Merge pull request #191 from antolinos/issue_190

Issue 190
ispyb · Nov 24, 2017 · c53b749 · c53b749
2 parents 66ef7cb + 77da484
commit c53b749
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diff --git a/a b/a
diff --git a/documentation/database/ISPyB_DataModel.mwb b/documentation/database/ISPyB_DataModel.mwb
diff --git a/ispyb-ejb/db/scripts/ahead/2017_10_22_EM.sql b/ispyb-ejb/db/scripts/ahead/2017_10_22_EM.sql
@@ -0,0 +1,158 @@
+insert into `pydb`.SchemaStatus (scriptName, schemaStatus) values ('20171022_EM.sql','ONGOING');
+
+CREATE TABLE IF NOT EXISTS `pydb`.`Movie` (
+  `movieId` INT(11) NOT NULL AUTO_INCREMENT,
+  `dataCollectionId` INT(11) UNSIGNED NULL DEFAULT NULL,
+  `movieNumber` INT NULL,
+  `movieFullPath` VARCHAR(255) NULL,
+  `positionX` VARCHAR(45) NULL,
+  `positionY` VARCHAR(45) NULL,
+  `micrographFullPath` VARCHAR(255) NULL,
+  `micrographSnapshotFullPath` VARCHAR(255) NULL,
+  `xmlMetaDataFullPath` VARCHAR(255) NULL,
+  `dosePerImage` VARCHAR(45) NULL,
+  `createdTimeStamp` TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+  PRIMARY KEY (`movieId`),
+  INDEX `dataCollectionToMovie_idx` (`dataCollectionId` ASC),
+  CONSTRAINT `dataCollectionToMovie`
+    FOREIGN KEY (`dataCollectionId`)
+    REFERENCES `pydb`.`DataCollection` (`dataCollectionId`)
+    ON DELETE NO ACTION
+    ON UPDATE NO ACTION);
+
+
+
+    CREATE TABLE `pydb`.`MotionCorrection` (
+  `motionCorrectionId` INT(11) NOT NULL AUTO_INCREMENT,
+  `movieId` INT(11) NULL,
+  `firstFrame` VARCHAR(45) NULL,
+  `lastFrame` VARCHAR(45) NULL,
+  `dosePerFrame` VARCHAR(45) NULL,
+  `doseWeight` VARCHAR(45) NULL,
+  `totalMotion` VARCHAR(45) NULL,
+  `averageMotionPerFrame` VARCHAR(45) NULL,
+  `driftPlotFullPath` VARCHAR(255) NULL,
+  `micrographFullPath` VARCHAR(255) NULL,
+  `micrographSnapshotFullPath` VARCHAR(255) NULL,
+  `correctedDoseMicrographFullPath` VARCHAR(255) NULL,
+  `patchesUsed` VARCHAR(45) NULL,
+  `logFileFullPath` VARCHAR(255) NULL,
+  `createdTimeStamp` TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+  PRIMARY KEY (`motionCorrectionId`),
+  INDEX `fk_MotionCorrection_1_idx` (`movieId` ASC),
+  CONSTRAINT `fk_MotionCorrection_1`
+    FOREIGN KEY (`movieId`)
+    REFERENCES `pydb`.`Movie` (`movieId`)
+    ON DELETE NO ACTION
+    ON UPDATE NO ACTION);
+
+
+
+CREATE TABLE `pydb`.`CTF` (
+  `CTFid` INT NOT NULL,
+  `motionCorrectionId` INT(11) NOT NULL,
+  `spectraImageThumbnailFullPath` VARCHAR(255) NULL,
+  `spectraImageFullPath` VARCHAR(255) NULL,
+  `defocusU` VARCHAR(45) NULL,
+  `defocusV` VARCHAR(45) NULL,
+  `angle` VARCHAR(45) NULL,
+  `crossCorrelationCoefficient` VARCHAR(45) NULL,
+  `resolutionLimit` VARCHAR(45) NULL,
+  `estimatedBfactor` VARCHAR(45) NULL,
+  `logFilePath` VARCHAR(255) NULL,
+   `createdTimeStamp` TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+  PRIMARY KEY (`CTFid`));
+
+
