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[Moose] ConfigOB - grepping the boolean config settings using ConfigOB #500

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merged 5 commits into from
Oct 18, 2019
Merged

[Moose] ConfigOB - grepping the boolean config settings using ConfigOB #500

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616213e
querying boolean config settings using ConfigOB instead of DBI::getCo…
cmadjar Oct 8, 2019
307a996
corrected typo
cmadjar Oct 8, 2019
952ee31
Nicolas's feedback
cmadjar Oct 15, 2019
80f6f50
fix MRIProcessingUtility.pm as suggested by Nicolas
cmadjar Oct 15, 2019
431a698
renamed getboolean to getBooleanRef
cmadjar Oct 16, 2019
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8 changes: 1 addition & 7 deletions batch_uploads_imageuploader.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -153,13 +153,7 @@ =head2 Methods
my $data_dir = $configOB->getDataDirPath();
my $mail_user = $configOB->getMailUser();
my $bin_dir = $configOB->getMriCodePath();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $is_qsub = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
my $is_qsub = $configOB->getIsQsub();



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7 changes: 1 addition & 6 deletions batch_uploads_tarchive.pl
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Expand Up @@ -185,14 +185,9 @@ =head1 AUTHORS
my $data_dir = $configOB->getDataDirPath();
my $tarchiveLibraryDir = $configOB->getTarchiveLibraryDir();
my $mail_user = $configOB->getMailUser();
my $is_qsub = $configOB->getIsQsub();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $is_qsub = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');


# define project space
my ($debug) = (0);
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8 changes: 1 addition & 7 deletions tools/batch_run_defacing_script.pl
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Expand Up @@ -144,13 +144,7 @@ =head1 AUTHORS
my $data_dir = $configOB->getDataDirPath();
my $mail_user = $configOB->getMailUser();
my $bin_dir = $configOB->getMriCodePath();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $is_qsub = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
my $is_qsub = $configOB->getIsQsub();



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8 changes: 1 addition & 7 deletions tools/batch_run_pipeline_qc_face_script.pl
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Expand Up @@ -157,13 +157,7 @@ =head1 AUTHORS
my $data_dir = $configOB->getDataDirPath();
my $mail_user = $configOB->getMailUser();
my $bin_dir = $configOB->getMriCodePath();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $is_qsub = &NeuroDB::DBI::getConfigSetting(\$dbh, 'is_qsub');
my $is_qsub = $configOB->getIsQsub();



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9 changes: 2 additions & 7 deletions tools/create_nifti_bval_bvec.pl
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Expand Up @@ -143,15 +143,10 @@ =head1 AUTHORS

my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);

my $data_dir = $configOB->getDataDirPath();
my $data_dir = $configOB->getDataDirPath();
my $create_nii = $configOB->getCreateNii();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $create_nii = NeuroDB::DBI::getConfigSetting(\$dbh, 'create_nii');



## exit if create_nii is set to No
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22 changes: 13 additions & 9 deletions uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm
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Expand Up @@ -498,7 +498,7 @@ sub determinePSC {
# ----------------------------------------------------------------
## Get config settings using ConfigOB
# ----------------------------------------------------------------
my $configOB = $this->{configOB};
my $configOB = $this->{'configOB'};
my $lookupCenterNameUsing = $configOB->getLookupCenterNameUsing();


Expand Down Expand Up @@ -1175,7 +1175,7 @@ sub registerScanIntoDB {
# ----------------------------------------------------------------
## Get config settings using ConfigOB
# ----------------------------------------------------------------
my $configOB = $this->{configOB};
my $configOB = $this->{'configOB'};
my $data_dir = $configOB->getDataDirPath();
my $prefix = $configOB->getPrefix();

Expand Down Expand Up @@ -1506,7 +1506,7 @@ sub moveAndUpdateTarchive {
# ----------------------------------------------------------------
## Get config settings using ConfigOB
# ----------------------------------------------------------------
my $configOB = $this->{configOB};
my $configOB = $this->{'configOB'};
my $tarchivePath = $configOB->getTarchiveLibraryDir();


Expand Down Expand Up @@ -1579,6 +1579,12 @@ sub CreateMRICandidates {
my ($subjectIDsref,$sex,$tarchiveInfo,$User,$centerID, $upload_id) = @_;
my ($message);

# ----------------------------------------------------------------
## Get config settings using ConfigOB
# ----------------------------------------------------------------
my $configOB = $this->{'configOB'};
my $createCandidates = $configOB->getCreateCandidates();

if ($tarchiveInfo->{'PatientSex'} eq 'F') {
$sex = "Female";
} elsif ($tarchiveInfo->{'PatientSex'} eq 'M') {
Expand All @@ -1589,11 +1595,9 @@ sub CreateMRICandidates {
## Create non-existent candidate if the profile allows for #####
## Candidate creation ##########################################
################################################################
if (!NeuroDB::MRI::subjectIDExists(
$subjectIDsref->{'CandID'},
$this->{dbhr}
)
&& (NeuroDB::DBI::getConfigSetting($this->{dbhr},'createCandidates'))
my $configOB = $this->{'configOB'};
if (!NeuroDB::MRI::subjectIDExists($subjectIDsref->{'CandID'}, $this->{dbhr})
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No need to instantiate $configOB again: it was already defined on line 1585. Also, the definition of $createCandidates should go here instead of further up.

