Merge pull request #40 from DiamondLightSource/new_release_1.14.0

New release 1.14.0

docs/list_of_procs.rst

@@ -74,6 +74,7 @@
  "**retrieve_proposal_title**","p_proposal_code varchar(5), p_proposal_number int","Returns a single-row, single-column result set with the title of the proposal p_proposal_code + p_proposal_number"
  "**retrieve_proposal_title**","p_proposal_code varchar(5), p_proposal_number int, p_authLogin varchar(45)","Returns a single-row, single-column result set with the title of the proposal p_proposal_code + p_proposal_number"
  "**retrieve_reprocessing_by_dc**","p_dcId int(11) unsigned","Retrieves reprocessing requests for a data collection (p_dcId)."
+ "**retrieve_sample**","p_id int unsigned, p_useContainerSession boolean, p_authLogin varchar(45)","Returns a single-row result-set with the sample for the given ID"
  "**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)",""

docs/list_of_tables_and_columns.rst

@@ -472,6 +472,8 @@
  ``componentSubTypeId``,int,""
  ``name``,varchar,""
  ``hasPh``,tinyint,""
+ ``proposalType``,varchar,""
+ ``active``,tinyint,"1=active, 0=inactive"
  **ComponentType**,table,""
  ``componentTypeId``,int,""
  ``name``,varchar,""
@@ -482,6 +484,8 @@
  ``concentrationTypeId``,int,""
  ``name``,varchar,""
  ``symbol``,varchar,""
+ ``proposalType``,varchar,""
+ ``active``,tinyint,"1=active, 0=inactive"
  **Container**,table,""
  ``containerId``,int,""
  ``dewarId``,int,""
@@ -749,6 +753,7 @@
  ``workflowId``,int,""
  ``xtalSnapshotFullPath``,varchar,""
  ``scanParameters``,longtext,""
+ ``experimentTypeId``,int,""
  **DataCollectionPlan_has_Detector**,table,""
  ``dataCollectionPlanHasDetectorId``,int,""
  ``dataCollectionPlanId``,int,""
@@ -898,6 +903,10 @@
  ``monoBandwidth``,double,""
  ``centringMethod``,enum,""
  ``userPath``,varchar,"User-specified relative "root" path inside the session directory to be used for holding collected data"
+ ``robotPlateTemperature``,float,"units: kelvin"
+ ``exposureTemperature``,float,"units: kelvin"
+ ``experimentTypeId``,int,""
+ ``purificationColumnId``,int,""
  **EMMicroscope**,table,""
  ``emMicroscopeId``,int,""
  ``instrumentName``,varchar,""
@@ -960,6 +969,11 @@
  ``dataCollectionType``,varchar,""
  ``dataCollectionKind``,varchar,""
  ``wedgeValue``,float,""
+ **ExperimentType**,table,"A lookup table for different types of experients"
+ ``experimentTypeId``,int,""
+ ``name``,varchar,""
+ ``proposalType``,varchar,""
+ ``active``,tinyint,"1=active, 0=inactive"
  **Frame**,table,""
  ``frameId``,int,""
  ``FRAMESETID``,int,""
@@ -1514,6 +1528,10 @@
  ``proteinhaspdbid``,int,""
  ``proteinid``,int,""
  ``pdbid``,int,""
+ **PurificationColumn**,table,"Size exclusion chromotography (SEC) lookup table for BioSAXS"
+ ``purificationColumnId``,int,""
+ ``name``,varchar,""
+ ``active``,tinyint,"1=active, 0=inactive"
  **RobotAction**,table,"Robot actions as reported by GDA"
  ``robotActionId``,int,""
  ``blsessionId``,int,""

grants/ispyb_acquisition.sql

@@ -50,3 +50,5 @@ GRANT EXECUTE ON PROCEDURE retrieve_dc_group_v2 TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE retrieve_sleeve TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE retrieve_sleeves TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE upsert_sleeve TO 'ispyb_acquisition';
+
+GRANT EXECUTE ON PROCEDURE retrieve_sample TO 'ispyb_acquisition';

