From bf6ae00f43bb939cbc8bf0d351bc182ff05660f6 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Mon, 13 Mar 2017 15:18:08 -0400 Subject: [PATCH 01/11] Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 --- .../17.1/2017-03-13_AddLorisMRIToConfig.sql | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql new file mode 100644 index 00000000000..211880529e9 --- /dev/null +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -0,0 +1,37 @@ +-- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; + + +-- default imaging_pipeline settings +INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="horizontalPics"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="no_nii"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "dcm2mnc" FROM ConfigSettings cs WHERE cs.Name="converter"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/dicomlib/" FROM ConfigSettings cs WHERE cs.Name="tarchiveLibraryDir"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "PatientName" FROM ConfigSettings cs WHERE cs.Name="lookupCenterNameUsing"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="createCandidates"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="is_qsub"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="if_site"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 65 FROM ConfigSettings cs WHERE cs.Name="DTI_volumes"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "adniT1" FROM ConfigSettings cs WHERE cs.Name="t1_scan_type"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 19 FROM ConfigSettings cs WHERE cs.Name="reject_thresh"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/opt/niak-0.6.4.1/" FROM ConfigSettings cs WHERE cs.Name="niak_path"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "INTERLACE_outputDWIFileNameSuffix" FROM ConfigSettings cs WHERE cs.Name="QCed2_step"; From 6d2d69ca3d0a9c1fedc1230ae4a537cdccef3ebd Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Tue, 14 Mar 2017 15:19:03 -0400 Subject: [PATCH 02/11] added the schema --- SQL/0000-00-03-ConfigTables.sql | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 4f9bd02ebf1..117d701795f 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -132,6 +132,25 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPrivate', 'Private Key for Google reCAPTCHA', 1, 0, 'text', ID, 'reCAPTCHA Private Key', 2 FROM ConfigSettings WHERE Name="APIKeys"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPublic', 'Public Key for Google reCaptcha', 1, 0, 'text', ID, 'reCAPTCHA Public Key', 3 FROM ConfigSettings WHERE Name="APIKeys"; +-- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; + -- -- Filling Config table with default values -- @@ -202,4 +221,22 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "Produced by LorisDB" FROM Confi SELECT 'Default API keys settings' as 'Filling Config table with default values'; INSERT INTO Config (ConfigID, Value) SELECT ID, "S3cret" FROM ConfigSettings WHERE Name="JWTKey"; +SELECT 'Default Imaging Pipeline settings' as 'Filling Config table with default values'; +INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="horizontalPics"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="no_nii"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "dcm2mnc" FROM ConfigSettings cs WHERE cs.Name="converter"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/dicomlib/" FROM ConfigSettings cs WHERE cs.Name="tarchiveLibraryDir"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "PatientName" FROM ConfigSettings cs WHERE cs.Name="lookupCenterNameUsing"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="createCandidates"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="is_qsub"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="if_site"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 65 FROM ConfigSettings cs WHERE cs.Name="DTI_volumes"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "adniT1" FROM ConfigSettings cs WHERE cs.Name="t1_scan_type"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 19 FROM ConfigSettings cs WHERE cs.Name="reject_thresh"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/opt/niak-0.6.4.1/" FROM ConfigSettings cs WHERE cs.Name="niak_path"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "INTERLACE_outputDWIFileNameSuffix" FROM ConfigSettings cs WHERE cs.Name="QCed2_step"; + SELECT 'Config import completed' as 'Status'; From ecb4a9bb65cca6b5cb2f5c1337471f9307201d3c Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Mon, 27 Mar 2017 13:29:07 -0400 Subject: [PATCH 03/11] Greg feedback on data_dir that could be different for different projects --- SQL/0000-00-03-ConfigTables.sql | 2 ++ SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql | 2 ++ 2 files changed, 4 insertions(+) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 117d701795f..fee4857ebd1 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -134,6 +134,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; @@ -222,6 +223,7 @@ SELECT 'Default API keys settings' as 'Filling Config table with default values' INSERT INTO Config (ConfigID, Value) SELECT ID, "S3cret" FROM ConfigSettings WHERE Name="JWTKey"; SELECT 'Default Imaging Pipeline settings' as 'Filling Config table with default values'; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="Loris-MRI Data Directory"; INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index 211880529e9..fb68f992de7 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -1,5 +1,6 @@ -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; @@ -19,6 +20,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- default imaging_pipeline settings +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="Loris-MRI Data Directory"; INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; From e402749cbdd844c3a03b462f9959d8606a270bd0 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Wed, 29 Mar 2017 12:25:03 -0400 Subject: [PATCH 04/11] Truncate the dcm2mnc description: Greg feedback --- SQL/0000-00-03-ConfigTables.sql | 2 +- SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index fee4857ebd1..92455a20e0c 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -140,7 +140,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index fb68f992de7..ff582b07062 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -6,7 +6,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; From 6445c01cbddb0bda2c4d24d0963d53712ad7bd9f Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Fri, 31 Mar 2017 16:29:12 -0400 Subject: [PATCH 05/11] Proper order number as opposed to all ordered to 1 --- SQL/0000-00-03-ConfigTables.sql | 32 +++++++++---------- .../17.1/2017-03-13_AddLorisMRIToConfig.sql | 32 +++++++++---------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 92455a20e0c..6c8e5022274 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -135,22 +135,22 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 2 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 3 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 6 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 7 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 10 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 11 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 12 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 13 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 14 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 15 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 16 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 17 FROM ConfigSettings WHERE Name="imaging_pipeline"; -- -- Filling Config table with default values diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index ff582b07062..07045edd974 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -1,22 +1,22 @@ -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 2 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 3 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 6 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 7 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 10 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 11 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 12 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 13 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 14 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 15 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 16 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 17 FROM ConfigSettings WHERE Name="imaging_pipeline"; -- default imaging_pipeline settings From e39982ec45275996686549400b46727b6904f9c6 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Mon, 13 Mar 2017 15:18:08 -0400 Subject: [PATCH 06/11] Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 --- .../17.1/2017-03-13_AddLorisMRIToConfig.sql | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql new file mode 100644 index 00000000000..211880529e9 --- /dev/null +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -0,0 +1,37 @@ +-- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; + + +-- default imaging_pipeline settings +INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="horizontalPics"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="no_nii"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "dcm2mnc" FROM ConfigSettings cs WHERE cs.Name="converter"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/dicomlib/" FROM ConfigSettings cs WHERE cs.Name="tarchiveLibraryDir"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "PatientName" FROM ConfigSettings cs WHERE cs.Name="lookupCenterNameUsing"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="createCandidates"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="is_qsub"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="if_site"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 65 FROM ConfigSettings cs WHERE cs.Name="DTI_volumes"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "adniT1" FROM ConfigSettings cs WHERE cs.Name="t1_scan_type"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 19 FROM ConfigSettings cs WHERE cs.Name="reject_thresh"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/opt/niak-0.6.4.1/" FROM ConfigSettings cs WHERE cs.Name="niak_path"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "INTERLACE_outputDWIFileNameSuffix" FROM ConfigSettings cs WHERE cs.Name="QCed2_step"; From c131f5aa07dd5af8d3f2375bc843b8878cf44fb7 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Tue, 14 Mar 2017 15:19:03 -0400 Subject: [PATCH 07/11] added the schema --- SQL/0000-00-03-ConfigTables.sql | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 4f9bd02ebf1..117d701795f 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -132,6 +132,25 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPrivate', 'Private Key for Google reCAPTCHA', 1, 0, 'text', ID, 'reCAPTCHA Private Key', 2 FROM ConfigSettings WHERE Name="APIKeys"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPublic', 'Public Key for Google reCaptcha', 1, 0, 'text', ID, 'reCAPTCHA Public Key', 3 FROM ConfigSettings WHERE Name="APIKeys"; +-- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; + -- -- Filling Config table with default values -- @@ -202,4 +221,22 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "Produced by LorisDB" FROM Confi SELECT 'Default API keys settings' as 'Filling Config table with default values'; INSERT INTO Config (ConfigID, Value) SELECT ID, "S3cret" FROM ConfigSettings WHERE Name="JWTKey"; +SELECT 'Default Imaging Pipeline settings' as 'Filling Config table with default values'; +INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="horizontalPics"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="no_nii"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "dcm2mnc" FROM ConfigSettings cs WHERE cs.Name="converter"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/dicomlib/" FROM ConfigSettings cs WHERE cs.Name="tarchiveLibraryDir"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "PatientName" FROM ConfigSettings cs WHERE cs.Name="lookupCenterNameUsing"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="createCandidates"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings cs WHERE cs.Name="is_qsub"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 1 FROM ConfigSettings cs WHERE cs.Name="if_site"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 65 FROM ConfigSettings cs WHERE cs.Name="DTI_volumes"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "adniT1" FROM ConfigSettings cs WHERE cs.Name="t1_scan_type"; +INSERT INTO Config (ConfigID, Value) SELECT ID, 19 FROM ConfigSettings cs WHERE cs.Name="reject_thresh"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/opt/niak-0.6.4.1/" FROM ConfigSettings cs WHERE cs.Name="niak_path"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "INTERLACE_outputDWIFileNameSuffix" FROM ConfigSettings cs WHERE cs.Name="QCed2_step"; + SELECT 'Config import completed' as 'Status'; From 3a169cdccdb1346ba4275cd145bcbb63b9dd5550 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Mon, 27 Mar 2017 13:29:07 -0400 Subject: [PATCH 08/11] Greg feedback on data_dir that could be different for different projects --- SQL/0000-00-03-ConfigTables.sql | 2 ++ SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql | 2 ++ 2 files changed, 4 insertions(+) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 117d701795f..fee4857ebd1 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -134,6 +134,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; @@ -222,6 +223,7 @@ SELECT 'Default API keys settings' as 'Filling Config