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[25.0 Release] Hotfixes for demo #8840

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merged 1 commit into from
Aug 8, 2023
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[25.0 Release] Hotfixes for demo #8840

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4 changes: 4 additions & 0 deletions .editorconfig
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Expand Up @@ -17,3 +17,7 @@ indent_size = 2

[*.md]
trim_trailing_whitespace = false

[*.yml]
indent_size = 2

6 changes: 6 additions & 0 deletions SQL/9999-99-99-drop_tables.sql
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@@ -1,11 +1,16 @@
-- 0000-00-05-ElectrophysiologyTables.sql
DROP TABLE IF EXISTS `physiological_event_parameter_category_level`;
DROP TABLE IF EXISTS `physiological_event_parameter`;
DROP TABLE IF EXISTS `physiological_event_archive`;
DROP TABLE IF EXISTS `physiological_event_file`;
DROP TABLE IF EXISTS `physiological_coord_system_electrode_rel`;
DROP TABLE IF EXISTS `physiological_coord_system_point_3d_rel`;
DROP TABLE IF EXISTS `point_3d`;
DROP TABLE IF EXISTS `physiological_coord_system`;
DROP TABLE IF EXISTS `physiological_coord_system_unit`;
DROP TABLE IF EXISTS `physiological_coord_system_name`;
DROP TABLE IF EXISTS `physiological_coord_system_type`;
DROP TABLE IF EXISTS `electrophysiology_uploader`;
DROP TABLE IF EXISTS `physiological_annotation_rel`;
DROP TABLE IF EXISTS `physiological_annotation_instance`;
DROP TABLE IF EXISTS `physiological_annotation_parameter`;
Expand Down Expand Up @@ -45,6 +50,7 @@ DROP TABLE IF EXISTS `issues`;
DROP TABLE IF EXISTS `issues_categories`;

-- 0000-00-02-Permission.sql
DROP TABLE IF EXISTS `testnames_permissions_rel`;
DROP TABLE IF EXISTS `user_perm_rel`;
DROP TABLE IF EXISTS `notification_modules_perm_rel`;
DROP TABLE IF EXISTS `permissions`;
Expand Down
0 ...up/2021-03-01-publication-add-columns.sql → ....0/2021-03-01-publication-add-columns.sql
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1 change: 1 addition & 0 deletions SQL/Archive/25.0/2022-03-03-AddHEDTags.sql
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Expand Up @@ -44,6 +44,7 @@ INSERT INTO physiological_event_file (PhysiologicalFileID, FilePath, FileType)
UPDATE physiological_task_event te
SET EventFileID=(SELECT EventFileID FROM physiological_event_file WHERE PhysiologicalFileID=te.PhysiologicalFileID)
;
SET FOREIGN_KEY_CHECKS= 1;
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I don't get why this is flagged as "IMPORTANT" in the description. It's a session variable, it'll be re-enabled after the patch is sourced even with this missing.

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@ridz1208 ridz1208 Jul 19, 2023 •
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the patch is the entire release patch because its concatenated into it. it also happens to be one of the first statements

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I think it is fine, the FOREIGN_KEY_CHECKS is disabled for the same set of statements on both patches.


-- Delete FilePath column in `physiological_task_event` table
ALTER TABLE physiological_task_event
Expand Down
214 changes: 136 additions & 78 deletions SQL/Release_patches/24.1_To_25.0_upgrade.sql
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@@ -1,11 +1,29 @@

SELECT 'Running: SQL/Archive/25.0/2021-03-01-publication-add-columns.sql';

ALTER TABLE publication
ADD COLUMN journal varchar(255) DEFAULT NULL,
ADD COLUMN doi text DEFAULT NULL,
ADD COLUMN datePublication date DEFAULT NULL,
ADD COLUMN link varchar(255) DEFAULT NULL,
ADD COLUMN publishingStatus enum('In Progress','Published') DEFAULT NULL,
ADD COLUMN project int(10) unsigned DEFAULT NULL,
ADD CONSTRAINT `FK_publication_project`
FOREIGN KEY (project) REFERENCES Project(ProjectID);