+  ALTER TABLE `pydb`.`CTF` 
+ADD INDEX `fk_CTF_1_idx` (`motionCorrectionId` ASC);
+ALTER TABLE `pydb`.`CTF` 
+ADD CONSTRAINT `fk_CTF_1`
+  FOREIGN KEY (`motionCorrectionId`)
+  REFERENCES `pydb`.`MotionCorrection` (`motionCorrectionId`)
+  ON DELETE NO ACTION
+  ON UPDATE NO ACTION;
+
+
+ALTER TABLE `pydb`.`CTF` 
+CHANGE COLUMN `CTFid` `CTFid` INT(11) NOT NULL AUTO_INCREMENT ;
+
+
+#ALTER TABLE `pydb`.`Movie` 
+#CHANGE COLUMN `createdTimeStamp` `createdTimeStamp` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ;
+
+#ALTER TABLE `pydb`.`Movie` 
+#CHANGE COLUMN `createdTimeStamp` `createdTimeStamp` DATETIME NULL DEFAULT CURRENT_TIMESTAMP ;
+
+#ALTER TABLE `pydb`.`MotionCorrection` 
+#CHANGE COLUMN `createdTimeStamp` `createdTimeStamp` DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ;
+
+ALTER TABLE `pydb`.`MotionCorrection` 
+CHANGE COLUMN `driftPlotFullPath` `driftPlotFullPath` VARCHAR(512) NULL DEFAULT NULL ,
+CHANGE COLUMN `micrographFullPath` `micrographFullPath` VARCHAR(512) NULL DEFAULT NULL ,
+CHANGE COLUMN `micrographSnapshotFullPath` `micrographSnapshotFullPath` VARCHAR(512) NULL DEFAULT NULL ,
+CHANGE COLUMN `correctedDoseMicrographFullPath` `correctedDoseMicrographFullPath` VARCHAR(512) NULL DEFAULT NULL ,
+CHANGE COLUMN `logFileFullPath` `logFileFullPath` VARCHAR(512) NULL DEFAULT NULL ;
+
+
+ALTER TABLE `pydb`.`BeamLineSetup` 
+ADD COLUMN `CS` FLOAT NULL AFTER `minTransmission`;
+
+ALTER TABLE `pydb`.`DataCollectionGroup` 
+CHANGE COLUMN `experimentType` `experimentType` ENUM('EM', 'SAD','SAD - Inverse Beam','OSC','Collect - Multiwedge','MAD','Helical','Multi-positional','Mesh','Burn','MAD - Inverse Beam','Characterization','Dehydration') NULL DEFAULT NULL COMMENT 'Experiment type flag' ;
+
+
+CREATE 
+    ALGORITHM = MERGE 
+    DEFINER = `pxadmin`@`%` 
+    SQL SECURITY DEFINER
+VIEW `pydb`.`v_em_movie` AS
+    SELECT 
+        `pydb`.`Movie`.`movieId` AS `Movie_movieId`,
+        `pydb`.`Movie`.`dataCollectionId` AS `Movie_dataCollectionId`,
+        `pydb`.`Movie`.`movieNumber` AS `Movie_movieNumber`,
+        `pydb`.`Movie`.`movieFullPath` AS `Movie_movieFullPath`,
+        `pydb`.`Movie`.`positionX` AS `Movie_positionX`,
+        `pydb`.`Movie`.`positionY` AS `Movie_positionY`,
+        `pydb`.`Movie`.`micrographFullPath` AS `Movie_micrographFullPath`,
+        `pydb`.`Movie`.`micrographSnapshotFullPath` AS `Movie_micrographSnapshotFullPath`,
+        `pydb`.`Movie`.`xmlMetaDataFullPath` AS `Movie_xmlMetaDataFullPath`,
+        `pydb`.`Movie`.`dosePerImage` AS `Movie_dosePerImage`,
+        `pydb`.`Movie`.`createdTimeStamp` AS `Movie_createdTimeStamp`,
+        `pydb`.`MotionCorrection`.`motionCorrectionId` AS `MotionCorrection_motionCorrectionId`,
+        `pydb`.`MotionCorrection`.`movieId` AS `MotionCorrection_movieId`,
+        `pydb`.`MotionCorrection`.`firstFrame` AS `MotionCorrection_firstFrame`,
