implement Site complementary informations
  • [GNP-2425] - Implement Trial complementary informations
  • [GNP-2429] - Insert GnpSeq data in GnpSeqNGS.
  • [GNP-2731] - Changement dans le formulaire de soumission

Story

  • [GNP-1734] - Isolate GnpSeq schema in GPI schema without ASTER views
  • [GNP-2157] - Merge association phenotypes in Ephesis
  • [GNP-2186] - GRC card : display new coordinator and curator.
  • [GNP-2289] - Migration of GPI::DB::Handler to use PostgreSQL
  • [GNP-2304] - Create a Talend to fill the static data sheets of submission files using SQL queries
  • [GNP-2311] - Allow external genetic resources distributors.
  • [GNP-2328] - Replace applications name by thematic
  • [GNP-2387] - Merge all database configuration parameters in build.properties
  • [GNP-2415] - Load new data in Wheat3BMine
  • [GNP-2436] - Improve SNP discovery interfaces
  • [GNP-2449] - Update Ephesis Talend to meet the standards established for the submit format
  • [GNP-2450] - Update Asso Talend to meet the standards established for the submit format
  • [GNP-2481] - Deal with big data: dependencies installation and project creation
  • [GNP-2484] - Benchmark: ElasticSearch Vs denormalized table
  • [GNP-2489] - iRODS file (with metadata) distribution test
  • [GNP-2503] - Release 14.1
  • [GNP-2540] - Generate indices for Transplant SolR
  • [GNP-2544] - Wheat IS portal
  • [GNP-2556] - Create a jenkins job to load denormalized tables
  • [GNP-2560] - Dygraph implementation for association graphs
  • [GNP-2562] - Release 13.3.1
  • [GNP-2574] - Update Public datamarts
  • [GNP-2586] - Add Phenotype data (Ephesis) in index and Taxon search.
  • [GNP-2590] - Hide links if the corresponding properties are not set in profiles.xml
  • [GNP-2692] - Insert descriptors to Grin Global.
  • [GNP-2709] - Hide links if the corresponding properties are not set in build.properties
  • [GNP-2710] - Insertion of Tomato Association public data
  • [GNP-2730] - Generic and Phenotype submission File validator
  • [GNP-2732] - Create load-tree-paths binary distribution
  • [GNP-2784] - Add 2 links to genetic resources and Siregal in GnpIS menu.
  • [GNP-2897] - Rename table ARRAY_T to TRANS_ARRAY_T

Task

  • [GNP-1548] - Merge SyntenyViewer forks into stable and maintainable application and database
  • [GNP-2400] - Continuous ignored/failing tests correction
  • [GNP-2476] - Create Dspace and Intermine project on Gitlab linked to github
  • [GNP-2559] - Launch orareverse on gpprod for AKER
  • [GNP-2579] - Update Forage GRC web site
  • [GNP-2582] - Create indexing configuration for wheat recent gbrowses (3B annotation and physical maps)
  • [GNP-2608] - Add new wheat physical maps
  • [GNP-2610] - Upgrade wheat 3B annotation
  • [GNP-2617] - Insert Apricot data from Avignon.
  • [GNP-2631] - Insert Graingenes: QTL
  • [GNP-2639] - GBrowse/JBrowse to mannage survey sequences (Curtis + Edward)
  • [GNP-2738] - Insert private melon makers in GnpIS
  • [GNP-2742] - Update annotation tomato for Gbrowse

Version 13.3.2 (2014/03/25)

Bug

  • [GNP-2707] - No Phenotyping Campaign filter for phenotypes
  • [GNP-2734] - Fix Grey trial (metadata only) handling

Version 13.3.1 (2014/02/24)

Bug

  • [GNP-2551] - Wrong image display in Siregal.
  • [GNP-2555] - Thematic restriction is not correctly applied to taxon result page
  • [GNP-2558] - Fix issues with GnpAsso prod

Version 13.3 (2014/02/05)

