[permissions] Renaming and organizing permissions phase 0

Dockerfile.test.db

@@ -3,8 +3,8 @@ FROM mysql:5.7
 ARG BASE_DIR
 
 COPY SQL/0000-00-00-schema.sql /0000-00-00-schema.sql
-COPY SQL/0000-00-01-Permission.sql /0000-00-01-Permission.sql
-COPY SQL/0000-00-02-Modules.sql /0000-00-02-Modules.sql
+COPY SQL/0000-00-01-Modules.sql /0000-00-01-Modules.sql
+COPY SQL/0000-00-02-Permission.sql /0000-00-02-Permission.sql
 COPY SQL/0000-00-03-ConfigTables.sql /0000-00-03-ConfigTables.sql
 COPY SQL/0000-00-04-Help.sql /0000-00-04-Help.sql
 COPY SQL/0000-00-05-ElectrophysiologyTables.sql /0000-00-05-ElectrophysiologyTables.sql
@@ -18,8 +18,8 @@ COPY raisinbread/RB_files/*.sql /RB_files/
 
 RUN echo "Use LorisTest;" | cat - \
     0000-00-00-schema.sql \
-    0000-00-01-Permission.sql \
-    0000-00-02-Modules.sql \
+    0000-00-01-Modules.sql \
+    0000-00-02-Permission.sql \
     0000-00-03-ConfigTables.sql \
     0000-00-04-Help.sql \
     0000-00-05-ElectrophysiologyTables.sql \

