Clean-up database scan type #1139
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I am having some troubles testing this PR because my dev database config got changed recently, but this should work. According to the files changed, only the DICOM to MINC ingestion pipeline needs to be tested. |
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@maximemulder there is a conflict in this PR. Could you rebase and let @nicolasbrossard and I when it is ready to test/review? Thank you :) |
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cmadjar
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Nov 12, 2024
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Tested following scripts:
- delete script 🟢
- minc_insertion.pl 🔴 see suggested code changes in functions
scan_type_text_to_idandscan_type_id_to_textofMRI.pm - imaging_non_minc_insertion.pl 🟢
- minc_to_bids_converter.pl 🔴 see suggested code change in function
getFileListoftools/minc_to_bids_converter.pl - get_dicom_files.pl 🟢
- run_defacing_script.pl 🔴 see suggested code change in function
check_if_deface_files_already_in_dbfunction oftools/run_defacing_script.pl - register_processed_data.pl 🟢
- run_dicom_archive_loader.py 🟢
🟢 = test successful 🥳
🔴 = bugs found, see attached comments for the bug resolution.
| @@ -650,9 +639,10 @@ sub scan_type_id_to_text { | |||
| my $mriScanTypeOB = NeuroDB::objectBroker::MriScanTypeOB->new( | |||
| db => $db | |||
| ); | |||
|
|
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| my $mriScanTypeRef = $mriScanTypeOB->get(0, { ID => $typeID }); | |||
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Suggested change
| my $mriScanTypeRef = $mriScanTypeOB->get(0, { ID => $typeID }); | |
| my $mriScanTypeRef = $mriScanTypeOB->get(0, { MriScanTypeID => $typeID }); |
| @@ -676,7 +666,7 @@ sub scan_type_text_to_id { | |||
| db => $db | |||
| ); | |||
| my $mriScanTypeRef = $mriScanTypeOB->get( | |||
| 0, { Scan_type => $type } | |||
| 0, { MriScanTypeName => $type } | |||
| ); | |||
|
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| return @$mriScanTypeRef ? $mriScanTypeRef->[0]->{'ID'} : undef; | |||
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Suggested change
| return @$mriScanTypeRef ? $mriScanTypeRef->[0]->{'ID'} : undef; | |
| return @$mriScanTypeRef ? $mriScanTypeRef->[0]->{'MriScanTypeID'} : undef; |
| @@ -427,7 +427,7 @@ sub getFileList { | |||
| SELECT | |||
| f.FileID, | |||
| File, | |||
| AcquisitionProtocolID, | |||
| MriScanTypeID, | |||
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Suggested change
| MriScanTypeID, | |
| mst.MriScanTypeID, |
Otherwise, get the following error:
DBD::mysql::st execute failed: Column 'MriScanTypeID' in field list is ambiguous at /data/preventAD/bin/mri/tools/minc_to_bids_converter.pl line 456.
| @@ -439,10 +439,10 @@ sub check_if_deface_files_already_in_db { | |||
| # base query | |||
| my $query = "SELECT COUNT(*) " | |||
| . " FROM files f " | |||
| . " JOIN mri_scan_type mst ON (mst.ID=f.AcquisitionProtocolID) "; | |||
| . " JOIN mri_scan_type mst USING (mst.MriScanTypeID=f.MriScanTypeID) "; | |||
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Suggested change
| . " JOIN mri_scan_type mst USING (mst.MriScanTypeID=f.MriScanTypeID) "; | |
| . " JOIN mri_scan_type mst ON (mst.MriScanTypeID=f.MriScanTypeID) "; |
otherwise, get the following error:
DBD::mysql::st execute failed: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '.MriScanTypeID=f.MriScanTypeID) WHERE (mst.MriScanTypeName = 't2-defaced' OR ms' at line 1 at tools/run_defacing_script.pl line 451.
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Complementary PR of LORIS #9304