Release notes
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Available versions
Version 19.3 (2021/07/05)
Bug
- [GNP-5745] - Fix display of name field for DataDiscovery
- [GNP-5749] - 404 error for accessions with puid
Story
- [GNP-5687] - Send SSR forward/reverse sequences to Sophie Bouchet
Task
- [GNP-4127] - Create Symphonie -> GnpIS data flow
- [GNP-4563] - Add new gene annotation (v3.1) in Populus v3 JBrowse
- [GNP-4758] - Insert PlantaExp Abies alba data (phenotypes + rg)
- [GNP-4992] - Update manage_release script to use develop branch instead of release branch (Erik part)
- [GNP-5318] - Merge WIPO into Wheat CO
- [GNP-5546] - Reindexation of Pea duplicated datasets
- [GNP-5563] - Implement BrAPI ET/L using new workflow management system
- [GNP-5582] - Insert PlantaExp Abies bornmuelleriana data (phenotypes + rg)
- [GNP-5583] - Insert PlantaExp Abies nordmanniana data (phenotypes + rg)
- [GNP-5584] - Insert PlantaExp Abies cephalonica data (phenotypes + rg)
- [GNP-5612] - Insert PlantaExp Pinus nigra data (phenotypes + rg)
- [GNP-5632] - Index updated EVA endpoint and reindex NIB/Terraref/WUR
- [GNP-5659] - Insert PlantaComp trials metadata in GnpIS
- [GNP-5676] - Index Ensembl Plants release 45 in WheatIS
- [GNP-5713] - Insert GenTree leaf traits in GnpIS
- [GNP-5714] - Update GenTree Quercus data from Pierroton in GnpIS
- [GNP-5724] - Update TABW280K track in jbrowse iwgsc
- [GNP-5725] - Tester avec un BAM Wheatomics dans le jbrowse iwgsc la track privée
- [GNP-5726] - Check mapping of gene catalog on IWGSC RefSeq gene names
- [GNP-5737] - Insert elm collection (RG) from CRGF
- [GNP-5751] - Add Pinus pinaster test dataset in Forest BRC
- [GNP-5758] - Create a job Jenkins to watch any modifications on team-documentation gitlab project
- [GNP-5765] - Configure dependabot-script for checking dependencies in our project
- [GNP-5767] - Add Cupressus sempervirens test dataset in Forest BRC
- [GNP-5768] - Add Sorbus domestica test dataset in Forest BRC
- [GNP-5770] - Index Ensembl Plants release 46 in WheatIS
- [GNP-5786] - Update data in RARe portal
- [GNP-5791] - Stress tests for WheatIS application
- [GNP-5799] - Open GenTree Metadata
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