SQL/0000-00-02-Permission.sql

@@ -0,0 +1,152 @@
+--
+-- Table structure for table `permissions_category`
+--
+
+CREATE TABLE `permissions_category` (
+  `ID` int(10) NOT NULL AUTO_INCREMENT,
+  `Description` varchar(255) NOT NULL,
+  PRIMARY KEY (`ID`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+INSERT INTO `permissions_category` VALUES
+  (1,'Roles'),
+  (2,'Permission');
+
+
+CREATE TABLE `permissions` (
+  `permID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `code` varchar(255) NOT NULL DEFAULT '',
+  `description` varchar(255) NOT NULL DEFAULT '',
+  `moduleID` int(11) unsigned,
+  `action` enum (
+      'View',
+      'Create',
+      'Edit',
+      'Download',
+      'Upload',
+      'Delete',
+      'View/Create',
+      'View/Edit',
+      'View/Download',
+      'View/Upload',
+      'View/Create/Edit',
+      'Create/Edit',
+      'Edit/Upload',
+      'Edit/Upload/Delete'),
+  `categoryID` int(10) NOT NULL DEFAULT '2',
+  PRIMARY KEY (`permID`),
+  UNIQUE KEY `code` (`code`),
+  KEY `fk_permissions_1_idx` (`categoryID`),
+  CONSTRAINT `fk_permissions_1`
+  FOREIGN KEY (`categoryID`)
+    REFERENCES `permissions_category` (`ID`)
+    ON DELETE NO ACTION
+    ON UPDATE NO ACTION,
+  CONSTRAINT `fk_permissions_2`
+  FOREIGN KEY (`moduleID`)
+    REFERENCES `modules` (`ID`)
+    ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+CREATE TABLE `user_perm_rel` (
+  `userID` int(10) unsigned NOT NULL default '0',
+  `permID` int(10) unsigned NOT NULL default '0',
+  PRIMARY KEY  (`userID`,`permID`),
+  KEY `FK_user_perm_rel_2` (`permID`),
+  CONSTRAINT `FK_user_perm_rel_2`
+  FOREIGN KEY (`permID`)
+    REFERENCES `permissions` (`permID`)
+    ON DELETE CASCADE
+    ON UPDATE CASCADE,
+  CONSTRAINT `FK_user_perm_rel_1`
+  FOREIGN KEY (`userID`)
+    REFERENCES `users` (`ID`)
+    ON DELETE CASCADE
+    ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+
+INSERT INTO `permissions` VALUES
+    (1,'superuser','Superuser - supersedes all permissions',NULL,NULL,'1'),
+    (2,'user_accounts','User Accounts - Own Sites',(SELECT ID FROM modules WHERE Name='user_accounts'),'View/Create/Edit','2'),
+    (3,'user_accounts_multisite','User Accounts - All Sites',(SELECT ID FROM modules WHERE Name='user_accounts'),'View/Create/Edit','2'),
+    (4,'context_help','Help documentation',(SELECT ID FROM modules WHERE Name='help_editor'),'Edit','2'),
+    (5,'bvl_feedback','Feedback Threads',(SELECT ID FROM modules WHERE Name='bvl_feedback'),'Create/Edit','1'),
+    (6,'imaging_browser_qc','Status',(SELECT ID FROM modules WHERE Name='imaging_browser'),'Edit','2'),
+    (7,'send_to_dcc','Send to DCC',(SELECT ID FROM modules WHERE Name='instrument_list'),NULL,'2'),
+    (8,'unsend_to_dcc','Reverse Send from DCC',(SELECT ID FROM modules WHERE Name='instrument_list'),NULL,'2'),
+    (9,'access_all_profiles','Candidates and Timepoints - All Sites',(SELECT ID FROM modules WHERE Name='candidate_list'),'View','2'),
+    (10,'data_entry','Candidates and Timepoints - Own Sites',(SELECT ID FROM modules WHERE Name='candidate_list'),'View/Create','1'),
+    (11,'examiner_view','Add and Certify Examiners - Own Sites',(SELECT ID FROM modules WHERE Name='examiner'),NULL,'2'),
+    (12,'examiner_multisite','Add and Certify Examiners - All Sites',(SELECT ID FROM modules WHERE Name='examiner'),NULL,'2'),
+    (13,'conflict_resolver','Resolve Conflicts',(SELECT ID FROM modules WHERE Name='conflict_resolver'),NULL,'2'),
+    (14,'data_dict_view','Parameter Type Descriptions',(SELECT ID FROM modules WHERE Name='datadict'),'View','2'),
+    (15,'violated_scans_view_allsites','Violated Scans - All Sites',(SELECT ID FROM modules WHERE Name='mri_violations'),'View','2'),
+    (16,'config','Settings',(SELECT ID FROM modules WHERE Name='configuration'),'View/Edit','2'),
+    (17,'imaging_browser_view_site','Imaging Scans - Own Sites',(SELECT ID FROM modules WHERE Name='imaging_browser'),'View','2'),
