Merge pull request #11 from DiamondLightSource/commits_for_1.6.0

Commits for 1.6.0

docs/list_of_procs.rst

@@ -71,12 +71,14 @@
  "**retrieve_reprocessing_by_dc**","p_dcId int(11) unsigned","Retrieves reprocessing requests for a data collection (p_dcId)."
  "**retrieve_samples_assigned_for_proposal**","IN p_proposalCode varchar(3), IN p_proposalNumber int","Retrieve the user friendly name and ID of all assigned instances"
  "**retrieve_samples_for_sample_group**","IN p_sampleGroupId int unsigned","Return multi-row result set with sample IDs, order in the group"
+ "**retrieve_samples_not_loaded_for_container_reg_barcode**","p_barcode varchar(20)",""
  "**retrieve_sample_groups_for_sample**","IN p_sampleId int unsigned","Return multi-row result-set with sample group IDs, order in the"
  "**retrieve_sample_type_for_sample**","IN p_sampleId int unsigned","Return single-row result set with sample type columns for sample"
  "**retrieve_sessions_for_beamline_and_run**","IN p_beamline varchar(15), IN p_run varchar(7)","Returns a multi-row result-set with the sessions (mx12345-123), their start and end dates for beamline p_beamline and run p_run"
  "**retrieve_sessions_for_person_login**","p_login varchar(45)","Returns a multi-row result-set with info about the sessions associated with a person with login=p_login"
  "**retrieve_session_id**","p_session varchar(15), OUT p_id int",""
  "**retrieve_session_id_v2**","p_session varchar(15), p_authLogin varchar(45)","Returns the session ID (an integer) for p_session (e.g. mx12345-123)"
+ "**retrieve_sleeve**","p_id tinyint unsigned",""
  "**retrieve_test**","","For testing the connection"
  "**update_container_assign**","IN p_beamline varchar(20), IN p_registry_barcode varchar(45), IN p_position int","Toggles assign status of container (p_barcode).Sets the s.c. position and beamline.If assigned then: 1) Also assign its dewar and shipping. 2) Unassigns other containers in the same proposal on that beamline and s.c. position.If unassign then:"
  "**update_container_ls_position**","IN p_barcode varchar(45), IN p_position int","Updates container sampleChangerLocation for barcode = p_barcode,"
@@ -132,6 +134,7 @@
  "**upsert_sample_image_analysis**","INOUT p_id int(11) unsigned, p_containerBarcode varchar(45), p_sampleLocation varchar(45), p_oavSnapshotBefore varchar(255), p_oavSnapshotAfter varchar(255), p_deltaX int, p_deltaY int, p_goodnessOfFit float, p_scaleFactor float, p_resultCode varchar(15), p_matchStartTS timestamp, p_matchEndTS timestamp","Insert or update info about the sample image analysis for the mo"
  "**upsert_session_for_proposal_code_number**","INOUT p_id int(11) unsigned, p_proposalCode varchar(3), p_proposalNumber int(11), p_visitNumber int(10) unsigned, p_beamLineSetupId int(10) unsigned, p_startDate datetime, p_endDate datetime, p_beamlineName varchar(45), p_title varchar(255), p_beamlineOperator varchar(45), p_nbShifts int(10) unsigned, p_scheduled tinyint(1), p_usedFlag tinyint(1), p_comments varchar(255), p_externalPkId int(11) unsigned, p_externalPkUUID varchar(32)","Inserts or updates a session for a proposal with given code and"
  "**upsert_session_has_person**","p_sessionId int(10) unsigned, p_personId int(10) unsigned, p_role varchar(100), p_remote tinyint(1)","Inserts or updates info about a session - person association (p_sessionId, p_personId).Mandatory columns:For insert: p_sessionId, p_personIdFor update: p_sessionId, p_personIdReturns: Nothing."
+ "**upsert_sleeve**","p_id tinyint unsigned, p_location tinyint unsigned, p_lastMovedToFreezer datetime, p_lastMovedFromFreezer datetime",""
  "**upsert_xfe_fluo_spectrum**","INOUT p_id int(11) unsigned, p_sessionId int(10) unsigned, p_sampleId int(10) unsigned, p_subSampleId int(11) unsigned, p_startTime datetime, p_endTime datetime, p_energy float, p_fileName varchar(255), p_annotatedPymcaSpectrum varchar(255), p_fittedDataFileFullPath varchar(255), p_jpegScanFileFullPath varchar(255), p_scanFileFullPath varchar(255), p_beamSizeHorizontal float, p_beamSizeVertical float, p_exposureTime float, p_transmission float, p_flux double, p_fluxEnd double, p_comments varchar(1024)","Inserts or updates info about a fluorescence spectrum measuremen"
  "**upsert_xray_centring_result**","INOUT p_id int(11) unsigned, p_gridInfoId int(11) unsigned, p_method varchar(15), p_status varchar(45), p_x float, p_y float","Inserts or updates info about an x-ray centring result (p_id).Mandatory columns:For insert: p_gridInfoId and p_statusFor update: p_id Returns: Record ID in p_id."
  "**Warnings**","",""

