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release_notes_on_web_application

Release notes on web application


  • beta 0.6.1 (Decembre 2018)
    • Minor changes:
      • [Improvement] : speed up initial request to list organisms and load taxo tree : initialy took ~10-12 seconds for 5000 genomes, now down to 5-6 seconds (2X improvement)
      • [Feature] : new script PrevalenceCDSsInOrthologsSynteny.java -byPairwiseComparisons : Prevalence CDSs In Orthologs and Synteny ; distribution of the number of pairwise comparison by the % of CDS in genome in ortho BDBH or synteny relationship
      • [Bug] : fixed bug missing data when displaying genomes with 2 elements somtimes : the lower bound pair was not inserted into getCumulatedLongWithinRangesAsIndividual as it should in the method convertSetLongToSortedRange_PositiveSingletonAsIndividualThenPositiveRangeAsPairThenNegativeSingletonAsIndividualThenNegativeRangeAsPair
      • [Bug] : fixed bug calculating pb distance between features when a CDS start had a start of 0pb relative to ORI
      • [Bug] : the use of the methodUtilitiesMethodsServer.excecuteCommandAndParseMultipleRowRS could cause “limit overhead problems” if the number of elements parsed was big. Bypass of this method.
      • [Improvement] : core / disp genome functionality : increase the limit for the maximum number of genomes in group plus minus combined to 300
      • [Bug] : fixed bug display was hung : on the genomic organisation tab when searching for a CDS within a synteny, the display could hung because the mask would stay forever and do not detect that the multiple request came back from the server
  • beta 0.6 (September 2018)
    • Major changes :
      • [Improvement] : revamped search tab : easier navigation, management of compared organisms, functionality for core genome improved
      • [Improvement] : suppport for organisms with a lot of contigs by speeding up display in the ortholog table view or the genomic context view. For a genome with ~500 contigs, it now takes ~1.5 seconds (it previsouly took ~5 minutes, a 85X improvement). Remark : transfering a large number of parameters (~300000) to postgresql was causing a 5 minutes long delay whereas the query itself just took a few miliseconds.
      • [Improvement] : suppport for organisms with a lot of contigs by allowing and speeding up searching for CDS in multiple contigs ; querying CDSs that match a specific genomic locations or qualifier (product, molecular fonction, lenght protein, etc…) filter when searching within ~500 contigs now takes ~300-450 milliseconds (it previsouly took ~4-5 seconds, a ~10-15X improvement) ; querying CDSs that match a specific presence / absence homologs filter when searching within ~500 contigs now takes ~2.4 seconds (it previsouly took 50 seconds, a ~20X improvement)
      • [Improvement] : Added management of result organisms (such as featuring, sorting, etc…) directly in the results tab, option “Result quick Navigation”
      • [Improvement] : To save disk space, tables related to syntenies and orthologs (alignment_params, alignments, alignment_pairs) have non redundant / mirror data.
