" FROM ConfigSettings WHERE Name="StudyDescription";
INSERT INTO Config (ConfigID, Value) SELECT ID, "images/neurorgb_web.jpg" FROM ConfigSettings WHERE Name="studylogo";
INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useEDC";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useDoB";
INSERT INTO Config (ConfigID, Value) SELECT ID, 8 FROM ConfigSettings WHERE Name="ageMin";
INSERT INTO Config (ConfigID, Value) SELECT ID, 11 FROM ConfigSettings WHERE Name="ageMax";
INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useFamilyID";
diff --git a/SQL/Cleanup_patches/2023-01-24-DropPresent.sql b/SQL/Cleanup_patches/2023-01-24-DropPresent.sql
new file mode 100644
index 00000000000..ab09d81bac8
--- /dev/null
+++ b/SQL/Cleanup_patches/2023-01-24-DropPresent.sql
@@ -0,0 +1 @@
+ALTER TABLE acknowledgements DROP COLUMN present;
diff --git a/SQL/Cleanup_patches/2024-04-24-InstrumentData_table.sql b/SQL/Cleanup_patches/2024-04-24-InstrumentData_table.sql
new file mode 100644
index 00000000000..f93796b648c
--- /dev/null
+++ b/SQL/Cleanup_patches/2024-04-24-InstrumentData_table.sql
@@ -0,0 +1,4 @@
+
+ALTER TABLE flag DROP COLUMN Data;
+-- Reclaim the space that was used by the column
+OPTIMIZE TABLE flag;
diff --git a/SQL/Cleanup_patches/2024-09-13-NoTestName.sql b/SQL/Cleanup_patches/2024-09-13-NoTestName.sql
new file mode 100644
index 00000000000..d6605cd5ca8
--- /dev/null
+++ b/SQL/Cleanup_patches/2024-09-13-NoTestName.sql
@@ -0,0 +1,2 @@
+ALTER TABLE flag DROP CONSTRAINT FK_flag_2;
+ALTER TABLE flag DROP COLUMN test_name;
diff --git a/SQL/New_patches/2020-10-28-Doc-Repo-Updates.sql b/SQL/New_patches/2020-10-28-Doc-Repo-Updates.sql
new file mode 100644
index 00000000000..040fa0e05f6
--- /dev/null
+++ b/SQL/New_patches/2020-10-28-Doc-Repo-Updates.sql
@@ -0,0 +1,29 @@
+-- create new permissions to upload and to hide files
+INSERT INTO permissions (code, description, moduleID, action, categoryID) VALUES
+ (
+ 'document_repository_categories',
+ 'Categories',
+ (SELECT ID FROM modules WHERE Name='document_repository'),
+ 'Edit/Upload/Delete',
+ 2
+ ),
+ (
+ 'document_repository_hidden',
+ 'Restricted files',
+ (SELECT ID FROM modules WHERE Name='document_repository'),
+ 'View',
+ 2
+ );
+
+UPDATE permissions
+ SET code='document_repository_upload_edit' WHERE code='document_repository_edit';
+
+-- give categories and hide permissions to admin
+INSERT INTO user_perm_rel (userID, permID) VALUES
+ ((SELECT ID FROM users WHERE UserID='admin'), (SELECT permID FROM permissions WHERE code='document_repository_categories')),
+ ((SELECT ID FROM users WHERE UserID='admin'), (SELECT permID FROM permissions WHERE code='document_repository_hidden'));
+
+
+-- create column to hide files
+ALTER TABLE document_repository
+ ADD COLUMN hidden_file enum('yes','no') DEFAULT NULL;
\ No newline at end of file
diff --git a/SQL/New_patches/2023-12-08_useDoB.sql b/SQL/New_patches/2023-12-08_useDoB.sql
new file mode 100644
index 00000000000..e96a7cf02e7
--- /dev/null
+++ b/SQL/New_patches/2023-12-08_useDoB.sql
@@ -0,0 +1,2 @@
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useDoB', 'Use DoB (Date of Birth)', 1, 0, 'boolean', ID, 'Use DoB', 31 FROM ConfigSettings WHERE Name="study";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useDoB";
diff --git a/SQL/New_patches/2024-04-24-InstrumentData_table.sql b/SQL/New_patches/2024-04-24-InstrumentData_table.sql
new file mode 100644
index 00000000000..79048478b02
--- /dev/null
+++ b/SQL/New_patches/2024-04-24-InstrumentData_table.sql
@@ -0,0 +1,22 @@
+CREATE TABLE `instrument_data` (
+ `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `Data` longtext CHARACTER SET utf8mb4 COLLATE utf8mb4_bin NOT NULL CHECK (json_valid(`Data`)),
+ PRIMARY KEY (`ID`)
+);
+
+-- we abuse the ID of the flag column for data migration
+-- by making it the same as the id in the new table, even
+-- though they're different primary keys
+INSERT INTO instrument_data SELECT ID, Data FROM flag WHERE Data IS NOT NULL;
+
+ALTER TABLE flag ADD COLUMN DataID int(10) unsigned;
+ALTER TABLE flag ADD FOREIGN KEY (DataID) REFERENCES instrument_data(ID);
+
+-- from this point forward they won't necessarily be the same id, but we don't
+-- care anymore now that the data is migrated and foreign keys were enforced
+UPDATE flag SET DataID=ID WHERE Data IS NOT NULL;
+
+-- FIXME: Put in a cleanup patch
+-- ALTER TABLE flag DROP COLUMN Data;
+-- Reclaim the space that was used by the column
+-- OPTIMIZE TABLE flag;
diff --git a/SQL/New_patches/2024-07-16-CleanDefault.sql b/SQL/New_patches/2024-07-16-CleanDefault.sql
new file mode 100644
index 00000000000..188b99c502e
--- /dev/null
+++ b/SQL/New_patches/2024-07-16-CleanDefault.sql
@@ -0,0 +1,148 @@
+-- Drop nonsensical defaults and put use right type for others.
