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

• [GNP-3556] - UML TODO
• [GNP-3585] - TODO

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

• [GNP-3644] - Service Layer And model Updates
• [GNP-3677] - RepetDB conf
• [GNP-3702] - Rename level to full uper case
• [GNP-3750] - TODO Web interface fixes
• [GNP-3751] - User friendly and perf
• [GNP-3760] - ressources génétiques
• [GNP-3785] - Pheno
• [GNP-3786] - geno

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

• [GNP-3481] - Jbrowse to index
• [GNP-3482] - Evaluate KarmaWeb as an alternative to shell/SQL
• [GNP-3554] - Variable parsing
• [GNP-3557] - Integrate data 2010

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

• [GNP-1946] - Functional tests environment setup
• [GNP-3488] - Hotfix 14.3.1

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

• [GNP-3175] - Hotfix 14.2.1

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

• [GNP-2282] - Ora2Pg evaluation
• [GNP-2288] - Evaluation of datamart creation

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

• [GNP-1656] - Display snp validation status.
• [GNP-1958] - Hot Fix release

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

• [GNP-1696] - Query parameter list.

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

• [GNP-1566] - Export results to excel file
• [GNP-1696] - Query parameter list.

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