docs/list_of_tables_and_columns.rst

@@ -1786,6 +1786,11 @@
  **ShippingHasSession**,table,""
  ``shippingId``,int,""
  ``sessionId``,int,""
+ **Sleeve**,table,"Registry of ice-filled sleeves used to cool plates whilst on the goniometer"
+ ``sleeveId``,tinyint,"The unique sleeve id 1...255 which also identifies its home location in the freezer"
+ ``location``,tinyint,"NULL == freezer, 1...255 for local storage locations"
+ ``lastMovedToFreezer``,timestamp,""
+ ``lastMovedFromFreezer``,timestamp,""
  **SpaceGroup**,table,""
  ``spaceGroupId``,int,"Primary key"
  ``spaceGroupNumber``,int,"ccp4 number pr IUCR"

grants/ispyb_acquisition.sql

@@ -45,3 +45,6 @@ GRANT EXECUTE ON PROCEDURE `retrieve_container_subsamples_v2` TO 'ispyb_acquisit
 GRANT EXECUTE ON PROCEDURE upsert_dc_group_v3 TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE retrieve_dc_group TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE retrieve_dc_group_v2 TO 'ispyb_acquisition';
+
+GRANT EXECUTE ON PROCEDURE retrieve_sleeve TO 'ispyb_acquisition';
+GRANT EXECUTE ON PROCEDURE upsert_sleeve TO 'ispyb_acquisition';

grants/ispyb_processing.sql

@@ -110,3 +110,4 @@ GRANT EXECUTE ON PROCEDURE retrieve_grid_info_for_dcg_v2 TO 'ispyb_processing';
 GRANT EXECUTE ON PROCEDURE retrieve_dewars_for_proposal_code_number_v2 TO 'ispyb_processing';
 GRANT EXECUTE ON PROCEDURE retrieve_dc_main_v2 TO 'ispyb_processing';
 GRANT EXECUTE ON PROCEDURE retrieve_dc TO 'ispyb_processing';
+GRANT EXECUTE ON PROCEDURE retrieve_samples_not_loaded_for_container_reg_barcode TO 'ispyb_processing';

schema/data.sql

@@ -1,8 +1,8 @@
--- MySQL dump 10.17 Distrib 10.3.14-MariaDB, for Linux (x86_64)
+-- MariaDB dump 10.17 Distrib 10.4.7-MariaDB, for Linux (x86_64)
 --
 -- Host: localhost Database: ispyb_build
 -- ------------------------------------------------------
--- Server version 10.3.14-MariaDB
+-- Server version 10.4.7-MariaDB
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -1591,6 +1591,15 @@ INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (474,339525)
 /*!40000 ALTER TABLE `ShippingHasSession` ENABLE KEYS */;
 UNLOCK TABLES;
 
+--
+-- Dumping data for table `Sleeve`
+--
+
+LOCK TABLES `Sleeve` WRITE;
+/*!40000 ALTER TABLE `Sleeve` DISABLE KEYS */;
+/*!40000 ALTER TABLE `Sleeve` ENABLE KEYS */;
+UNLOCK TABLES;
+
 --
 -- Dumping data for table `SpaceGroup`
 --
@@ -1774,4 +1783,4 @@ UNLOCK TABLES;
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2019-04-23 11:38:32
+-- Dump completed on 2019-08-15 9:49:01

schema/lookups.sql

@@ -1,8 +1,8 @@
--- MariaDB dump 10.17 Distrib 10.4.6-MariaDB, for Linux (x86_64)
+-- MariaDB dump 10.17 Distrib 10.4.7-MariaDB, for Linux (x86_64)
 --
 -- Host: localhost Database: ispyb_build
 -- ------------------------------------------------------
--- Server version 10.4.6-MariaDB
+-- Server version 10.4.7-MariaDB
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -20,7 +20,7 @@
 