Technical task

  • [GNP-452] - Accession passeport form: display country names instead of textual code.
  • [GNP-1981] - Accession passport form : display institution in alphabetic order.
  • [GNP-2164] - Varietal List to trial direct linking: add data for existing trials
  • [GNP-2176] - Interface optimization for GnpAsso Beta
  • [GNP-2324] - Restore all GnpIS development database schemas with clean dumps
  • [GNP-2329] - Talend for Project submission (Project & Contact & Institution & Address) insertion.
  • [GNP-2330] - Update perl data tools (Refactor Contact).
  • [GNP-2333] - Address.country_id are missing.
  • [GNP-2337] - Make ObservationVarVO a sublclass of OntologyTermVO, ensuring the usability by TreeWidget
  • [GNP-2338] - Add message when no results
  • [GNP-2344] - Feed recussive linking of parent study subject : bloc|1;rep|a25
  • [GNP-2345] - Filter studySubject by ObsVar : not doable with SLQ
  • [GNP-2347] - EphesisTrialPresenter : list trialIds from a dedicated query rather than only from current page
  • [GNP-2368] - Rename <set name="lots" table="TRIAL_LOT" order-by="LOT*S*_ID" l
  • [GNP-2386] - UML TODO 2
  • [GNP-2395] - UML TODO 3
  • [GNP-2398] - Refactor and fix StudySubjectServiceImpl.handleGenerateExportFile(
  • [GNP-2402] - Create ETL script to feed test data for continuous integration
  • [GNP-2499] - Finisih GWT TrialCard

Bug

  • [GNP-1995] - Set group_id and insertion_date to not null in site_t table.
  • [GNP-2196] - Phenotyping Dates are not loaded in the database
  • [GNP-2302] - Export of private genome variant fails
  • [GNP-2303] - Bug in GnpSNP rc when selecting CnvMaize analysis in GenomeVariantForm.jsp
  • [GNP-2305] - 404 error when trying to download private raw data files
  • [GNP-2325] - Basket export does not work anymore
  • [GNP-2341] - Bad species group value for Quercus robur genetic maps
  • [GNP-2366] - Strange results when querying contact form (from GnpSNP)
  • [GNP-2388] - Contact form returns wrong results.
  • [GNP-2404] - Bad chromosome order in manhattan plots
  • [GNP-2405] - Fix artefacts on the GnpAsso's gwt interface
  • [GNP-2462] - Can not read the full popup at the end of page
  • [GNP-2467] - Missing separator between details list
  • [GNP-2470] - Problem in Ontology viewer with TO only
  • [GNP-2472] - "Reset" button doesn't work
  • [GNP-2479] - Experiment results, error on link to taxon card
  • [GNP-2480] - Software card: bad links for doc and get URL
  • [GNP-2513] - Wrong values in "Sort result by" dropdown
  • [GNP-2514] - Fail to refresh the association count (and results) when removing a filter
  • [GNP-2517] - No ref. seq loaded when typing in snpform
  • [GNP-2531] - Gene name is not displayed when hovering the gene

Epic

  • [GNP-1947] - Continuous integration chain improvement. (Transversal O13)
  • [GNP-2056] - Data submission for GnpIS (interface and submission files) (Transversal/O8)
  • [GNP-2075] - Schemas fusion (Transversal/O6)
  • [GNP-2168] - Implement EFPA needs (phenotypes and genetic ressources).
  • [GNP-2283] - Oracle to PostgreSQL migration (Transversal/O11)
  • [GNP-2372] - Improve Phenotype user interface (Epehsis/O1)
  • [GNP-2376] - Create Oak GnpIS (genomic and genetic data) (EFPA/O2)
  • [GNP-2377] - Update Genetic Resources data
  • [GNP-2381] - Continuous data integration

Exploratory Task

Improvement

  • [GNP-1928] - Add filters in asso results
  • [GNP-2076] - Improve constraints in database schema (unicity, triggers, indicies...)
  • [GNP-2275] - Create indexes on GnpAsso tables
  • [GNP-2365] - Hide empty files in Map card
  • [GNP-2393] - Use common jsp to download files in GnpSeqNGS and Ephesis.
  • [GNP-2458] - Portal modifications for GnpAsso production

New Feature

  • [GNP-2169] - Implement trial type and status
  • [GNP-2183] - SNP Discovery interface V2