+
+ALTER TABLE `users`
+ ALTER `Privilege` SET DEFAULT 0;
+
+ALTER TABLE `candidate`
+ ALTER `CandID` DROP DEFAULT;
+
+ALTER TABLE `candidate`
+ ALTER `RegistrationCenterID` DROP DEFAULT;
+
+ALTER TABLE `session`
+ ALTER `CandID` DROP DEFAULT;
+
+ALTER TABLE `instrument_subtests`
+ ALTER `Order_number` SET DEFAULT 0;
+
+ALTER TABLE `flag`
+ ALTER `SessionID` DROP DEFAULT;
+
+ALTER TABLE `tarchive`
+ ALTER `AcquisitionCount` SET DEFAULT 0;
+
+ALTER TABLE `tarchive`
+ ALTER `NonDicomFileCount` SET DEFAULT 0;
+
+ALTER TABLE `tarchive`
+ ALTER `DicomFileCount` SET DEFAULT 0;
+
+ALTER TABLE `tarchive`
+ ALTER `sumTypeVersion` SET DEFAULT 0;
+
+ALTER TABLE `tarchive`
+ ALTER `uploadAttempt` SET DEFAULT 0;
+
+ALTER TABLE `tarchive`
+ ALTER `PendingTransfer` SET DEFAULT 0;
+
+ALTER TABLE `tarchive_series`
+ ALTER `TarchiveID` DROP DEFAULT;
+
+ALTER TABLE `tarchive_series`
+ ALTER `SeriesNumber` SET DEFAULT 0;
+
+ALTER TABLE `tarchive_series`
+ ALTER `NumberOfFiles` SET DEFAULT 0;
+
+ALTER TABLE `tarchive_files`
+ ALTER `TarchiveID` DROP DEFAULT;
+
+ALTER TABLE `hrrt_archive`
+ ALTER `EcatFileCount` SET DEFAULT 0;
+
+ALTER TABLE `hrrt_archive`
+ ALTER `NonEcatFileCount` SET DEFAULT 0;
+
+ALTER TABLE `hrrt_archive_files`
+ ALTER `HrrtArchiveID` DROP DEFAULT;
+
+ALTER TABLE `mri_processing_protocol`
+ ALTER `InsertTime` SET DEFAULT 0;
+
+ALTER TABLE `files`
+ ALTER `SessionID` DROP DEFAULT;
+
+ALTER TABLE `files`
+ ALTER `InsertTime` SET DEFAULT 0;
+
+ALTER TABLE `files`
+ ALTER `SourceFileID` DROP DEFAULT;
+
+ALTER TABLE `mri_upload`
+ ALTER `InsertionComplete` SET DEFAULT 0;
+
+ALTER TABLE `mri_upload`
+ ALTER `IsTarchiveValidated` SET DEFAULT 0;
+
+ALTER TABLE `document_repository_categories`
+ ALTER `parent_id` DROP DEFAULT;
+
+ALTER TABLE `document_repository`
+ ALTER `EARLI` SET DEFAULT 0;
+
+ALTER TABLE `document_repository`
+ ALTER `hide_video` SET DEFAULT 0;
+
+ALTER TABLE `notification_types`
+ ALTER `private` SET DEFAULT 0;
+
+ALTER TABLE `notification_spool`
+ ALTER `NotificationTypeID` DROP DEFAULT;
+
+ALTER TABLE `notification_spool`
+ ALTER `ProcessID` DROP DEFAULT;
+
+ALTER TABLE `participant_status`
+ ALTER `CandID` DROP DEFAULT;
+
+ALTER TABLE `participant_status_history`
+ ALTER `CandID` DROP DEFAULT;
+
+ALTER TABLE `certification`
+ ALTER `examinerID` DROP DEFAULT;
+
+ALTER TABLE `media`
+ ALTER `hide_file` SET DEFAULT 0;
+
+ALTER TABLE `parameter_type`
+ ALTER `Queryable` SET DEFAULT 1;
+
+ALTER TABLE `parameter_type`
+ ALTER `IsFile` SET DEFAULT 0;
+
+ALTER TABLE `parameter_type_category_rel`
+ ALTER `ParameterTypeID` DROP DEFAULT;
+
