Load the "WebReady" tables #50
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…le_CompoundAttributes to createTable_PathwayReactions, 3) move createTable_PathwayNodes after createTable_PathwayReactions, and 4) temporarily comment out createTable_GroupDomainAttribute for testing
…w into denorm-tables
jbrestel
commented
Jun 24, 2025
| my $taxonId = $self->getOrganismInfo($test, $organismAbbrev, $gusConfigFile)->getTaxonId(); | ||
| $args = "--mode $mode --psqlDirPath $psqlDirPath --tableName $tableName --schema $schema --projectId $projectId --organismAbbrev $organismAbbrev --taxonId $taxonId"; | ||
| } else { | ||
| $args = "--mode $mode --psqlDirPath $psqlDirPath --tableName $tableName --schema $schema --projectId $projectId --taxonId 1"; |
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Why is the "taxonId" hard coded to 1 here? that may bite us
…_product in previous tunning table
…criptattributes will make the gene_product column
* Adding previousGroups file to persistent cache * Busco ApiCommonWorkflow (#48) * initial dev for busco in reflow * add busco and mapper calls * fix typo * fix syntax errors * debug of $clusterServer * fix typo * debug lineage_dataset_map.txt * outputFilePrefix is not required * max retries for nextflow job --------- Co-authored-by: Sufen Hu <[email protected]> * Adding Orthomcl Dependent graph * Creating new ortho web ready tables. Loading ortho group blast values for orthomcl ec prediction * Readding orthomcl ec prediction * Adding previousGroups file to persistent cache * Busco ApiCommonWorkflow (#48) * initial dev for busco in reflow * add busco and mapper calls * fix typo * fix syntax errors * debug of $clusterServer * fix typo * debug lineage_dataset_map.txt * outputFilePrefix is not required * max retries for nextflow job --------- Co-authored-by: Sufen Hu <[email protected]> * Adding Orthomcl Dependent graph * Creating new ortho web ready tables. Loading ortho group blast values for orthomcl ec prediction * Readding orthomcl ec prediction * fix a typo * Removing duplicate predictEcNumbers step * Resolving predictEc dependency name error * Changing order for dependencies * add the -C option to tar to specify the target directory when extracting files * Resolving path to comparative table for create * Adding comparative tables to orthomcl peripheral workflow * debug $outputDir * Removing duplicate EcNumberGenus step * Adding new argument for insertOrthoGroupBlastValue * Changing path for fifo file * Changing path for fifo file to absolute path * Changing dependency for Phyletic Pattern * Resolving dependency issue for webready tables * Removing checkForCompleted file and merging OrthoMCLDependent and orthomclDerivedEC * Add additional output file parameter for predictEcNumbers * fix typo * Primary key functionality * add gusConfigFile * fix gusConfigFile * debug $inputFile * add gusConfigFile * add paramValue gusConfigFile * fix syntax error * fix syntax error * add subgraph MakeComparativeWebTables * Removing unneeded gus config argument * Removing unneeded gusConfig argument lines * Removing unneeded instances of gus config file * Removing more unneeded instances of gus config file * Removing more unneeded instances of gus config file --------- Co-authored-by: Richard Demko <[email protected]> Co-authored-by: Sufen Hu <[email protected]>
* fix depends for webtables for all org specific steps * add GeneProduct * add splice site transcript table and insert rows using perl script * wrong Step class for some ortho webready tables * Add step for PathwayEc table * Added steps for TranscriptEC and TranscriptPathway. Removed dependent steps * add junction tables (wip) * Workflow step class to run LoadDenormalizedTable plugin * Add step to load TranscriptPathway * wip; move some orthomcl webready tables * Add some commentary about the purpose of this step class * Clean up and remove tables that will be loaded in the comparative graph * add intronsupport level * Step to create empty PathwaysGeneTable * Step to load PathwaysGeneTable --------- Co-authored-by: Kathryn Crouch <[email protected]>
…anismAbbrev}_*" to fix error: step XXXX_MakeChildWebTables depends on step XXXX_MakeChildWebTables which is not above it in the XML file
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