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allow for multiple external database specs #89

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798b8e2
allow for multiple external database specs
jbrestel Sep 19, 2025
eea9a5a
fix undo for multiple extdb rls
jbrestel Sep 23, 2025
71219c7
Merge branch 'master' into eda-study-extdbrls
jbrestel Dec 1, 2025
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62 changes: 37 additions & 25 deletions Load/lib/perl/InstallEdaStudyFromArtifacts.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@ use JSON qw( decode_json );
use File::Copy;
use ApiCommonData::Load::Psql;

use Data::Dumper;

my $SQLLDR_STREAM_SIZE = 512000;
my $SQLLDR_ROWS = 5000;
my $SQLLDR_BINDSIZE = 2048000;
Expand Down Expand Up @@ -83,7 +85,7 @@ sub isDryRun {defined $_[0]->{DRYRUN} ? 1 : 0 }
# these 2 are needed for installing and uninstalling internal datasets
# because we are running batches in nextflow, we do not keep the original install.json
sub skipPreexistingTables { defined $_[0]->{SKIP_PREEXISTING_TABLES} ? 1 : 0 }
sub getExternalDatabaseName { $_[0]->{EXTERNAL_DATABASE_NAME} }
sub getExternalDatabaseRlsSpecs { $_[0]->{EXTERNAL_DATABASE_RLS_SPECS} || [] }


sub getConfigsArrayFromInstallJsonFile {
Expand Down Expand Up @@ -114,70 +116,77 @@ sub getInstallJsonFile {
sub uninstallDataFromExternalDatabase {
my ($self) = @_;



my $dbh = $self->getDbh();
my $schema = $self->getDbSchema();

my $externalDatabaseName = $self->getExternalDatabaseName();
my $externalDatabaseRlsSpecs = $self->getExternalDatabaseRlsSpecs();

print STDERR "Uninstall Study with extDbName=$externalDatabaseName\n";
my @extDbRlsIds;

my $externalDatabaseReleaseIdQuery = "select r.external_database_release_id
from sres.externaldatabase d
join sres.externaldatabaserelease r
on d.external_database_id = r.external_database_id
where d.name = ?";
where d.name = ?
and r.version like ?";

my $sh_db = $dbh->prepare($externalDatabaseReleaseIdQuery);
$sh_db->execute($externalDatabaseName);

my %extDbRlsIds;
while(my ($extDbRlsId) = $sh_db->fetchrow_array()) {
$extDbRlsIds{$extDbRlsId} = 1;
}
$sh_db->finish();
my @uniqueExtDbRlsIds = keys(%extDbRlsIds);
unless(scalar(@uniqueExtDbRlsIds) == 1) {
die "Must be one externaldatabaserelease for $externalDatabaseName";
foreach my $spec (@$externalDatabaseRlsSpecs) {
my ($extDbName, $extDbVer) = split(/\|/, $spec);

print STDERR "EXTDBNAME=$extDbName\n";
print STDERR "EXTDBVER=$extDbVer\n";

$sh_db->execute($extDbName, $extDbVer);

while(my ($extDbRlsId) = $sh_db->fetchrow_array()) {
push @extDbRlsIds, $extDbRlsId;
}
$sh_db->finish();
}
my $externalDatabaseReleaseId = $uniqueExtDbRlsIds[0];

my $studyIdQuery = "select s.study_id from eda.study s where s.external_database_release_id = ?";
my $placeholders = join(",", map { "?" } @extDbRlsIds);
my $studyIdQuery = "select s.study_id
from eda.study s inner join eda.studyexternaldatabaserelease ser
on s.study_id = ser.study_id
where ser.external_database_release_id in ($placeholders)";

my $sh_study = $dbh->prepare($studyIdQuery);
$sh_study->execute($externalDatabaseReleaseId);
$sh_study->execute(@extDbRlsIds);

my %studyIds;
while(my ($studyId) = $sh_study->fetchrow_array()) {
print STDERR "STUDY_ID=$studyId\n";