+ALTER TABLE `parameter_type_category_rel`
+ ALTER `ParameterTypeCategoryID` DROP DEFAULT;
+
+ALTER TABLE `parameter_candidate`
+ ALTER `CandID` DROP DEFAULT;
+
+ALTER TABLE `parameter_candidate`
+ ALTER `ParameterTypeID` DROP DEFAULT;
+
+ALTER TABLE `parameter_candidate`
+ ALTER `InsertTime` SET DEFAULT 0;
+
+ALTER TABLE `parameter_session`
+ ALTER `SessionID` DROP DEFAULT;
+
+ALTER TABLE `parameter_session`
+ ALTER `ParameterTypeID` DROP DEFAULT;
+
+ALTER TABLE `parameter_session`
+ ALTER `InsertTime` SET DEFAULT 0;
+
+ALTER TABLE `SNP_candidate_rel`
+ ALTER `SNPID` DROP DEFAULT;
+
+ALTER TABLE `SNP_candidate_rel`
+ ALTER `CandID` DROP DEFAULT;
+
+ALTER TABLE `feedback_mri_predefined_comments`
+ ALTER `CommentTypeID` DROP DEFAULT;
+
+ALTER TABLE `feedback_mri_comments`
+ ALTER `CommentTypeID` DROP DEFAULT;
diff --git a/SQL/New_patches/2024-08-13-issuetracker-AddWatchingToIssuesHistory.sql b/SQL/New_patches/2024-08-13-issuetracker-AddWatchingToIssuesHistory.sql
new file mode 100644
index 00000000000..8eedae2578c
--- /dev/null
+++ b/SQL/New_patches/2024-08-13-issuetracker-AddWatchingToIssuesHistory.sql
@@ -0,0 +1,2 @@
+ALTER TABLE `issues_history`
+ MODIFY `fieldChanged` enum('assignee','status','comment','sessionID','centerID','title','category','module','lastUpdatedBy','priority','candID', 'description', 'watching') NOT NULL DEFAULT 'comment';
diff --git a/SQL/New_patches/2024-09-13-TestID.sql b/SQL/New_patches/2024-09-13-TestID.sql
new file mode 100644
index 00000000000..b2131bf97f4
--- /dev/null
+++ b/SQL/New_patches/2024-09-13-TestID.sql
@@ -0,0 +1,6 @@
+ALTER TABLE flag ADD COLUMN TestID int(10) unsigned AFTER test_name;
+ALTER TABLE flag ADD CONSTRAINT FOREIGN KEY (TestID) REFERENCES test_names(ID);
+
+UPDATE flag f SET TestID=(SELECT ID FROM test_names tn WHERE f.test_name=tn.test_name);
+
+ALTER TABLE flag MODIFY COLUMN TestID int(10) unsigned NOT NULL;
diff --git a/docker-compose.yml b/docker-compose.yml
index 36f6a6d60c8..2b20f2ccfb5 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,4 +1,4 @@
-version: '2'
+version: '3.8'
services:
db:
build:
@@ -13,12 +13,9 @@ services:
- MYSQL_RANDOM_ROOT_PASSWORD=yes
selenium:
- image: selenium/standalone-firefox-debug:3.141.59-zirconium
- volumes:
- - /dev/shm:/dev/shm
+ image: selenium/standalone-firefox:4.25
ports:
- "5900:5900"
-
web:
build:
context: .
@@ -62,58 +59,3 @@ services:
- selenium
- web
entrypoint: /app/test/wait-for-services.sh
-
- selenium-debug:
- image: selenium/standalone-firefox-debug:3.141.59-zirconium
- links:
- - web-debug:web
- ports:
- - "5901:5900"
-
- web-debug:
- build:
- context: .