Story

  • [GNP-1784] - Improve web design in 'how to order' page.
  • [GNP-1944] - Continuous integration on database orchestration script.
  • [GNP-1996] - Remove all references to RawValue and RawValueSet
  • [GNP-2040] - Analysis of the GnpIS (modules/portal) architecture
  • [GNP-2041] - Design unified interface mockup
  • [GNP-2053] - Improved consistency for Taxon accross Portal and thematic apps
  • [GNP-2156] - Single form for Pheno data (GxE and Asso) and trials
  • [GNP-2163] - Create Phenotyping result page in Association Form
  • [GNP-2200] - Refactor Institution-Contact-Person
  • [GNP-2201] - Mise en production d'asso
  • [GNP-2218] - Load BreedWheat data (Pheno & Polym)
  • [GNP-2222] - Accession outside BRC : data tools, RG Home page.
  • [GNP-2230] - Release 13.3
  • [GNP-2294] - Create association denormalized table (big data optimization)
  • [GNP-2297] - Insert complete data association for Arabidopsis
  • [GNP-2312] - Clean *_OLD and explain plan tables in deprecated owners
  • [GNP-2313] - Disable queries on Siregal home page.
  • [GNP-2332] - Automatize Association insertion for continuous integration
  • [GNP-2334] - Test on database restore with only one processor
  • [GNP-2346] - Improve SNP discovery interface V2
  • [GNP-2364] - Link polymorphic loci without refseq to a refseq using their subsnps
  • [GNP-2367] - Rationalize SNP positions in SNP_card and SNP_results

Task

  • [GNP-1961] - Release GnpIS 13.2 modules
  • [GNP-2059] - Simple submission interface: URGI web site + Gimli
  • [GNP-2162] - GnpAsso Preparation for workshop 30/09
  • [GNP-2175] - Dspace iRods: insertion of NGS test data
  • [GNP-2212] - Configure Intermine instance for Wheat data (stands for GRS)
  • [GNP-2310] - Remove public access restriction on PlantSyntenyViewer (data + app)

Version 13.2 (2013/09/06)

Technical task

  • [GNP-1338] - Order form : change "Result" button to "Validate order" button.
  • [GNP-1830] - Accession card.synonym : don't display [] when language is empty.
  • [GNP-2077] - Create URGI unit ontology
  • [GNP-2078] - integrate Soil, Meteo and ITK file
  • [GNP-2153] - Handle Variable Tab correctly

Bug

  • [GNP-1913] - Missing default value for DATA_FILE_T.INSERTION_DATE.
  • [GNP-1942] - Problem with varray type to copy from prod to dev instance
  • [GNP-1953] - Error on name for SG views
  • [GNP-2007] - URL link produces an error on GRS when coming from the GnpIS portal
  • [GNP-2129] - XDoclet runtime error
  • [GNP-2154] - Display taxonomy list in passeport accession form
  • [GNP-2165] - Ancestral chromosomes (and sometimes taxons) are not displayed in drop down when a species restriction group is selected
  • [GNP-2251] - Misplaced footer
  • [GNP-2252] - Data : Link to private grape CMAP doesn't work.
  • [GNP-2253] - Data : Link to GRIN database for taxon doesn't work
  • [GNP-2255] - Phenotypes used informations are missing.
  • [GNP-2256] - Bad help icon used on taxon card
  • [GNP-2257] - Taxon Card show wrong number and accession link doesn't work.
  • [GNP-2258] - Shuffle bug : Sometime, genotype card take 3 min to load.
  • [GNP-2259] - Genetic map submission bug in GnpIS (database)
  • [GNP-2262] - Typo in Ephesis header choice page
  • [GNP-2266] - Species group versus BRC : the 2 drop downs are not linked.
  • [GNP-2267] - Siregal Preferences click: hide both drop downs.
  • [GNP-2268] - Internal server error for passport form on chesnut GRC.
  • [GNP-2269] - Accession passport form takes too much time to be displayed.
  • [GNP-2270] - Inconsistent Phenotyping campaign management
  • [GNP-2272] - Create mandatory indicies
  • [GNP-2273] - Need a busy wheel on phenotyping campaign widget
  • [GNP-2276] - Add static information on accession order form.
  • [GNP-2278] - Missing indicies in Siregal tables
  • [GNP-2279] - In the marker card, polymorphic locus associated are not display.
  • [GNP-2281] - Odd number in taxonomy tree diplay
  • [GNP-2300] - Bad link to release notes page

Exploratory Task

  • [GNP-1619] - Configure & implement first test using Mockito

Improvement

  • [GNP-1856] - Improvement of UML schema after fusion of all modules
  • [GNP-1949] - Implement Servlet in GnpIS to handle (un-)authentified file download
  • [GNP-1959] - Implement functional tests with selenium - Session 3
  • [GNP-1974] - Add a tag "isVirtual" in StudySubject to manage Trial without levels.
  • [GNP-1986] - SnpForm: make the chromosome list dependent on the selected genome
  • [GNP-2291] - "Wilcard" mispelling.