SELECT 'Running: SQL/Archive/25.0/2021-09-13_fix_project_primary_key.sql';

-- Add a unique constraint on Project.Name
CREATE UNIQUE INDEX `u_ProjectName` ON `Project` (`Name`);

ALTER TABLE `Project`
MODIFY `Name` VARCHAR(255) NOT NULL;

SELECT 'Running: SQL/Archive/25.0/2021-12-01-make_subproject_titles_unique.sql';

ALTER TABLE subproject ADD UNIQUE (`title`);
ALTER TABLE session
ADD COLUMN Date_status_change date DEFAULT NULL AFTER Date_visit;-- ############################## CAPTURE HEDVersion ########################## --

SELECT 'Running: SQL/Archive/25.0/2022-03-03-AddHEDTags.sql';

-- ############################## CAPTURE HEDVersion ########################## --
-- HEDVersion from dataset_description.json to be added to parameter_type
-- Entry in physiological_parameter_file will be added on dataset import**
INSERT INTO parameter_type (Name, Type, Description, SourceFrom) VALUES
Expand Down Expand Up @@ -51,6 +69,7 @@ INSERT INTO physiological_event_file (PhysiologicalFileID, FilePath, FileType)
UPDATE physiological_task_event te
SET EventFileID=(SELECT EventFileID FROM physiological_event_file WHERE PhysiologicalFileID=te.PhysiologicalFileID)
;
SET FOREIGN_KEY_CHECKS= 1;

-- Delete FilePath column in `physiological_task_event` table
ALTER TABLE physiological_task_event
Expand Down Expand Up @@ -98,27 +117,9 @@ CREATE TABLE `physiological_event_parameter_category_level` (
CONSTRAINT `FK_event_param_ID` FOREIGN KEY (`EventParameterID`) REFERENCES `physiological_event_parameter` (`EventParameterID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8
;
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createVisit', 'Enable visit creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable visit creation', 11 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_project', 'Default project used when creating scan candidate or visit', 1, 0, 'text', ID, 'Default project', 12 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_cohort', 'Default cohort used when creating scan visit', 1, 0, 'text', ID, 'Default cohort', 13 FROM ConfigSettings WHERE Name="imaging_pipeline";

UPDATE ConfigSettings SET Label = 'Enable candidate creation' WHERE Name = 'createCandidates';
SELECT 'Running: SQL/Archive/25.0/2022-11-22-eeg-additional-events-table.sql';

UPDATE ConfigSettings SET OrderNumber = 14 WHERE Name = 'default_bids_vl';
UPDATE ConfigSettings SET OrderNumber = 15 WHERE Name = 'is_qsub';
UPDATE ConfigSettings SET OrderNumber = 16 WHERE Name = 'DTI_volumes';
UPDATE ConfigSettings SET OrderNumber = 17 WHERE Name = 't1_scan_type';
UPDATE ConfigSettings SET OrderNumber = 18 WHERE Name = 'reject_thresh';
UPDATE ConfigSettings SET OrderNumber = 19 WHERE Name = 'niak_path';
UPDATE ConfigSettings SET OrderNumber = 20 WHERE Name = 'QCed2_step';
UPDATE ConfigSettings SET OrderNumber = 21 WHERE Name = 'excluded_series_description';
UPDATE ConfigSettings SET OrderNumber = 22 WHERE Name = 'ComputeDeepQC';
UPDATE ConfigSettings SET OrderNumber = 23 WHERE Name = 'MriConfigFile';
UPDATE ConfigSettings SET OrderNumber = 24 WHERE Name = 'EnvironmentFile';
UPDATE ConfigSettings SET OrderNumber = 25 WHERE Name = 'compute_snr_modalities';
UPDATE ConfigSettings SET OrderNumber = 26 WHERE Name = 'reference_scan_type_for_defacing';
UPDATE ConfigSettings SET OrderNumber = 27 WHERE Name = 'modalities_to_deface';
UPDATE ConfigSettings SET OrderNumber = 28 WHERE Name = 'MriPythonConfigFile';
-- Create `physiological_task_event_opt` table
-- tracks additional events from bids archives
CREATE TABLE `physiological_task_event_opt` (
Expand All @@ -130,34 +131,9 @@ CREATE TABLE `physiological_task_event_opt` (
CONSTRAINT `FK_event_task_opt`
FOREIGN KEY (`PhysiologicalTaskEventID`)
REFERENCES `physiological_task_event` (`PhysiologicalTaskEventID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;-- Create EEG upload table
CREATE TABLE `electrophysiology_uploader` (
`UploadID` int(10) unsigned NOT NULL AUTO_INCREMENT,
`UploadedBy` varchar(255) NOT NULL,
`UploadDate` DateTime NOT NULL,
`UploadLocation` varchar(255) NOT NULL,
`Status` enum('Not Started', 'Extracted', 'In Progress', 'Complete', 'Failed', 'Archived') DEFAULT 'Not Started',
`SessionID` int(10) unsigned,
`Checksum` varchar(40) DEFAULT NULL,
`MetaData` TEXT DEFAULT NULL,
PRIMARY KEY (`UploadID`),
KEY (`SessionID`),
CONSTRAINT `FK_eegupload_SessionID`
FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`),
CONSTRAINT `FK_eegupload_UploadedBy`
FOREIGN KEY (`UploadedBy`) REFERENCES `users` (`UserID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
SELECT 'Running: SQL/Archive/25.0/2022-11-24-electrode-coord-system.sql';