table with default values' INSERT INTO Config (ConfigID, Value) SELECT ID, "S3cret" FROM ConfigSettings WHERE Name="JWTKey"; SELECT 'Default Imaging Pipeline settings' as 'Filling Config table with default values'; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="Loris-MRI Data Directory"; INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index 211880529e9..fb68f992de7 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -1,5 +1,6 @@ -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; @@ -19,6 +20,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- default imaging_pipeline settings +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="Loris-MRI Data Directory"; INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info"; From b8f5e0c17c20f3cf8272ee13d846e78485745a78 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Wed, 29 Mar 2017 12:25:03 -0400 Subject: [PATCH 09/11] Truncate the dcm2mnc description: Greg feedback --- SQL/0000-00-03-ConfigTables.sql | 2 +- SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index fee4857ebd1..92455a20e0c 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -140,7 +140,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index fb68f992de7..ff582b07062 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -6,7 +6,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; From 14a0112d3cbc7abbc764b9a5914f20672ef4cd9b Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Fri, 31 Mar 2017 16:29:12 -0400 Subject: [PATCH 10/11] Proper order number as opposed to all ordered to 1 --- SQL/0000-00-03-ConfigTables.sql | 32 +++++++++---------- .../17.1/2017-03-13_AddLorisMRIToConfig.sql | 32 +++++++++---------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 92455a20e0c..6c8e5022274 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/SQL/0000-00-03-ConfigTables.sql @@ -135,22 +135,22 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 2 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 3 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 6 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 7 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 10 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 11 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 12 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 13 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 14 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 15 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 16 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 17 FROM ConfigSettings WHERE Name="imaging_pipeline"; -- -- Filling Config table with default values diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index ff582b07062..07045edd974 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -1,22 +1,22 @@ -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12); INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; -INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'prefix', 'Study prefix or study name', 1, 0, 'text', ID, 'Study Name', 2 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'mail_user', 'User to be notified during imaging pipeline execution', 1, 0, 'text', ID, 'User to notify when executing the pipeline', 3 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'get_dicom_info', 'Full path to get_dicom_info.pl', 1, 0, 'text', ID, 'Full path to get_dicom_info.pl script', 4 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'horizontalPics', 'Generate horizontal pictures', 1, 0, 'boolean', ID, 'Horizontal pictures creation', 5 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'no_nii', 'Create NIFTII files if set to 0', 1, 0, 'boolean', ID, 'NIFTII file creation', 6 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 7 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'tarchiveLibraryDir', 'Location of storing the library of used tarchives. If this is not set, they will not be moved', 1, 0, 'text', ID, 'Path to Tarchives', 8 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'lookupCenterNameUsing', 'The element of the tarchive table to be used in getPSC(), being either PatientID or PatientName', 1, 0, 'text', ID, 'Center name lookup variable', 9 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createCandidates', 'Creation of candidates if set to 1', 1, 0, 'boolean', ID, 'Upload creation of candidates', 10 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'is_qsub', 'Do not use batch management if qsub is set to 0', 1, 0, 'boolean', ID, 'Project batch management used', 11 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'if_site', 'Use site if set to 1', 1, 0, 'boolean', ID, 'If site is used', 12 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'DTI_volumes', 'Number of volumes in native DTI acquisitions', 1, 0, 'text', ID, 'Number of volumes in native DTI acquisitions', 13 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 't1_scan_type', 'Scan type of native T1 acquisition (as in the mri_scan_type table)', 1, 0, 'text', ID, 'Scan type of native T1 acquisition', 14 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reject_thresh', 'Max number of directions that can be rejected to PASS QC', 1, 0, 'text', ID, 'Max number of DTI rejected directions for passing QC', 15 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'niak_path', 'Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl)', 1, 0, 'text', ID, 'NIAK Path', 16 FROM ConfigSettings WHERE Name="imaging_pipeline"; +INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'QCed2_step', 'DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep)', 1, 0, 'text', ID, 'Secondary QCed dataset', 17 FROM ConfigSettings WHERE Name="imaging_pipeline"; -- default imaging_pipeline settings From 82edf6c3b3bffda9bceec791c5254059061763d5 Mon Sep 17 00:00:00 2001 From: MounaSafiHarab Date: Fri, 7 Jul 2017 09:20:35 -0400 Subject: [PATCH 11/11] Greg good catch --- SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql index 07045edd974..ba71642216b 100644 --- a/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql +++ b/SQL/Archive/17.1/2017-03-13_AddLorisMRIToConfig.sql @@ -20,7 +20,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, -- default imaging_pipeline settings -INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="Loris-MRI Data Directory"; +INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/DATA/location" FROM ConfigSettings cs WHERE cs.Name="dataDirBasepath"; INSERT INTO Config (ConfigID, Value) SELECT ID, "project" FROM ConfigSettings cs WHERE cs.Name="prefix"; INSERT INTO Config (ConfigID, Value) SELECT ID, "yourname\@example.com" FROM ConfigSettings cs WHERE cs.Name="mail_user"; INSERT INTO Config (ConfigID, Value) SELECT ID, "/PATH/TO/get_dicom_info.pl" FROM ConfigSettings cs WHERE cs.Name="get_dicom_info";