$studyIds{$studyId} = 1;
}
$sh_study->finish();

my @uniqueStudyIds = keys(%studyIds);

if(scalar(@uniqueStudyIds) == 0) {
print STDERR "No studyId found for externaldatabasename $externalDatabaseName... nothing to do\n";
print STDERR "No studyId found for externaldatabasename ... nothing to do\n";
return;
}

unless(scalar(@uniqueStudyIds) == 1) {
die "Must be one study id for externaldatabasereleaseid=$externalDatabaseReleaseId";
die "Must be one study id for externaldatabasereleaseid";
}

my $studyId = $uniqueStudyIds[0];

my $viewsQuery = $self->getQueryForTableOrViewNames("views", $schema);
my $sh_view = $dbh->prepare($viewsQuery);
$sh_view->execute($externalDatabaseReleaseId);
$sh_view->execute($studyId);
while(my ($viewName) = $sh_view->fetchrow_array()) {
$self->dropTableOrView('view', "${schema}.${viewName}");
}
$sh_view->finish();

my $tablesQuery = $self->getQueryForTableOrViewNames("tables", $schema);
my $sh_table = $dbh->prepare($tablesQuery);
$sh_table->execute($externalDatabaseReleaseId);
$sh_table->execute($studyId);
my $tableCount;

while(my ($tableName) = $sh_table->fetchrow_array()) {
Expand All @@ -186,16 +195,19 @@ where d.name = ?";
}
$sh_table->finish();

die "No artifact tables found for externaldatabase=$externalDatabaseName" unless($tableCount);
print STDERR "No artifact tables found. " unless($tableCount);

my $delEntityTypeGraph = " delete from $schema.entitytypegraph where study_id = $studyId";
print STDERR "RUNNING SQL: $delEntityTypeGraph\n\n";
$dbh->do($delEntityTypeGraph) || die "Failed running sql: $delEntityTypeGraph\n" unless $self->isDryRun();

my $delStudyExternalDatabaseRelease = " delete from $schema.studyexternaldatabaserelease where study_id = $studyId";
print STDERR "RUNNING SQL: $delStudyExternalDatabaseRelease\n\n";
$dbh->do($delStudyExternalDatabaseRelease) || die "Failed running sql: $delEntityTypeGraph\n" unless $self->isDryRun();

my $delStudy = "delete from $schema.study where study_id = $studyId";
print STDERR "RUNNING SQL: $delStudy\n\n";
$dbh->do($delStudy) || die "Failed running sql: $delStudy\n" unless $self->isDryRun();

}

sub getQueryForTableOrViewNames {
Expand All @@ -207,7 +219,7 @@ join ${schema}.entitytypegraph etg
on s.study_id = etg.study_id
join information_schema.${tablesOrViews} t
on lower(t.table_name) like '%' || lower(s.internal_abbrev) || '_' || lower(etg.internal_abbrev)
where s.external_database_release_id = ?
where s.study_id = ?
and lower(t.table_schema) = lower('$schema') ";
}

Expand Down
78 changes: 39 additions & 39 deletions Load/plugin/perl/InsertEdaStudyFromArtifacts.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,7 @@ use strict;

use GUS::Model::EDA::Study;
use GUS::Model::EDA::EntityTypeGraph;

use ApiCommonData::Load::InstallEdaStudyFromArtifacts;
use GUS::Model::EDA::StudyExternalDatabaseRelease;

use Data::Dumper;

Expand Down Expand Up @@ -49,7 +48,7 @@ my $argsDeclaration =
descr => 'External Database Spec for this study',
reqd => 1,
constraintFunc => undef,
isList => 0, }),
isList => 1, }),

];

Expand Down Expand Up @@ -84,6 +83,7 @@ sub run {
my ($self) = @_;

my $extDbRlsSpec = $self->getArg('extDbRlsSpec');

my $inputDir = $self->getArg("inputDirectory");
my $outputDir = $self->getArg("outputDirectory");
my $gusConfigFile = $self->getArg("gusConfigFile");
Expand All @@ -92,34 +92,44 @@ sub run {
$self->userError("Output Directory already Exists");
}

my $extDbRlsId = $self->getExtDbRlsId($extDbRlsSpec);
#my $extDbRlsId = $self->getExtDbRlsId($extDbRlsSpec);
my $installer = $self->makeInstaller($inputDir, $outputDir, $gusConfigFile, $extDbRlsSpec);

my $installJsonFile = $installer->getInstallJsonFile($inputDir);
my $configsArray = $installer->getConfigsArrayFromInstallJsonFile($installJsonFile);

my ($studyConfig) = grep { $_->{type} eq 'table' && $_->{name} eq 'study' } @$configsArray;
my $studyHash = $self->preexistingTable($studyConfig, 'study.cache');