New Feature

  • [GNP-1809] - Link Accessions directly to BRC.
  • [GNP-1920] - Display genealogy data in Accession Card.
  • [GNP-1921] - Integrate genealogy data
  • [GNP-1948] - Create script generating Apache httpd configuration needed for managing access to authenticated files
  • [GNP-1951] - Configure Wheat GRS on Chado data

Story

  • [GNP-1895] - Update of admin tools for GnpIS after fusion
  • [GNP-1925] - Display numbers in decimal format
  • [GNP-1927] - Add experimental condition columns in asso results
  • [GNP-1929] - Dynamic update by Taxon in asso form
  • [GNP-1930] - Add Panel and Accession criteria in asso form
  • [GNP-1931] - Add chromosomic criteria in asso form
  • [GNP-1934] - QQPlots and manhattan plots in asso results
  • [GNP-1954] - Evaluate Isa Tabs for Phenotyping Data
  • [GNP-1980] - Integrate Wheat network (Factor*mod=Treatment)
  • [GNP-1982] - Correct misleading taxonomy count
  • [GNP-1983] - Update Asso code (Dao, context, tests)
  • [GNP-1989] - Manage Xref links in GnpAsso for Gbrowse
  • [GNP-1990] - Change Taxon Form to drop-down list in Asso form
  • [GNP-1991] - Update data export in asso results
  • [GNP-1999] - Use mock API in services layer unit tests
  • [GNP-2250] - Migrate code coverage tool from Cobertura to JaCoCo
  • [GNP-2290] - Display Another option for accession distribution restriction on accession card

Task

  • [GNP-905] - Merge all UML files.
  • [GNP-1719] - Display traits to select within an ontology tree
  • [GNP-1837] - Release GnpIS 13.1 modules
  • [GNP-1851] - Database patch orchestration script for GnpIS 13.1.
  • [GNP-1873] - Fusion of Aster.Gene_t and Transcriptome.Gene_t
  • [GNP-1936] - Extract data from RAW_VALUE to files
  • [GNP-1938] - Remove on the fly generation of raw_value data and change it to simple file download
  • [GNP-1939] - Rename RAW_VALUE_T and RAW_VALUE_SET_T to *_OLD
  • [GNP-1943] - SNP discovery (no ref. genome) model changes
  • [GNP-1960] - Database patch orchestration script for GnpIS 13.2.
  • [GNP-1961] - Release GnpIS 13.2 modules
  • [GNP-1978] - Check/clean and merge UML schemas
  • [GNP-1979] - Delete bio_type_t tables in osnp and otrans
  • [GNP-2011] - Production: functional validation for GnpIS 13.2
  • [GNP-2021] - Release candidate: functional validation for GnpIS 13.2

Version 13.1 (2013/07/22)

Sub-task

  • [GNP-1532] - Bugs hunt for species restriction
  • [GNP-1533] - Write functional tests using Selenium on Taxon form for species restriction
  • [GNP-1729] - Move to aster and deduplicate data for protocol_T
  • [GNP-1779] - Move to aster and deduplicate data for Software_T
  • [GNP-1780] - Move to aster and deduplicate data for hardware_T
  • [GNP-1781] - Move to aster and deduplicate data for population_T
  • [GNP-1782] - Move to aster and deduplicate data for Defined_Type_T

