Bump Version to 1.30.0, update history, refresh schema files

HISTORY.rst

@@ -5,6 +5,31 @@ History
 Unreleased / master
 -------------------
 
+1.30.0 (2022-06-22)
+-------------------
+
+New tables (for cryo-ET and electrin diffraction):
+
+* ``Tomogram``: For storing per-sample, per-position data analysis results (reconstruction)
+* ``TiltImageAlignment``: For storing per-movie analysis results (reconstruction)
+
+New columns (for cryo-ET and electron diffraction):
+
+* angle
+* fluence
+* numberOfFrames
+
+Other changes:
+
+* Add JNB (Jupyter Notebook) option to ``app`` enum in ``Pod`` table
+* Add execute privilege to ``ispyb_acquisition`` role on:
+ * procedure ``upsert_dc``
+ * function ``retrieve_visit_id``
+
+* Make it possible to delete from ``BeamCalendar`` without deleting ``BLSessions`` (no longer cascading delete)
+* Add index on ``recordTimeStamp`` in ``SW_onceToken``
+
+
 1.29.0 (2022-02-14)
 -------------------
 

schemas/ispyb/lookups.sql

@@ -10,7 +10,7 @@
 /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
 
 /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */;
-INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.29.0');
+INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.30.0');
 /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */;
@@ -190,7 +190,12 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
 (215,'2022_01_12_Container_and_ContainerHistory_update.sql','DONE','2022-02-14 11:02:17'),
 (216,'2022_01_20_Container_priorityPipelineId_default.sql','DONE','2022-02-14 11:02:18'),
 (217,'2022_02_04_Pod.sql','DONE','2022-02-14 11:02:18'),
-(218,'2022_02_14_AdminVar_bump_version.sql','DONE','2022-02-14 11:02:18');
+(218,'2022_02_14_AdminVar_bump_version.sql','DONE','2022-02-14 11:02:18'),
+(219,'2022_03_07_SW_onceToken_recordTimeStamp_idx.sql','DONE','2022-06-22 12:09:07'),
+(220,'2022_04_12_BLSession_fk_beamCalendarId_set_null.sql','DONE','2022-06-22 12:09:07'),
+(221,'2022_05_12_Pod_app_modify_enum.sql','DONE','2022-06-22 12:09:07'),
+(222,'2022_06_22_AdminVar_bump_version.sql','DONE','2022-06-22 12:09:07'),
+(223,'2022_06_22_cryo-ET_tables.sql','DONE','2022-06-22 12:09:07');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;