-- Add to module table
INSERT INTO modules (Name, Active) VALUES ('electrophysiology_uploader', 'Y');

-- Add new configurations for eeg uploader
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber)
SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigSettings WHERE Name="paths";

-- Add new permissions for eeg uploader
INSERT INTO permissions (code, description, moduleID, action, categoryID) VALUES
('monitor_eeg_uploads','Monitor EEG uploads',(SELECT ID FROM modules WHERE Name='electrophysiology_uploader'),NULL,'2');
-- -----------------------------------------------------
-- ADDED
-- Table `physiological_coord_system_type`
Expand Down Expand Up @@ -410,30 +386,9 @@ ALTER TABLE physiological_electrode
DROP FOREIGN KEY FK_phys_file_FileID_3;
ALTER TABLE physiological_electrode
DROP COLUMN PhysiologicalFileID;
INSERT INTO ConfigSettings
(
Name,
Description,
Visible,
AllowMultiple,
DataType,
Parent,
Label,
OrderNumber
)
SELECT
'UserMaximumDaysInactive',
'The maximum number of days since last login before making a user inactive',
1,
0,
'text',
ID,
'Maximum Days Before Making User Inactive',
30
FROM ConfigSettings
WHERE Name="study";

INSERT INTO Config (ConfigID, Value) SELECT ID, "365" FROM ConfigSettings WHERE Name="UserMaximumDaysInactive";
SELECT 'Running: SQL/Archive/25.0/2022-12-01-subprojects_no_more.sql';

ALTER TABLE subproject RENAME TO cohort;
ALTER TABLE project_subproject_rel RENAME TO project_cohort_rel;
ALTER TABLE visit_project_subproject_rel RENAME TO visit_project_cohort_rel;
Expand Down Expand Up @@ -466,11 +421,9 @@ ALTER TABLE mri_protocol_group_target CHANGE `CohortID` `SubprojectID` int(10) u
ALTER TABLE visit_project_subproject_rel CHANGE `VisitProjectCohortRelID` `VisitProjectSubprojectRelID` int(10) unsigned NOT NULL AUTO_INCREMENT;
ALTER TABLE visit_project_subproject_rel CHANGE `ProjectCohortRelID` `ProjectSubprojectRelID` int(10) unsigned NOT NULL;
*/
-- ---------------------------------------------------------------------------------------------
-- alter MRICandidateErrors table to add PhaseEncodingDirection and EchoNumber
-- ---------------------------------------------------------------------------------------------
ALTER TABLE MRICandidateErrors ADD COLUMN `PhaseEncodingDirection` VARCHAR(3) DEFAULT NULL;
ALTER TABLE MRICandidateErrors ADD COLUMN `EchoNumber` VARCHAR(20) DEFAULT NULL;