+        `pydb`.`MotionCorrection`.`lastFrame` AS `MotionCorrection_lastFrame`,
+        `pydb`.`MotionCorrection`.`dosePerFrame` AS `MotionCorrection_dosePerFrame`,
+        `pydb`.`MotionCorrection`.`doseWeight` AS `MotionCorrection_doseWeight`,
+        `pydb`.`MotionCorrection`.`totalMotion` AS `MotionCorrection_totalMotion`,
+        `pydb`.`MotionCorrection`.`averageMotionPerFrame` AS `MotionCorrection_averageMotionPerFrame`,
+        `pydb`.`MotionCorrection`.`driftPlotFullPath` AS `MotionCorrection_driftPlotFullPath`,
+        `pydb`.`MotionCorrection`.`micrographFullPath` AS `MotionCorrection_micrographFullPath`,
+        `pydb`.`MotionCorrection`.`micrographSnapshotFullPath` AS `MotionCorrection_micrographSnapshotFullPath`,
+        `pydb`.`MotionCorrection`.`correctedDoseMicrographFullPath` AS `MotionCorrection_correctedDoseMicrographFullPath`,
+        `pydb`.`MotionCorrection`.`patchesUsed` AS `MotionCorrection_patchesUsed`,
+        `pydb`.`MotionCorrection`.`logFileFullPath` AS `MotionCorrection_logFileFullPath`,
+        `pydb`.`CTF`.`CTFid` AS `CTF_CTFid`,
+        `pydb`.`CTF`.`motionCorrectionId` AS `CTF_motionCorrectionId`,
+        `pydb`.`CTF`.`spectraImageThumbnailFullPath` AS `CTF_spectraImageThumbnailFullPath`,
+        `pydb`.`CTF`.`spectraImageFullPath` AS `CTF_spectraImageFullPath`,
+        `pydb`.`CTF`.`defocusU` AS `CTF_defocusU`,
+        `pydb`.`CTF`.`defocusV` AS `CTF_defocusV`,
+        `pydb`.`CTF`.`angle` AS `CTF_angle`,
+        `pydb`.`CTF`.`crossCorrelationCoefficient` AS `CTF_crossCorrelationCoefficient`,
+        `pydb`.`CTF`.`resolutionLimit` AS `CTF_resolutionLimit`,
+        `pydb`.`CTF`.`estimatedBfactor` AS `CTF_estimatedBfactor`,
+        `pydb`.`CTF`.`logFilePath` AS `CTF_logFilePath`,
+        `pydb`.`CTF`.`createdTimeStamp` AS `CTF_createdTimeStamp`,
+        `pydb`.`Proposal`.`proposalId` AS `Proposal_proposalId`,
+        `pydb`.`BLSession`.`sessionId` AS `BLSession_sessionId`
+    FROM
+        ((((((`pydb`.`Movie`
+        LEFT JOIN `pydb`.`MotionCorrection` ON ((`pydb`.`MotionCorrection`.`movieId` = `pydb`.`Movie`.`movieId`)))
+        LEFT JOIN `pydb`.`DataCollection` ON ((`pydb`.`DataCollection`.`dataCollectionId` = `pydb`.`Movie`.`dataCollectionId`)))
+        LEFT JOIN `pydb`.`DataCollectionGroup` ON ((`pydb`.`DataCollectionGroup`.`dataCollectionGroupId` = `pydb`.`DataCollection`.`dataCollectionGroupId`)))
+        LEFT JOIN `pydb`.`BLSession` ON ((`pydb`.`BLSession`.`sessionId` = `pydb`.`DataCollectionGroup`.`sessionId`)))
+        LEFT JOIN `pydb`.`Proposal` ON ((`pydb`.`Proposal`.`proposalId` = `pydb`.`BLSession`.`proposalId`)))
+        LEFT JOIN `pydb`.`CTF` ON ((`pydb`.`CTF`.`motionCorrectionId` = `pydb`.`MotionCorrection`.`motionCorrectionId`)));
+update `pydb`.SchemaStatus set schemaStatus = 'DONE' where scriptName = '20171022_EM.sql';