schemas/ispyb/tables.sql

@@ -731,7 +731,8 @@ CREATE TABLE `BLSession` (
  KEY `Session_FKIndexBeamLineName` (`beamLineName`),
  KEY `Session_FKIndexEndDate` (`endDate`),
  KEY `Session_FKIndexStartDate` (`startDate`),
- KEY `BLSession_ibfk_3` (`beamCalendarId`),
+ KEY `BLSession_fk_beamCalendarId` (`beamCalendarId`),
+ CONSTRAINT `BLSession_fk_beamCalendarId` FOREIGN KEY (`beamCalendarId`) REFERENCES `BeamCalendar` (`beamCalendarId`) ON DELETE SET NULL ON UPDATE CASCADE,
  CONSTRAINT `BLSession_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `BLSession_ibfk_2` FOREIGN KEY (`beamLineSetupId`) REFERENCES `BeamLineSetup` (`beamLineSetupId`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `BLSession_ibfk_3` FOREIGN KEY (`beamCalendarId`) REFERENCES `BeamCalendar` (`beamCalendarId`)
@@ -889,6 +890,7 @@ CREATE TABLE `BeamLineSetup` (
  `monoBandwidthMin` double DEFAULT NULL COMMENT 'unit: percentage',
  `monoBandwidthMax` double DEFAULT NULL COMMENT 'unit: percentage',
  `preferredDataCentre` varchar(30) DEFAULT NULL COMMENT 'Relevant datacentre to use to process data from this beamline',
+ `amplitudeContrast` float DEFAULT NULL COMMENT 'Needed for cryo-ET',
  PRIMARY KEY (`beamLineSetupId`),
  KEY `BeamLineSetup_ibfk_1` (`detectorId`),
  CONSTRAINT `BeamLineSetup_ibfk_1` FOREIGN KEY (`detectorId`) REFERENCES `Detector` (`detectorId`)
@@ -2500,6 +2502,9 @@ CREATE TABLE `Movie` (
  `positionX` float DEFAULT NULL,
  `positionY` float DEFAULT NULL,
  `nominalDefocus` float unsigned DEFAULT NULL COMMENT 'Nominal defocus, Units: A',
+ `angle` float DEFAULT NULL COMMENT 'unit: degrees relative to perpendicular to beam',
+ `fluence` float DEFAULT NULL COMMENT 'accumulated electron fluence from start to end of acquisition of this movie (commonly, but incorrectly, referred to as ‘dose’)',
+ `numberOfFrames` int(11) unsigned DEFAULT NULL COMMENT 'number of frames per movie. This should be equivalent to the number of MotionCorrectionDrift entries, but the latter is a property of data analysis, whereas the number of frames is an intrinsic property of acquisition.',
  PRIMARY KEY (`movieId`),
  KEY `Movie_ibfk1` (`dataCollectionId`),
  CONSTRAINT `Movie_ibfk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`)
@@ -2851,7 +2856,7 @@ CREATE TABLE `Pod` (
  `podId` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `personId` int(10) unsigned NOT NULL COMMENT 'Pod owner defined by the logged in SynchWeb user who requested the pod start up',
  `filePath` varchar(255) COLLATE utf8mb3_unicode_ci DEFAULT NULL COMMENT 'File or directory path to mount into the Pod if required',
- `app` enum('MAXIV HDF5 Viewer','H5Web') COLLATE utf8mb3_unicode_ci NOT NULL,
+ `app` enum('MAXIV HDF5 Viewer','H5Web','JNB') COLLATE utf8mb3_unicode_ci NOT NULL,
  `podName` varchar(255) COLLATE utf8mb3_unicode_ci DEFAULT NULL,
  `status` varchar(25) COLLATE utf8mb3_unicode_ci DEFAULT NULL,
  `ip` varchar(15) COLLATE utf8mb3_unicode_ci DEFAULT NULL,
@@ -3328,6 +3333,7 @@ CREATE TABLE `SW_onceToken` (
  PRIMARY KEY (`onceTokenId`),
  KEY `SW_onceToken_fk1` (`personId`),
  KEY `SW_onceToken_fk2` (`proposalId`),
+ KEY `SW_onceToken_recordTimeStamp_idx` (`recordTimeStamp`),
  CONSTRAINT `SW_onceToken_fk1` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`),
  CONSTRAINT `SW_onceToken_fk2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`)
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='One-time use tokens needed for token auth in order to grant access to file downloads and webcams (and some images)';
@@ -3980,6 +3986,52 @@ CREATE TABLE `SubtractionToAbInitioModel` (
  CONSTRAINT `substractionToSubstraction` FOREIGN KEY (`subtractionId`) REFERENCES `Subtraction` (`subtractionId`) ON DELETE CASCADE ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `TiltImageAlignment`;
+/*!40101 SET @saved_cs_client = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `TiltImageAlignment` (
+ `movieId` int(11) unsigned NOT NULL COMMENT 'FK to Movie table',
+ `tomogramId` int(11) unsigned NOT NULL COMMENT 'FK to Tomogram table; tuple (movieID, tomogramID) is unique',
+ `defocusU` float DEFAULT NULL COMMENT 'unit: Angstroms',
+ `defocusV` float DEFAULT NULL COMMENT 'unit: Angstroms',
+ `psdFile` varchar(255) DEFAULT NULL,
+ `resolution` float DEFAULT NULL COMMENT 'unit: Angstroms',
+ `fitQuality` float DEFAULT NULL,
+ `refinedMagnification` float DEFAULT NULL COMMENT 'unitless',
+ `refinedTiltAngle` float DEFAULT NULL COMMENT 'units: degrees',
+ `refinedTiltAxis` float DEFAULT NULL COMMENT 'units: degrees',
+ `residualError` float DEFAULT NULL COMMENT 'Residual error, unit: nm',
+ PRIMARY KEY (`movieId`,`tomogramId`),
+ KEY `TiltImageAlignment_fk_tomogramId` (`tomogramId`),
+ CONSTRAINT `TiltImageAlignment_fk_movieId` FOREIGN KEY (`movieId`) REFERENCES `Movie` (`movieId`) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT `TiltImageAlignment_fk_tomogramId` FOREIGN KEY (`tomogramId`) REFERENCES `Tomogram` (`tomogramId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For storing per-movie analysis results (reconstruction)';
+/*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `Tomogram`;
+/*!40101 SET @saved_cs_client = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `Tomogram` (
+ `tomogramId` int(11) unsigned NOT NULL AUTO_INCREMENT,
+ `dataCollectionId` int(11) unsigned DEFAULT NULL COMMENT 'FK to DataCollection table',
+ `autoProcProgramId` int(10) unsigned DEFAULT NULL COMMENT 'FK, gives processing times/status and software information',
+ `volumeFile` varchar(255) DEFAULT NULL COMMENT '.mrc file representing the reconstructed tomogram volume',
+ `stackFile` varchar(255) DEFAULT NULL COMMENT '.mrc file containing the motion corrected images ordered by angle used as input for the reconstruction',
+ `sizeX` int(11) unsigned DEFAULT NULL COMMENT 'unit: pixels',
+ `sizeY` int(11) unsigned DEFAULT NULL COMMENT 'unit: pixels',
+ `sizeZ` int(11) unsigned DEFAULT NULL COMMENT 'unit: pixels',
+ `pixelSpacing` float DEFAULT NULL COMMENT 'Angstrom/pixel conversion factor',
+ `residualErrorMean` float DEFAULT NULL COMMENT 'Alignment error, unit: nm',
+ `residualErrorSD` float DEFAULT NULL COMMENT 'Standard deviation of the alignment error, unit: nm',
+ `xAxisCorrection` float DEFAULT NULL COMMENT 'X axis angle (etomo), unit: degrees',
+ `tiltAngleOffset` float DEFAULT NULL COMMENT 'tilt Axis offset (etomo), unit: degrees',
+ `zShift` float DEFAULT NULL COMMENT 'shift to center volumen in Z (etomo)',
+ PRIMARY KEY (`tomogramId`),
+ KEY `Tomogram_fk_dataCollectionId` (`dataCollectionId`),
+ KEY `Tomogram_fk_autoProcProgramId` (`autoProcProgramId`),
+ CONSTRAINT `Tomogram_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE,
+ CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For storing per-sample, per-position data analysis results (reconstruction)';
+/*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `UserGroup`;
 /*!40101 SET @saved_cs_client = @@character_set_client */;
 /*!40101 SET character_set_client = utf8 */;

schemas/ispyb/updates/2022_06_22_AdminVar_bump_version.sql

@@ -0,0 +1,5 @@
+INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2022_06_22_AdminVar_bump_version.sql', 'ONGOING');
+
+UPDATE AdminVar SET `value` = '1.30.0' WHERE `name` = 'schemaVersion';
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2022_06_22_AdminVar_bump_version.sql';