SELECT 'Running: SQL/Archive/25.0/2022-12-05-AddVizConfig.sql';

-- Adds the option to toggle the EEG Browser visualization components (disabled by default).
INSERT INTO ConfigSettings
(
Expand Down Expand Up @@ -498,7 +451,8 @@ INSERT INTO ConfigSettings
Name="gui";

INSERT INTO Config (ConfigID, Value) SELECT ID, 'false' FROM ConfigSettings WHERE Name="useEEGBrowserVisualizationComponents";
CREATE INDEX `i_violations_resolved_extid_type` ON `violations_resolved` (`ExtID`, `TypeTable`);

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I don't think we should be changing this. Was there a problem with the order that it was, even if it wasn't chronological? That's the order that the patch was in when it was tested.

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we don't know.... we were disabling foreign keys in the same patch

SELECT 'Running: SQL/Archive/25.0/2022-12-20-instrumentpermissions.sql';

CREATE TABLE `testnames_permissions_rel` (
`TestID` int(10) unsigned NOT NULL,
Expand All @@ -507,3 +461,107 @@ CREATE TABLE `testnames_permissions_rel` (
CONSTRAINT `FK_testnames_permissions_rel_test` FOREIGN KEY (`TestID`) REFERENCES `test_names` (`ID`),
CONSTRAINT `FK_testnames_permissions_rel_perm` FOREIGN KEY (`permID`) REFERENCES `permissions` (`permID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

SELECT 'Running: SQL/Archive/25.0/2022-12-20-project-name-not-null.sql';

ALTER TABLE `Project`
MODIFY `Name` VARCHAR(255) NOT NULL;

SELECT 'Running: SQL/Archive/25.0/2023-01-19_add_index_on_violations_resolved.sql';

CREATE INDEX `i_violations_resolved_extid_type` ON `violations_resolved` (`ExtID`, `TypeTable`);


SELECT 'Running: SQL/Archive/25.0/2023-01-31-add-date-stage-change.sql';

ALTER TABLE session
ADD COLUMN Date_status_change date DEFAULT NULL AFTER Date_visit;
SELECT 'Running: SQL/Archive/25.0/2023-02-17-imaging-new-config.sql';

INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'createVisit', 'Enable visit creation in the imaging pipeline', 1, 0, 'boolean', ID, 'Enable visit creation', 11 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_project', 'Default project used when creating scan candidate or visit', 1, 0, 'text', ID, 'Default project', 12 FROM ConfigSettings WHERE Name="imaging_pipeline";
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'default_cohort', 'Default cohort used when creating scan visit', 1, 0, 'text', ID, 'Default cohort', 13 FROM ConfigSettings WHERE Name="imaging_pipeline";

UPDATE ConfigSettings SET Label = 'Enable candidate creation' WHERE Name = 'createCandidates';

UPDATE ConfigSettings SET OrderNumber = 14 WHERE Name = 'default_bids_vl';
UPDATE ConfigSettings SET OrderNumber = 15 WHERE Name = 'is_qsub';
UPDATE ConfigSettings SET OrderNumber = 16 WHERE Name = 'DTI_volumes';
UPDATE ConfigSettings SET OrderNumber = 17 WHERE Name = 't1_scan_type';
UPDATE ConfigSettings SET OrderNumber = 18 WHERE Name = 'reject_thresh';
UPDATE ConfigSettings SET OrderNumber = 19 WHERE Name = 'niak_path';
UPDATE ConfigSettings SET OrderNumber = 20 WHERE Name = 'QCed2_step';
UPDATE ConfigSettings SET OrderNumber = 21 WHERE Name = 'excluded_series_description';
UPDATE ConfigSettings SET OrderNumber = 22 WHERE Name = 'ComputeDeepQC';
UPDATE ConfigSettings SET OrderNumber = 23 WHERE Name = 'MriConfigFile';
UPDATE ConfigSettings SET OrderNumber = 24 WHERE Name = 'EnvironmentFile';
UPDATE ConfigSettings SET OrderNumber = 25 WHERE Name = 'compute_snr_modalities';
UPDATE ConfigSettings SET OrderNumber = 26 WHERE Name = 'reference_scan_type_for_defacing';
UPDATE ConfigSettings SET OrderNumber = 27 WHERE Name = 'modalities_to_deface';
UPDATE ConfigSettings SET OrderNumber = 28 WHERE Name = 'MriPythonConfigFile';