- dockerfile: Dockerfile.test.php8.debug
- volumes:
- - ./:/app
- - ./test/test_instrument:/app/project/instruments
- environment:
- - LORIS_DB_CONFIG=/app/test/config.xml
- - XDEBUG_CONFIG=remote_host=${XDEBUG_REMOTE_HOST}
- - PHP_IDE_CONFIG=serverName=LorisTests
- depends_on:
- - db
- command: php -S 0.0.0.0:8000 -t /app/htdocs /app/htdocs/router.php
-
- unit-tests-debug:
- build:
- context: .
- dockerfile: Dockerfile.test.php8.debug
- volumes:
- - ./:/app
- working_dir: /app
- environment:
- - LORIS_DB_CONFIG=test/config.xml
- - XDEBUG_CONFIG=remote_host=${XDEBUG_REMOTE_HOST}
- - PHP_IDE_CONFIG=serverName=LorisTests
- depends_on:
- - db
- entrypoint: /app/test/wait-for-services.sh
-
- integration-tests-debug:
- build:
- context: .
- dockerfile: Dockerfile.test.php8.debug
- volumes:
- - ./:/app
- working_dir: /app
- environment:
- - LORIS_DB_CONFIG=test/config.xml
- - SELENIUM_REQUIRED=true
- - XDEBUG_CONFIG=remote_host=${XDEBUG_REMOTE_HOST}
- - PHP_IDE_CONFIG=serverName=LorisTests
- links:
- - db
- - selenium-debug:selenium
- - web-debug:web
- entrypoint: /app/test/wait-for-services.sh
diff --git a/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md b/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md
index 5f4f132ebe2..c77ecdbf548 100644
--- a/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md
+++ b/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md
@@ -10,9 +10,9 @@ For further details on the install process, please see the LORIS GitHub Wiki Cen
# System Requirements - Install dependencies
Default dependencies installed by CentOS 7.x may not meet the version requirements for LORIS deployment or development:
-* MariaDB 10.3 is supported for LORIS 25.
+* MariaDB 10.3 is supported for LORIS 26.
-* PHP 8.1 (or higher) is supported for LORIS 25.
+* PHP 8.2 (or higher) is supported for LORIS 26.
In addition to the above, the following packages should be installed with `yum` and may also differ from the packages referenced in the main (Ubuntu) [LORIS Readme](../../../../../README.md). Detailed command examples are provided below (`sudo` privilege may be required depending on your system).
* Apache 2.4 or higher
diff --git a/htdocs/AjaxHelper.php b/htdocs/AjaxHelper.php
index 09dff46b3db..a9521b74b95 100644
--- a/htdocs/AjaxHelper.php
+++ b/htdocs/AjaxHelper.php
@@ -1,4 +1,5 @@
- {
- let combined;
- if (remainder.length == 0) {
- combined = value;
- } else {
- combined = new Uint8Array(
- value.length + remainder.length
- );
- for (let i = 0; i < remainder.length; i++) {
- combined[i] = remainder[i];
- }
- for (let i = 0; i < value.length; i++) {
- combined[i+remainder.length] = value[i];
- }
- }
- return processLines(combined, rowcb, endstreamcb);
- }).then(({remainder: rem, eos}) => {
- chunkcb(eos);
- doneLoop = eos;
- remainder = rem;
- }).catch((err) => {
- console.error(err);
- doneLoop = true;
- });
- }
+ let remainder = [];
+ let doneLoop = false;
+ while (!doneLoop) {
+ await reader.read().then(({done, value}) => {
+ let combined;
+ if (remainder.length == 0) {
+ combined = value;
+ } else {
+ combined = new Uint8Array(
+ value.length + remainder.length
+ );
+ for (let i = 0; i < remainder.length; i++) {
+ combined[i] = remainder[i];
+ }
+ for (let i = 0; i < value.length; i++) {
+ combined[i+remainder.length] = value[i];
+ }
+ }
+ return processLines(combined, rowcb, endstreamcb);
+ }).then(({remainder: rem, eos}) => {
+ chunkcb(eos);
+ doneLoop = eos;
+ remainder = rem;
+ }).catch((err) => {
+ console.error(err);
+ doneLoop = true;
+ });
+ }
}
export default fetchDataStream;
diff --git a/jsx/Breadcrumbs.js b/jsx/Breadcrumbs.js
index cef326354d6..c5ab758b09b 100644
--- a/jsx/Breadcrumbs.js
+++ b/jsx/Breadcrumbs.js
@@ -106,9 +106,9 @@ class Breadcrumbs extends Component {
} else {
breadcrumbs.push(
+ href={url}
+ className='btn btn-primary'
+ onClick={onClick}>