Technical task

Bug

  • [GNP-1618] - URL prefix not managed in common method to download file
  • [GNP-1629] - Allow an url to take several param
  • [GNP-1800] - Web service API stabilization
  • [GNP-1829] - GnpIS modules are badly translated in English.
  • [GNP-1831] - Improve graphical display in GnpSeq NGS sequence form.
  • [GNP-1832] - Improve Sequence result page to display only unique samples.
  • [GNP-1866] - Bad links toward pool results from marker card.
  • [GNP-1876] - Bad URL when linking a genome variant to its subrun.
  • [GNP-1878] - Update Siregal description.
  • [GNP-1880] - Gwt compilation errors.
  • [GNP-1909] - Structure Matrix doesn't display all data
  • [GNP-1910] - Asso results doesn't always display Number of associated markers
  • [GNP-1911] - Alphabetical order for Structure group instead of alphanumerical
  • [GNP-1919] - Accession passport form does not longer work
  • [GNP-1922] - Struts does not populate correctly nested form beans attributes with non standards setter methods
  • [GNP-1942] - Problem with varray type to copy from prod to dev instance
  • [GNP-1962] - Correct problem with Generic pager on Ephesis
  • [GNP-1988] - Photo description is not displayed.
  • [GNP-1997] - Refresh problem with site list. Even if whe clean ...
  • [GNP-1998] - Export capability from trial card is broken. Simpl...
  • [GNP-2000] - Triger form update method when clicling on any Tab...
  • [GNP-2003] - Can't display marker card with marker PIE017 (marker_id=49982)
  • [GNP-2004] - Bad configuration for genome-chado-functional instances
  • [GNP-2005] - Can't display marker results with Anchored clone n...
  • [GNP-2046] - Bad redirection from sequence result page to analysis and experiment cards.
  • [GNP-2047] - Can't display protocol results tab, when I want to...
  • [GNP-2048] - On ephesis result page, the lotNumber column displ...
  • [GNP-2049] - Bad link generated in SNP card as a cross ref
  • [GNP-2052] - Error with species group when linking from Portal ...

Improvement

  • [GNP-1257] - Bad design on Accession card.
  • [GNP-1718] - Add view on all table without species group and with group_id to load with Talend
  • [GNP-1732] - Add estimator to linkage disequilibrium data.
  • [GNP-1854] - Display exon name and gene name when snp hits an exon
  • [GNP-1863] - Add experimental conditions to association form criteria
  • [GNP-1875] - Association Form optimization
  • [GNP-1879] - Implement functional tests with selenium.
  • [GNP-1914] - Improve Preference drop downs in Siregal.

New Feature

  • [GNP-1808] - Create QQPlot graphs for association results
  • [GNP-1864] - Manhattan Plot for association results

Story

  • [GNP-1717] - Add trial list to accession_card
  • [GNP-1786] - Add sort on columns in the Kinship Table
  • [GNP-1833] - Improve confidentiality views performances
  • [GNP-1853] - Add timeout to gwt compilations.
  • [GNP-1855] - Ephesis form : Header choice helpers
  • [GNP-1871] - Trial tab query helpers : Trial Name autocomplete
  • [GNP-1872] - Trial tab query helpers : Site Liste autoupdate
  • [GNP-1977] - Remove ontology related webservice from GnpIS

Task

  • [GNP-1644] - Database patch orchestration script for GnpIS 12.4.
  • [GNP-1669] - Rename mapping_localisation_t in genome_t.
  • [GNP-1762] - Release GnpIS 12.4
  • [GNP-1817] - Delete SEQUENCES_T table (empty and unused table) in OSNP
  • [GNP-1822] - QQplot form in trait tab of GnpAsso form
  • [GNP-1834] - Fix bugs from continuous integration
  • [GNP-1859] - Pivot table Structure in Panel Card
  • [GNP-1861] - Add MAF column in association results
  • [GNP-1862] - Display number of results of associations
  • [GNP-1869] - Add a link to genomeView browser in genome variant result/form

Version 12.4.1 (2013/05/17)

Bug

  • [GNP-1972] - Error during raw data export

Version 12.4 (2013/04/12)

Sub-task

  • [GNP-815] - Choose genotype caracteristics to export (accession, lot, taxon, etc...).
  • [GNP-1409] - Functional validation for release of Synteny_1_0_3
  • [GNP-1411] - Functional validation for release of GnpAsso_1_0_0
  • [GNP-1670] - Refactor AssignmentDaoImpl.FindCytogeneticQtlsByCriteria() in criteria.
  • [GNP-1714] - Prepare phenotype display order.
  • [GNP-1715] - Improve accession card and form to display phenotype in a given order.