+    (18,'imaging_browser_view_allsites', 'Imaging Scans - All Sites',(SELECT ID FROM modules WHERE Name='imaging_browser'),'View', '2'),
+    (19,'dicom_archive_view_allsites', 'DICOMs - All Sites',(SELECT ID FROM modules WHERE Name='dicom_archive'),'View', '2'),
+    (20,'instrument_builder', 'Instrument Forms',(SELECT ID FROM modules WHERE Name='instrument_builder'),'Create/Edit', '2'),
+    (21,'data_dict_edit','Parameter Type Descriptions',(SELECT ID FROM modules WHERE Name='datadict'),'Edit','2'),
+    (22,'candidate_parameter_view','Candidate Information',(SELECT ID FROM modules WHERE Name='candidate_parameters'),'View','2'),
+    (23,'candidate_parameter_edit','Candidate Information',(SELECT ID FROM modules WHERE Name='candidate_parameters'),'Edit','2'),
+    (24,'genomic_browser_view_site','Genomic Data - Own Sites',(SELECT ID FROM modules WHERE Name='genomic_browser'),'View','2'),
+    (25,'genomic_browser_view_allsites','Genomic Data - All Sites',(SELECT ID FROM modules WHERE Name='genomic_browser'),'View','2'),
+    (26,'document_repository_view','Documents',(SELECT ID FROM modules WHERE Name='document_repository'),'View','2'),
+    (27,'document_repository_delete','Documents',(SELECT ID FROM modules WHERE Name='document_repository'),'Delete','2'),
+    (28,'server_processes_manager','Processes',(SELECT ID FROM modules WHERE Name='server_processes_manager'),'View','2'),
+    (29,'imaging_uploader','Imaging Scans',(SELECT ID FROM modules WHERE Name='imaging_uploader'),'View/Upload','2'),
+    (30,'acknowledgements_view','Acknowledgee List',(SELECT ID FROM modules WHERE Name='acknowledgements'),'View','2'),
+    (31,'acknowledgements_edit','Acknowledgee List',(SELECT ID FROM modules WHERE Name='acknowledgements'),'Edit','2'),
+    (32,'dataquery_view','Cross-Modality Data',(SELECT ID FROM modules WHERE Name='dataquery'),'View/Download','2'),
+    (33,'genomic_data_manager','Genomic Files',(SELECT ID FROM modules WHERE Name='genomic_browser'),'Upload','2'),
+    (34,'media_write','Candidate Media Files',(SELECT ID FROM modules WHERE Name='media'),'Edit/Upload/Delete','2'),
+    (35,'media_read','Candidate Media Files',(SELECT ID FROM modules WHERE Name='media'),'View/Download','2'),
+    (36,'issue_tracker_reporter', 'Create/Edit Own Issues and Comment on All Issues',(SELECT ID FROM modules WHERE Name='issue_tracker'),NULL, 2),
+    (37,'issue_tracker_developer', 'Close/Edit/Re-assign/Comment on All Issues',(SELECT ID FROM modules WHERE Name='issue_tracker'),NULL, 2),
+    (38,'imaging_browser_phantom_allsites', 'Phantom Scans - All Sites',(SELECT ID FROM modules WHERE Name='imaging_browser'),'View', 2),
+    (39,'imaging_browser_phantom_ownsite', 'Phantom Scans - Own Sites',(SELECT ID FROM modules WHERE Name='imaging_browser'),'View', 2),
+    (40,'data_release_view', 'Release Files',(SELECT ID FROM modules WHERE Name='data_release'),'View', 2),
+    (41,'data_release_upload', 'Release Files',(SELECT ID FROM modules WHERE Name='data_release'),'Upload', 2),
+    (42,'data_release_edit_file_access', 'Grant Other Users Access to Releases',(SELECT ID FROM modules WHERE Name='data_release'),NULL, 2),
+    (43,'instrument_manager_read', 'Installed Instruments',(SELECT ID FROM modules WHERE Name='instrument_manager'),'View', 2),
+    (44,'instrument_manager_write', 'Upload and Install Instruments',(SELECT ID FROM modules WHERE Name='instrument_manager'),NULL, 2),
+    (45,'publication_view', 'Publication Projects',(SELECT ID FROM modules WHERE Name='publication'),'View', 2),
+    (46,'publication_propose', 'Propose Publication Projects',(SELECT ID FROM modules WHERE Name='publication'),NULL, 2),
+    (47,'publication_approve', 'Accept/Reject Publication Projects',(SELECT ID FROM modules WHERE Name='publication'),NULL, 2),