$studyHash->{'external_database_release_id'} = $extDbRlsId;
my $studyArray = $self->preexistingTable($studyConfig, 'study.cache');
if(scalar @$studyArray != 1) {
$self->error("study.cache must contain one row of data");
}

my $study = GUS::Model::EDA::Study->new($studyHash);
my $study = GUS::Model::EDA::Study->new($studyArray->[0]);

my ($entityTypeGraphConfig) = grep { $_->{type} eq 'table' && $_->{name} eq 'entitytypegraph' } @$configsArray;
my $entityTypeGraphArray = $self->preexistingTable($entityTypeGraphConfig, 'entitytypegraph.cache');

foreach my $entityTypeGraphHash (@$entityTypeGraphArray) {
my $entityTypeGraph = GUS::Model::EDA::EntityTypeGraph->new($entityTypeGraphHash);
$entityTypeGraph->setParent($study);
}

my $entityTypeGraphHash = $self->preexistingTable($entityTypeGraphConfig, 'entitytypegraph.cache');
my $entityTypeGraph = GUS::Model::EDA::EntityTypeGraph->new($entityTypeGraphHash);
foreach my $spec (@{$extDbRlsSpec}) {
my $extDbRlsId = $self->getExtDbRlsId($spec);

my $studyExtDbRls = GUS::Model::EDA::StudyExternalDatabaseRelease->new({external_database_release_id => $extDbRlsId});
$studyExtDbRls->setParent($study);
}

$entityTypeGraph->setParent($study);
$entityTypeGraph->submit();
$study->submit();

if($self->getArg('commit')) {
# now install the artifacts
$installer->installData();
}
return("Loaded an EDA Study for external_database_release_id = $extDbRlsId");


return("Loaded an EDA Study for ");
}

sub preexistingTable {
Expand All @@ -129,30 +139,24 @@ sub preexistingTable {

open(FILE, $cacheFileFullPath) or $self->error("Could not open file $cacheFileFullPath for reading: $!");

my @data = ();

my $count;
my $rv = [];
while(<FILE>) {
chomp;
my @line = split(/\t/, $_);
@data = @line;
$count++;
}

$self->userError("cache file $cacheFile must contain exactly one row") if($count != 1);

my $rv = {};
my $row = {};
foreach my $field (@{$config->{fields}}) {
next if($field->{macro});

foreach my $field (@{$config->{fields}}) {
next if($field->{macro});
my $key = $field->{name};
my $index = $field->{cacheFileIndex};
my $value = $line[$index];

my $key = $field->{name};
my $index = $field->{cacheFileIndex};
my $value = $data[$index];
$rv->{$key} = $value;
$row->{$key} = $value;
}
push @$rv, $row;
}


close FILE;
return $rv;
}
Expand All @@ -166,8 +170,6 @@ sub makeInstaller {

die "gus.confg $gusConfigFile does not exist" unless -e $gusConfigFile;

my ($extDbName, $extDbVersion) = split(/\|/, $extDbRlsSpec);

my $gusconfig = GUS::Supported::GusConfig->new($gusConfigFile);
my ($host, $port, $dbname);
my $dsn = $gusconfig->getDbiDsn();
Expand Down Expand Up @@ -215,7 +217,7 @@ sub makeInstaller {
'DATA_FILES' => $outputDir,
'INPUT_DIR' => $inputDir,
'SKIP_PREEXISTING_TABLES' => 1, # we are loading these rows here not in the VDI artifact loader
'EXTERNAL_DATABASE_NAME' => $extDbName, # This is needed for Undo only
'EXTERNAL_DATABASE_RLS_SPECS' => $extDbRlsSpec, # This is needed for Undo only
);

return ApiCommonData::Load::InstallEdaStudyFromArtifacts->new(\%requiredVars);
Expand All @@ -229,10 +231,12 @@ sub undoTables {
sub undoPreprocess {
my($self, $dbh, $rowAlgInvocationList) = @_;

my $gusConfigFile = $self->getAlgorithmParam($dbh,$rowAlgInvocationList,'gusConfigFile');
my $gusConfigFile = $self->getAlgorithmParam($dbh,$rowAlgInvocationList,'gusConfigFile')->[0];


my $extDbRlsSpec = $self->getAlgorithmParam($dbh,$rowAlgInvocationList,'extDbRlsSpec');

unless(-e $gusConfigFile && $extDbRlsSpec) {
unless(-e $gusConfigFile && scalar @$extDbRlsSpec > 0) {
$self->error("Required algorithm param missing OR does not exist gusConfigFile=$gusConfigFile, extDbRlsSpec=$extDbRlsSpec");
}

Expand Down Expand Up @@ -263,11 +267,7 @@ sub getAlgorithmParam {

my @values = keys %paramValues;

if(scalar keys %paramValues != 1) {
$self->error("Odd looking param values for $paramKey: \n" . Dumper(\%paramValues));
}

return $values[0];
return \@values;
}


Expand Down