Technical task

Bug

  • [GNP-794] - StudySubject form: no focus on help popup.
  • [GNP-800] - Bug GnpSeq : cross reference from GnpMap to GnpSeq
  • [GNP-1132] - Biomercator export message (more than 1000 elements) is displayed when QTL search by loci returns 0 result
  • [GNP-1134] - Loci search using QTL results (reciprocally) search throws error
  • [GNP-1574] - No data when selecting lots and accession of the same trial
  • [GNP-1592] - Can't open BioMercator.
  • [GNP-1652] - BUG: export in GnpArray.
  • [GNP-1658] - Quick search publique : Absence de marqueurs de group_id = 0
  • [GNP-1707] - Panel redirection goes wrong when id is wrong
  • [GNP-1724] - Gwt variable tab: last term of ontology is partially hidden
  • [GNP-1725] - Select a marker_set and a marker in association form provokes an error
  • [GNP-1733] - Kinship pager is not displayed in GnpAsso panel card.
  • [GNP-1737] - Build error because of no space left on tmp directory.
  • [GNP-1785] - QTL and Map web services fail using ID
  • [GNP-1828] - Load-tree-paths is not executed every night.
  • [GNP-1850] - Can't display project card from Pool set card
  • [GNP-1880] - Gwt compilation errors.
  • [GNP-1882] - Error on siregal accession passport form with wheat species group.
  • [GNP-1883] - Two 'preferences' menus are displayed with enabled species restriction.
  • [GNP-1884] - Remove deprecated class SeqDbXref.
  • [GNP-1885] - On taxon card, the linked object count disapear when species restriction is enabled.
  • [GNP-1886] - Error on trait card.
  • [GNP-1887] - Table header on the sequence results page forwards to the home page.
  • [GNP-1888] - Fake link on Siregal home page.
  • [GNP-1889] - Database error when loading /snp/createSnpSangerSelect action forward
  • [GNP-1890] - The accession form show/hide memory is not working on rc.
  • [GNP-1900] - Error on extract card
  • [GNP-1901] - Error when exporting wheat hybridizations
  • [GNP-1905] - Keep GRC names in uppercase, in left menu.
  • [GNP-1906] - Error on some cards with wheat species group restriction.
  • [GNP-1908] - Error when switching species filter on/off on every GWT applications
  • [GNP-1912] - Genome variant form: the species group restriction does not apply on analysis list
  • [GNP-1915] - Non wheat data are displayed with wheat restriction.

Epic

  • [GNP-397] - Improve the data model to accept accessions outside BRC.
  • [GNP-1560] - Migrate Ephesis experimental data search to GWT
  • [GNP-1650] - Fusion of prepared tables for all modules

Improvement

  • [GNP-399] - Accession card & form: display the phenotypes in a given order.
  • [GNP-1131] - Migrate all Siregal tables in Aster.
  • [GNP-1448] - Accession passport form : don't display criteria without data.
  • [GNP-1612] - Update GnpIS error message to include the case where the data are private
  • [GNP-1621] - Add metaQTL link in QTL card (assignment table)
  • [GNP-1622] - Add metaQTL link in locus card (assignment table)
  • [GNP-1641] - Modify SNPFormAction to load only usefull dropdowns
  • [GNP-1645] - Add metaQTL link in marker card (assignment table)
  • [GNP-1673] - Improve access to run card.
  • [GNP-1706] - Use common version in deployment script.
  • [GNP-1721] - Add a pop up to specify the order ref/var of a genotype
  • [GNP-1722] - Modify association links toward table storing traits information and allele_group in GnpAsso tables.
  • [GNP-1742] - Display samples names alphabetically in GnpSeqNGS experiment card.
  • [GNP-1777] - Add a pop up to variation cards to specify the order REF/VAR
  • [GNP-1801] - Update deployment script to use git repository instead of cvs one.
  • [GNP-1824] - Use parallelization for JUnit tests.

New Feature

  • [GNP-445] - Allow the users to update the status of a SNP to validated.
  • [GNP-1442] - Export deletion bin under BioMercator XML format.
  • [GNP-1671] - Add CNIL information on GnpIS.
  • [GNP-1704] - Allow download of .CEL file linked to hybridization
  • [GNP-1893] - Include JIRA issue collector tool.