&& ($createCandidates)
) {
chomp($User);
unless ($subjectIDsref->{'CandID'}) {
Expand Down Expand Up @@ -1888,7 +1892,7 @@ sub computeSNR {
# ----------------------------------------------------------------
## Get config settings using ConfigOB
# ----------------------------------------------------------------
my $configOB = $this->{configOB};
my $configOB = $this->{'configOB'};
my $data_dir = $configOB->getDataDirPath();

my $modalities = NeuroDB::DBI::getConfigSetting(
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64 changes: 64 additions & 0 deletions uploadNeuroDB/NeuroDB/objectBroker/ConfigOB.pm
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Expand Up @@ -81,6 +81,10 @@ use constant LOOK_UP_CENTER_NAME_USING => 'lookupCenterNameUsing';
use constant DEFACING_REF_SCAN_TYPE => 'reference_scan_type_for_defacing';
use constant LEGO_PHANTOM_REGEX => 'LegoPhantomRegex';
use constant LIVING_PHANTOM_REGEX => 'LivingPhantomRegex';
use constant CREATE_NII => 'create_nii';
use constant HORIZONTAL_PICS => 'horizontalPics';
use constant IS_QSUB => 'is_qsub';
use constant CREATE_CANDIDATES => 'createCandidates';

=pod

Expand Down Expand Up @@ -348,6 +352,66 @@ sub getLivingPhantomRegex {
return &$getConfigSettingRef($self, LIVING_PHANTOM_REGEX);
}

=head3 getCreateNii()

Get the create_nii Config setting.

RETURN: (boolean) 1 if create_nii is set to Yes in the Config module, 0 otherwise

=cut
sub getCreateNii {
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@nicolasbrossard nicolasbrossard Oct 15, 2019 •
edited
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I think it would be a good idea to have a private function getBoolean that the other methods would call instead of "hardcoding" the logic inside each method. What do you think?

Oh and here's how you declare/used a private function:

my $privatePrintMethodRef = sub {
    my($arg) = @_;
    print "$arg.\n";
};
.
.
.
sub myPublicSayHelloMethod {
    $myPrivatePrintMethodRef->('Hello');
}

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I agree!

my $self = shift;

my $value = &$getConfigSettingRef($self, CREATE_NII);

return ($value eq "true" || $value == 1) ? 1 : 0;
}

=head3 getHorizontalPics()

Get the horizontalPics Config setting.

RETURN: (boolean) 1 if horizontalPics is set to Yes in the Config module, 0 otherwise

=cut
sub getHorizontalPics {
my $self = shift;

my $value = &$getConfigSettingRef($self, HORIZONTAL_PICS);

return ($value eq "true" || $value == 1) ? 1 : 0;
}

=head3 getIsQsub()

Get the is_qsub Config setting.

RETURN: (boolean) 1 if is_qsub is set to Yes in the Config module, 0 otherwise

=cut
sub getIsQsub {
my $self = shift;

my $value = &$getConfigSettingRef($self, IS_QSUB);

return ($value eq "true" || $value == 1) ? 1 : 0;
}

=head3 getCreateCandidates()

Get the createCandidates Config setting.

RETURN: (boolean) 1 if createCandidates is set to Yes in the Config module, 0 otherwise

=cut
sub getCreateCandidates {
my $self = shift;

my $value = &$getConfigSettingRef($self, IS_QSUB);

return ($value eq "true" || $value == 1) ? 1 : 0;
}

1;


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10 changes: 2 additions & 8 deletions uploadNeuroDB/mass_pic.pl
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Expand Up @@ -124,14 +124,8 @@ =head1 DESCRIPTION

my $configOB = NeuroDB::objectBroker::ConfigOB->new(db => $db);

my $data_dir = $configOB->getDataDirPath();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $horizontalPics = &NeuroDB::DBI::getConfigSetting(\$dbh, 'horizontalPics');
my $data_dir = $configOB->getDataDirPath();
my $horizontalPics = $configOB->getHorizontalPics();



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10 changes: 2 additions & 8 deletions uploadNeuroDB/minc_insertion.pl
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Expand Up @@ -284,14 +284,8 @@ =head2 Methods

my $data_dir = $configOB->getDataDirPath();
my $tarchiveLibraryDir = $configOB->getTarchiveLibraryDir();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $create_nii = NeuroDB::DBI::getConfigSetting(\$dbh, 'create_nii' );
my $horizontalPics = NeuroDB::DBI::getConfigSetting(\$dbh, 'horizontalPics');
my $create_nii = $configOB->getCreateNii();
my $horizontalPics = $configOB->getHorizontalPics();



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7 changes: 1 addition & 6 deletions uploadNeuroDB/register_processed_data.pl
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Expand Up @@ -177,14 +177,9 @@ =head2 Methods

my $data_dir = $configOB->getDataDirPath();
my $lookupCenterName = $configOB->getLookupCenterNameUsing();
my $horizontalPics = $configOB->getHorizontalPics();


# -----------------------------------------------------------------
## Get config setting using the old database calls
# -----------------------------------------------------------------

my $horizontalPics = &NeuroDB::DBI::getConfigSetting(\$dbh,'horizontalPics');




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