    • Minor changes :
      • [Improvement] :updated home page to display the links to the multiple Insyght public website available
      • [Bug] : gene name was not displayed properly on canvas
      • [Feature] : improved search for organisms and taxons : return a close best match if no exact match are found
      • [Improvement] : web app is now compatible with database schema v3 (see release notes on database schema for more details)
      • [Improvement] : migration to GWT 2.8.2 → GWT2.8 + junit.jar + validation-api-1.0.0.GA.jar in war/WEB-INF ; fixed Error at compile time The template code generator cannot guarantee HTML-safety of the template
      • [Bug] : fixed bug : the full list of organism didn't come back after (1) searching for a particular organism, (2) adding it to the featured list, (3) closing the ManageListComparedOrganisms, (4) re-opening ManageListComparedOrganisms and adding the full list of organisms again by clearing the filter
      • [Improvement] : the web app doesn't display organisms if their computation process (comparison with all other species) is not finished
      • [Improvement] : update link to Ensemblgenome : http://ensemblgenomes.org/id/
      • [Bug] : fixed bug in handling taxonomic node when restricting list of compared organisms
      • [Improvement] : automatic display of selected gene set when adding genes to it from core/disp genome browser
      • [Bug] : fixed bug in moving compared organisms up and down when managing those lists
      • [Bug] : fixed bug when navigating orthologs table to see the last compared organisms using the next result button : IndexOutOfBoundsException due to scrollQuickNavToEnsureVisible
      • [Bug] : fixed bug in managing list compared organism : main list was not listing all the non features compared organisms if a filter by the user on a taxonomic node was still active
      • [Bug] : fixed bug not able to display genomic location if organisms had no strain information
      • [Improvement] : new functionality to set compared organism as reference (mirror view) directly from context specific menu while browsing results
      • [Improvement] : new functionality to export list of CDS sequence from compared organism as fasta
      • [Improvement] : url Api &listReferenceOrigamiGeneSetIds= empty if dealing with whole organism
      • [Improvement] : Search for organism or taxonomic group in the taxonomix browser for the functionality core / dispensable set of CDSs for reference node
      • [Bug] : fixed bug wrong processing of encapsulated CDSs when opening synteny in mirror view (negative alignment_id)
      • [Bug] : Synteny info about query subject start and stop were mixed up
      • [Bug] : bug automatic setting of score scope to whole genome if the gene set size was 1
      • [Bug] : fixed bug when contextual menu → selected symbol → list reference genes : error unrecognized case if the synteny number was negative
      • [Bug] : fixed Bug Export sequence from search tab → Reference CDSs → Build your reference gene set : All compared CDSs in the selected gene set was sometimes available
      • [Bug] : fixed bug selected ref organisms or nodes was not taken into account when clicking on the menu Reference CDSs
      • [Bug] : fixed bug when listing gene from core genome and searching them using filters, nothing was happening
      • [Improvement] : SharedAppParams MAX_NUMBER_IN_GENE_SET_ALLOWED is now 20000 instead of 200 ; MAX_NUMBER_FEATURED_ORGA_ALLOWED is now 20000 instead of 300 ; public static final int MAX_NUMBER_EXCLUDED_ORGA_ALLOWED is now 20000 instead of 1000
      • [Improvement] : prevent interacting with dispplay when data takes a long time loading
      • [Bug] : fixed bug transitioning from “Build your reference gene set” to “Whole proteome or Core / dispensable set of CDSs” showed the wrong display
      • [Bug] : fixed bug not to allow searching for Presence orthologs in group + and absence in group - while browsing core/disp genome : This functionality is disabled, it needs at least 1 organism in group + that is not the reference or 1 organism in group -
      • [Improvement] : set a compared organism as the reference organism (mirror view) from the ortholog table view or the genomic context view
      • [Improvement] : modified method getGeneNameLocusTagStrandWithGeneId to take advantage of newer database schema with direct access to the locus tag field (UtilitiesMethodsServer.isDatabaseGenesElementsGenomeAssemblyConvenience(conn))
      • [Bug] : fixed problem displaying appropriate message when no organism are available in the database
      • [Improvement] : faster intial display of browser for core / disp genome with lot of organisms as root : method setDefaultRefGenomeWithSelectedRefTaxoNode in SearchViewImpl. From ~1.6 seconds to ~120 milliseconds for ~300 orga (~ 14 times faster) ; From ~3.1 minutes to ~0.6 seconds for ~2600 orga (~ 330 times faster)
      • [Improvement] : getting the Reference Genes Most Represented among a set of 200 organisms took ~1.5 minutes, now take ~10 seconds (use of table aligment_params + alignments instead of homologies) ⇒ 9X faster
      • [Feature] : set a maximum number of genomes to be compared for presence / absence homology : 100 as above 190 can cause GC overhead limit exceeded
release_notes_on_web_application.txt · Last modified: 2018/12/03 13:41 by thomas.lacroix@inra.fr