SELECT 'Running: SQL/Archive/25.0/2023-02-24-electrophysiology_uploader.sql';

-- Create EEG upload table
CREATE TABLE `electrophysiology_uploader` (
`UploadID` int(10) unsigned NOT NULL AUTO_INCREMENT,
`UploadedBy` varchar(255) NOT NULL,
`UploadDate` DateTime NOT NULL,
`UploadLocation` varchar(255) NOT NULL,
`Status` enum('Not Started', 'Extracted', 'In Progress', 'Complete', 'Failed', 'Archived') DEFAULT 'Not Started',
`SessionID` int(10) unsigned,
`Checksum` varchar(40) DEFAULT NULL,
`MetaData` TEXT DEFAULT NULL,
PRIMARY KEY (`UploadID`),
KEY (`SessionID`),
CONSTRAINT `FK_eegupload_SessionID`
FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`),
CONSTRAINT `FK_eegupload_UploadedBy`
FOREIGN KEY (`UploadedBy`) REFERENCES `users` (`UserID`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

-- Add to module table
INSERT INTO modules (Name, Active) VALUES ('electrophysiology_uploader', 'Y');

-- Add new configurations for eeg uploader
INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber)
SELECT 'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', ID, 'EEG Incoming Directory', 7 FROM ConfigSettings WHERE Name="paths";

-- Add new permissions for eeg uploader
INSERT INTO permissions (code, description, moduleID, action, categoryID) VALUES
('monitor_eeg_uploads','Monitor EEG uploads',(SELECT ID FROM modules WHERE Name='electrophysiology_uploader'),NULL,'2');

SELECT 'Running: SQL/Archive/25.0/2023-02-28_create_max_days_inactive_config_for_users.sql';

INSERT INTO ConfigSettings
(
Name,
Description,
Visible,
AllowMultiple,
DataType,
Parent,
Label,
OrderNumber
)
SELECT
'UserMaximumDaysInactive',
'The maximum number of days since last login before making a user inactive',
1,
0,
'text',
ID,
'Maximum Days Before Making User Inactive',
30
FROM ConfigSettings
WHERE Name="study";

INSERT INTO Config (ConfigID, Value) SELECT ID, "365" FROM ConfigSettings WHERE Name="UserMaximumDaysInactive";

SELECT 'Running: SQL/Archive/25.0/2023-04-24_add_phase_enc_dir_and_echo_number_to_MRICandidateErrors.sql';

-- ---------------------------------------------------------------------------------------------
-- alter MRICandidateErrors table to add PhaseEncodingDirection and EchoNumber
-- ---------------------------------------------------------------------------------------------
ALTER TABLE MRICandidateErrors ADD COLUMN `PhaseEncodingDirection` VARCHAR(3) DEFAULT NULL;
ALTER TABLE MRICandidateErrors ADD COLUMN `EchoNumber` VARCHAR(20) DEFAULT NULL;
2 changes: 2 additions & 0 deletions modules/configuration/.gitignore
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Expand Up @@ -3,3 +3,5 @@
# we can just ignore the whole directory.
js/CohortRelations.js
js/configuration_helper.js
js/CohortRelations.js.map
js/configuration_helper.js.map
11 changes: 0 additions & 11 deletions raisinbread/RB_files/RB_project_subproject_rel.sql
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9 changes: 0 additions & 9 deletions raisinbread/RB_files/RB_subproject.sql
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