Story

  • [GNP-1607] - Merge PROTOCOL_DEFAULT & PROTOCOL_DESCRIPTION with PROTOCOL
  • [GNP-1647] - Move specific and single tables of each module
  • [GNP-1649] - Prepare BIO_TYPE_T for fusion
  • [GNP-1723] - Create RELEASE table.
  • [GNP-1727] - UML/SQL : TrialSet + Varietal List and Variable list direct link in database
  • [GNP-1728] - Interface : trial Set param in existing forms
  • [GNP-1788] - Test species restriction performance using SNP_T as partitioned table
  • [GNP-1802] - Add variant simple search (GWT interface) in left menu
  • [GNP-1803] - Reorganize the sidebar of GnpSNP
  • [GNP-1826] - Add variation pattern in genome variant result page

Task

  • [GNP-1386] - Merge experiment_file_t and analysis_output_file_t with data_file_t in GnpSeqNGS.
  • [GNP-1646] - Prepare DEFINED_TYPE for fusion
  • [GNP-1651] - Fusion DATABASE_SCHEMAS
  • [GNP-1653] - Release GnpIS 12.3
  • [GNP-1702] - Create Sequences query form for GnpSeq.
  • [GNP-1807] - Create bio_type_t tuples for genotyping

Version 12.3 (2012/10/09)

Sub-task

  • [GNP-808] - Add trial information in studysubject export and previsualisation.
  • [GNP-815] - Choose genotype caracteristics to export (accession, lot, taxon, etc...).
  • [GNP-1409] - Functional validation for release of Synteny_1_0_3
  • [GNP-1411] - Functional validation for release of GnpAsso_1_0_0
  • [GNP-1509] - Data model : non CRB accession
  • [GNP-1522] - Update BioMercator XML to export deletion bin.
  • [GNP-1533] - Write functional tests using Selenium on Taxon form for species restriction
  • [GNP-1670] - Refactor AssignmentDaoImpl.FindCytogeneticQtlsByCriteria() in criteria.

Technical task

Bug

  • [GNP-794] - StudySubject form: no focus on help popup.
  • [GNP-1056] - Fix wildcard accesion search
  • [GNP-1132] - Biomercator export message (more than 1000 elements) is displayed when QTL search by loci returns 0 result
  • [GNP-1134] - Loci search using QTL results (reciprocally) search throws error
  • [GNP-1592] - Can't open BioMercator.
  • [GNP-1632] - Manage an empty start/end position field in variant export

Epic

  • [GNP-397] - Improve the data model to accept accessions outside BRC.
  • [GNP-1560] - Migrate Ephesis experimental data search to GWT
  • [GNP-1623] - Migrate Accession search form into GWT.

Improvement

  • [GNP-694] - Update nullable constraints for Taxon_t.
  • [GNP-837] - Handle timeout for long queries in search by loci.
  • [GNP-994] - Update common Contact card and general display to avoid data deduplication.
  • [GNP-1122] - On taxon result page, replace term 'object' by something more biological.
  • [GNP-1204] - Memory leaks hunt
  • [GNP-1354] - Improve taxon associated information.
  • [GNP-1446] - Improve Accession search.
  • [GNP-1447] - Add a drop down list for collecting countries.
  • [GNP-1448] - Simplify accession passport form.
  • [GNP-1519] - Improve accession search form.
  • [GNP-1612] - Update GnpIS error message to include the case where the data are private
  • [GNP-1621] - Add metaQTL link in QTL card (assignment table)
  • [GNP-1622] - Add metaQTL link in locus card (assignment table)
  • [GNP-1624] - Add snp effect in criterias of snp form
  • [GNP-1641] - Modify SNPFormAction to load only usefull dropdowns
  • [GNP-1645] - Add metaQTL link in marker card (assignment table)
  • [GNP-1647] - Move specific and single tables of each module

New Feature

  • [GNP-1123] - Taxon form: add autocompletion on scientific name.
  • [GNP-1165] - Global Taxon form : add restriction to scientific object (acessions, snps, ...)
  • [GNP-1395] - Preparation of GnpMap package and MetaQTL insertion tools for distribution.
  • [GNP-1442] - Export deletion bin under BioMercator XML format.
  • [GNP-1525] - Update UML model and DDL to store marker location onto chromosomes

Story

  • [GNP-1567] - Rationalize and unify version system

Task

  • [GNP-310] - Name the child parent relation of StudySubject.
  • [GNP-355] - Rename TrialSearchCriteria.trialAccessions to TrialSearchCriteria.trialAccessionsNames.
  • [GNP-905] - Merge all UML files.
  • [GNP-1057] - Refactor phenotyping campain.
  • [GNP-1646] - Prepare DEFINED_TYPE for fusion
  • [GNP-1649] - Prepare BIO_TYPE_T for fusion
  • [GNP-1650] - Fusion of prepared tables for all modules
  • [GNP-1651] - Fusion DATABASE_SCHEMAS