 LOCK TABLES `AdminVar` WRITE;
 /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */;
-INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.5.2');
+INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.6.0');
 /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -30,7 +30,7 @@ UNLOCK TABLES;
 
 LOCK TABLES `SchemaStatus` WRITE;
 /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */;
-INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `recordTimeStamp`) VALUES (6,'20180213_BLSample_subLocation.sql','DONE','2018-02-13 13:27:19'),(12,'20180213_DataCollectionFileAttachment_fileType.sql','DONE','2018-02-13 15:12:54'),(16,'20180303_v_run_to_table.sql','DONE','2018-07-25 15:11:18'),(19,'20180328_ImageQualityIndicators_alter_table.sql','DONE','2018-07-25 15:11:18'),(22,'20180410_BeamLineSetup_alter.sql','DONE','2018-07-25 15:11:18'),(25,'20180413_BeamLineSetup_and_Detector_alter.sql','DONE','2018-07-25 15:11:18'),(28,'20180501_DataCollectionGroup_experimentType_enum.sql','DONE','2018-07-25 15:11:18'),(31,'20180531_ScreeningOutput_alignmentSuccess.sql','DONE','2018-07-25 15:11:18'),(34,'20180629_DataCollection_imageContainerSubPath.sql','DONE','2018-07-25 15:11:18'),(35,'20180913_BeamCalendar.sql','DONE','2018-09-19 09:52:45'),(36,'2018_09_19_DataCollection_imageDirectory_comment.sql','DONE','2018-09-19 12:38:01'),(37,'2018_09_27_increase_schema_version.sql','DONE','2018-09-27 13:17:15'),(38,'2018_11_01_XrayCenteringResult.sql','DONE','2018-11-01 13:36:53'),(39,'2018_11_01_AutoProcProgram_dataCollectionId.sql','DONE','2018-11-01 15:10:38'),(40,'2018_11_01_AutoProcProgramMessage.sql','DONE','2018-11-01 15:28:17'),(44,'2018_11_01_DiffractionPlan_centeringMethod.sql','DONE','2018-11-01 22:51:36'),(45,'2018_11_02_DataCollectionGroup_experimentType_enum.sql','DONE','2018-11-02 11:54:15'),(47,'2018_11_05_spelling_of_centring.sql','DONE','2018-11-05 15:31:38'),(48,'2018_11_09_AutoProcProgram_update_processing_program.sql','DONE','2018-11-09 16:38:34'),(49,'2018_11_14_AutoProcProgramMessage_autoinc.sql','DONE','2018-11-14 10:15:27'),(50,'2018_11_22_AutoProcProgram_processingStatus_update.sql','DONE','2018-11-22 16:11:15'),(51,'2018_12_04_EnergyScan_and_XFEFluorescenceSpectrum_add_axisPosition.sql','DONE','2018-12-04 14:13:23'),(52,'2018_12_20_DataCollectionGroup_scanParameters.sql','DONE','2018-12-20 17:30:04'),(53,'2019_01_14_Proposal_state.sql','DONE','2019-01-14 12:13:31'),(54,'2019_01_14_ProcessingJobParameter_parameterValue.sql','DONE','2019-01-14 14:00:02'),(57,'2019_01_15_Detector_localName.sql','DONE','2019-01-15 23:01:15'),(58,'2019_02_04_BLSession_unique_index.sql','DONE','2019-02-04 13:52:19'),(59,'2019_03_29_BLSession_archived.sql','DONE','2019-04-03 14:43:08'),(60,'2019_04_03_UserGroup_and_Permission.sql','DONE','2019-04-03 14:51:04'),(61,'2019_04_07_AdminVar_bump_version.sql','DONE','2019-04-07 11:35:06'),(62,'2019_04_08_AdminVar_bump_version.sql','DONE','2019-04-08 15:38:01'),(63,'2019_04_23_AdminVar_bump_version.sql','DONE','2019-04-23 11:13:27'),(64,'2019_04_23_drop_v_run_view.sql','DONE','2019-04-23 11:13:35'),(67,'2019_04_23_v_run_additional_runs.sql','DONE','2019-04-23 12:39:47'),(68,'2019_05_28_AdminVar_bump_version.sql','DONE','2019-05-28 13:29:27'),(72,'2019_07_17_BLSample_crystalId_default.sql','DONE','2019-07-17 15:21:59');
+INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `recordTimeStamp`) VALUES (6,'20180213_BLSample_subLocation.sql','DONE','2018-02-13 13:27:19'),(12,'20180213_DataCollectionFileAttachment_fileType.sql','DONE','2018-02-13 15:12:54'),(16,'20180303_v_run_to_table.sql','DONE','2018-07-25 15:11:18'),(19,'20180328_ImageQualityIndicators_alter_table.sql','DONE','2018-07-25 15:11:18'),(22,'20180410_BeamLineSetup_alter.sql','DONE','2018-07-25 15:11:18'),(25,'20180413_BeamLineSetup_and_Detector_alter.sql','DONE','2018-07-25 15:11:18'),(28,'20180501_DataCollectionGroup_experimentType_enum.sql','DONE','2018-07-25 15:11:18'),(31,'20180531_ScreeningOutput_alignmentSuccess.sql','DONE','2018-07-25 15:11:18'),(34,'20180629_DataCollection_imageContainerSubPath.sql','DONE','2018-07-25 15:11:18'),(35,'20180913_BeamCalendar.sql','DONE','2018-09-19 09:52:45'),(36,'2018_09_19_DataCollection_imageDirectory_comment.sql','DONE','2018-09-19 12:38:01'),(37,'2018_09_27_increase_schema_version.sql','DONE','2018-09-27 13:17:15'),(38,'2018_11_01_XrayCenteringResult.sql','DONE','2018-11-01 13:36:53'),(39,'2018_11_01_AutoProcProgram_dataCollectionId.sql','DONE','2018-11-01 15:10:38'),(40,'2018_11_01_AutoProcProgramMessage.sql','DONE','2018-11-01 15:28:17'),(44,'2018_11_01_DiffractionPlan_centeringMethod.sql','DONE','2018-11-01 22:51:36'),(45,'2018_11_02_DataCollectionGroup_experimentType_enum.sql','DONE','2018-11-02 11:54:15'),(47,'2018_11_05_spelling_of_centring.sql','DONE','2018-11-05 15:31:38'),(48,'2018_11_09_AutoProcProgram_update_processing_program.sql','DONE','2018-11-09 16:38:34'),(49,'2018_11_14_AutoProcProgramMessage_autoinc.sql','DONE','2018-11-14 10:15:27'),(50,'2018_11_22_AutoProcProgram_processingStatus_update.sql','DONE','2018-11-22 16:11:15'),(51,'2018_12_04_EnergyScan_and_XFEFluorescenceSpectrum_add_axisPosition.sql','DONE','2018-12-04 14:13:23'),(52,'2018_12_20_DataCollectionGroup_scanParameters.sql','DONE','2018-12-20 17:30:04'),(53,'2019_01_14_Proposal_state.sql','DONE','2019-01-14 12:13:31'),(54,'2019_01_14_ProcessingJobParameter_parameterValue.sql','DONE','2019-01-14 14:00:02'),(57,'2019_01_15_Detector_localName.sql','DONE','2019-01-15 23:01:15'),(58,'2019_02_04_BLSession_unique_index.sql','DONE','2019-02-04 13:52:19'),(59,'2019_03_29_BLSession_archived.sql','DONE','2019-04-03 14:43:08'),(60,'2019_04_03_UserGroup_and_Permission.sql','DONE','2019-04-03 14:51:04'),(61,'2019_04_07_AdminVar_bump_version.sql','DONE','2019-04-07 11:35:06'),(62,'2019_04_08_AdminVar_bump_version.sql','DONE','2019-04-08 15:38:01'),(63,'2019_04_23_AdminVar_bump_version.sql','DONE','2019-04-23 11:13:27'),(64,'2019_04_23_drop_v_run_view.sql','DONE','2019-04-23 11:13:35'),(67,'2019_04_23_v_run_additional_runs.sql','DONE','2019-04-23 12:39:47'),(68,'2019_05_28_AdminVar_bump_version.sql','DONE','2019-05-28 13:29:27'),(72,'2019_07_17_BLSample_crystalId_default.sql','DONE','2019-07-17 15:21:59'),(73,'2019_08_15_Sleeve.sql','DONE','2019-08-15 08:34:34'),(74,'2019_08_15_AdminVar_bump_version.sql','DONE','2019-08-15 08:57:37');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -195,4 +195,4 @@ UNLOCK TABLES;
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2019-07-17 16:23:11
+-- Dump completed on 2019-08-15 9:58:13