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apicommonmodel's Introduction

ApiCommonModel

Extends EbrModelCommon.

It includes xml files with basic data types definitions, and their structured searches, for genomic sites. Api stands for ‘Apicomplexan’. These are the first organisms included in our websites when they were first time publicly released as ApiDB BRC (Bioinformatics Resource Center), back in 2002.

Dependencies

  • yarn / npm / ant
  • WEBAPP_PROP_FILE file (file with one property for the webapp target directory) webappTargetDir=BLAH
  • environment variables for GUS_HOME and PROJECT_HOME
  • Internal Dependencies
    • WDK, CBIL, ReFlow, EbrcModelCommon

Installation instructions.

  • bld ApiCommonModel
  • changes to wdk model xml files requires reload of tomcat instance

Operating instructions.

  • Installation is successful if you can run “wdkXml -model $MODEL_NAME” without error

Manifest

Model/bin
scripts referenced in tuning manager config and other tuning scripts (portallinker); scripts for creating jbrowse configuration
Model/lib/dst
dataset template files
Model/lib/jbrowse
jbrowse configuration; common and organism specific tracks
Model/lib/perl
utils for datasets and jbrowse
Model/lib/wdk
xml files which define wdk records, searches, params.
Model/lib/xml
tuning manager configuration, jbrowse queries, global dataset presenter xml
Model/src/main/java/org/apidb/apicommon/model/datasetInjector
java code per data class for managing template injection
Model/src/main/java/org/apidb/apicommon/model/report
reporters referenced in wdk xml
Model/src/main/java/org/apidb/apicommon/model/userdataset
Type Handlers for User Datasets

apicommonmodel's People

Contributors

jbrestel avatar haimingw-git avatar kathryncrouch avatar brunkb01 avatar aurreco-uga avatar ryanrdoherty avatar steve-fischer-200 avatar markhick avatar swfeltz avatar iodice avatar dmfalke avatar linxu123-git avatar mheiges avatar edliaw avatar fungiecfg14 avatar sufenhu avatar d-callan avatar sybah2 avatar asizemore avatar jtlong3rd avatar jernestmyers avatar axl-bernal avatar wbazant avatar tsucheta avatar foxcapades avatar mvnural avatar dmgaldi avatar rossmadden-glasgow avatar bobular avatar jaycolin avatar

Stargazers

Bindu Gajria avatar

Watchers

 avatar  avatar James Cloos avatar  avatar  avatar Daniel Lawson avatar Daniel Beiting avatar  avatar  avatar Samuel Rund avatar Mikkel Christensen avatar jie zheng avatar Stuart Brown avatar Robert Wieck avatar Omar Harb avatar David Starns avatar  avatar  avatar  avatar DK avatar Brett avatar Matthieu Barba avatar  avatar  avatar  avatar  avatar

apicommonmodel's Issues

Fix large dataset param performance

(this issue was triggered by the connection timeout in VB on July 25-26 , seems the cause was a user running geneId slow searches, each trying to create a new cache table and some got stuck in oracle)

This issue has been co-opted from the description below to instead rework how dataset param data is imported into a WDK cache table. Reading data over the DB link as a subquery has been shown to be consistently slow and exponentially slower as data size grows. Thus, maybe we can get a speed-up if we create a temp table in appDb containing the dataset_values rows for a particular dataset and use, as the dataset param's internal value, a select * from the_tmp_table. This would not be hard to set up (would just need to build the table when asked for the dataset param's internal value), but we will have to add a mechanism to tear the table down when complete. Steve suggested reusing tables (one per dataset_id) but this would require additional concurrency logic akin to the WDK cache. Or we could just let them sit out there and add their deletion to the wdkCache clearing logic.

First step, however is to confirm that ID query's ID sql is significantly faster when reading from a tmp table in appDb than it is when reading from dataset_values over the db link AND make sure that create table as (select from dataset_values) is not so slow that it offsets any performance gains. In short, check to make sure creating a tmp table from select over db_link + reading from tmp table is significantly faster than selecting directly over db_link.

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