+    (48, 'candidate_dob_edit', 'Dates of Birth',(SELECT ID FROM modules WHERE Name='candidate_parameters'),'Edit', 2),
+    (49,'electrophysiology_browser_view_allsites', 'EEGs - All Sites',(SELECT ID FROM modules WHERE Name='electrophysiology_browser'),'View', 2),
+    (50,'electrophysiology_browser_view_site', 'EEGs - Own Sites',(SELECT ID FROM modules WHERE Name='electrophysiology_browser'),'View', 2),
+    (51,'battery_manager_view','Battery Entries',(SELECT ID FROM modules WHERE Name='battery_manager'),'View',2),
+    (52,'battery_manager_edit','Battery Entries',(SELECT ID FROM modules WHERE Name='battery_manager'),'Create/Edit',2),
+    (53,'module_manager_view', 'Installed Modules',(SELECT ID FROM modules WHERE Name='module_manager'),'View', 2),
+    (54,'module_manager_edit', 'Installed Modules',(SELECT ID FROM modules WHERE Name='module_manager'),'Edit', 2),
+    (55,'candidate_dod_edit', 'Dates of Death',(SELECT ID FROM modules WHERE Name='candidate_parameters'),'Edit', 2),
+    (56,'violated_scans_view_ownsite','Violated Scans - Own Sites',(SELECT ID FROM modules WHERE Name='mri_violations'),'View','2'),
+    (57,'document_repository_edit','Documents',(SELECT ID FROM modules WHERE Name='document_repository'),'Edit/Upload','2'),
+    (58,'survey_accounts_view', 'Candidate Surveys',(SELECT ID FROM modules WHERE Name='survey_accounts'),'View', 2),
+    (59,'imaging_quality_control_view','Flagged Imaging Entries',(SELECT ID FROM modules WHERE Name='imaging_qc'),'View','2'),
+    (60,'behavioural_quality_control_view','Flagged Behavioural Entries',(SELECT ID FROM modules WHERE Name='behavioural_qc'),'View','2');
+
+INSERT INTO `user_perm_rel` (userID, permID)
+  SELECT u.ID, p.permID
+  FROM users u JOIN permissions p
+  WHERE u.userid = 'admin'
+  ORDER BY p.permID;
+
+-- permissions for each notification module
+DROP TABLE IF EXISTS `notification_modules_perm_rel`;
+CREATE TABLE `notification_modules_perm_rel` (
+      `notification_module_id` int(10) unsigned NOT NULL,
+      `perm_id` int(10) unsigned NOT NULL default '0',
+      CONSTRAINT `FK_notification_modules_perm_rel_1` FOREIGN KEY (`notification_module_id`) REFERENCES `notification_modules` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
+      CONSTRAINT `FK_notification_modules_perm_rel_2` FOREIGN KEY (`perm_id`) REFERENCES `permissions` (`permID`) ON DELETE CASCADE ON UPDATE CASCADE,
+      PRIMARY KEY (`notification_module_id`,`perm_id`)
+) ENGINE=InnoDB DEFAULT CHARSET='utf8';
+
+-- populate notification perm table
+INSERT INTO notification_modules_perm_rel SELECT nm.id, p.permID FROM notification_modules nm JOIN permissions p WHERE nm.module_name='media' AND (p.code='media_write' OR p.code='media_read');
+INSERT INTO notification_modules_perm_rel SELECT nm.id, p.permID FROM notification_modules nm JOIN permissions p WHERE nm.module_name='document_repository' AND (p.code='document_repository_view' OR p.code='document_repository_delete');
+INSERT INTO notification_modules_perm_rel SELECT nm.id, p.permID FROM notification_modules nm JOIN permissions p WHERE nm.module_name='publication' AND (p.code='publication_view' OR p.code='publication_propose' OR p.code='publication_approve');

SQL/9999-99-99-drop_tables.sql

@@ -28,10 +28,10 @@ DROP TABLE IF EXISTS `issues_comments`;
 DROP TABLE IF EXISTS `issues`;
 DROP TABLE IF EXISTS `issues_categories`;
 
--- 0000-00-02-Modules.sql
+-- 0000-00-01-Modules.sql
 DROP TABLE IF EXISTS `modules`;
 
--- 0000-00-01-Permission.sql
+-- 0000-00-02-Permission.sql
 DROP TABLE IF EXISTS `user_perm_rel`;
 DROP TABLE IF EXISTS `notification_modules_perm_rel`;
 DROP TABLE IF EXISTS `permissions`;

SQL/Cleanup_patches/2021-01-31-deleting_permissions.sql

@@ -0,0 +1,4 @@
+DELETE FROM permissions WHERE code='training';
+DELETE FROM permissions WHERE code='timepoint_flag';
+DELETE FROM permissions WHERE code='timepoint_flag_evaluate';
+DELETE FROM permissions WHERE code='mri_efax';