schema/routines.sql

@@ -1,8 +1,8 @@
--- MariaDB dump 10.17 Distrib 10.4.13-MariaDB, for Linux (x86_64)
+-- MariaDB dump 10.17 Distrib 10.5.6-MariaDB, for Linux (x86_64)
 --
 -- Host: localhost Database: ispyb_build
 -- ------------------------------------------------------
--- Server version 10.4.13-MariaDB
+-- Server version 10.5.6-MariaDB
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -3960,6 +3960,138 @@ DELIMITER ;
 /*!50003 SET character_set_client = @saved_cs_client */ ;
 /*!50003 SET character_set_results = @saved_cs_results */ ;
 /*!50003 SET collation_connection = @saved_col_connection */ ;
+/*!50003 DROP PROCEDURE IF EXISTS `retrieve_sample` */;
+/*!50003 SET @saved_cs_client = @@character_set_client */ ;
+/*!50003 SET @saved_cs_results = @@character_set_results */ ;
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client = utf8 */ ;
+/*!50003 SET character_set_results = utf8 */ ;
+/*!50003 SET collation_connection = utf8_general_ci */ ;
+/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
+/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+DELIMITER ;;
+CREATE PROCEDURE `retrieve_sample`(p_id int unsigned, p_useContainerSession boolean, p_authLogin varchar(45))
+ READS SQL DATA
+ COMMENT 'Returns a single-row result-set with the sample for the given ID'
+BEGIN
+ IF p_id IS NOT NULL THEN
+
+ IF p_useContainerSession = True THEN
+
+ IF p_authLogin IS NOT NULL THEN
+
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ bs.sessionId "sessionId",
+ bs.visit_number "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN BLSession bs ON c.sessionId = bs.sessionId
+ INNER JOIN Proposal p ON p.proposalId = bs.proposalId
+ INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId
+ INNER JOIN Person pe ON pe.personId = shp.personId
+ WHERE pe.login = p_authLogin AND bls.blSampleId = p_id;
+
+ ELSE
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ bs.sessionId "sessionId",
+ bs.visit_number "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN BLSession bs ON c.sessionId = bs.sessionId
+ INNER JOIN Proposal p ON p.proposalId = bs.proposalId
+ WHERE bls.blSampleId = p_id;
+
+ END IF;
+
+ ELSE
+
+ IF p_authLogin IS NOT NULL THEN
+
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ NULL "sessionId",
+ NULL "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN Dewar d ON d.dewarId = c.dewarId
+ INNER JOIN Shipping s ON s.shippingId = d.shippingId
+ INNER JOIN Proposal p ON p.proposalId = s.proposalId
+ INNER JOIN BLSession bs ON bs.proposalId = p.proposalId
+ INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId
+ INNER JOIN Person pe ON pe.personId = shp.personId
+ WHERE pe.login = p_authLogin AND bls.blSampleId = p_id;
+
+ ELSE
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ NULL "sessionId",
+ NULL "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN Dewar d ON d.dewarId = c.dewarId
+ INNER JOIN Shipping s ON s.shippingId = d.shippingId
+ INNER JOIN Proposal p ON p.proposalId = s.proposalId
+ WHERE bls.blSampleId = p_id;
+
+ END IF;
+
+ END IF;
+
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_id can not be NULL';
+ END IF;
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode = @saved_sql_mode */ ;
+/*!50003 SET character_set_client = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection = @saved_col_connection */ ;
 /*!50003 DROP PROCEDURE IF EXISTS `retrieve_samples_assigned_for_proposal` */;
 /*!50003 SET @saved_cs_client = @@character_set_client */ ;
 /*!50003 SET @saved_cs_results = @@character_set_results */ ;
@@ -7960,12 +8092,12 @@ DELIMITER ;
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2020-07-13 20:02:24
--- MariaDB dump 10.17 Distrib 10.4.13-MariaDB, for Linux (x86_64)
+-- Dump completed on 2020-10-16 17:05:55
+-- MariaDB dump 10.17 Distrib 10.5.6-MariaDB, for Linux (x86_64)
 --
 -- Host: localhost Database: ispyb_build
 -- ------------------------------------------------------
--- Server version 10.4.13-MariaDB
+-- Server version 10.5.6-MariaDB
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -8006,4 +8138,4 @@ DELIMITER ;
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2020-07-13 20:02:24
+-- Dump completed on 2020-10-16 17:05:55

schema/stored_programs/sp_retrieve_sample.sql

@@ -0,0 +1,120 @@
+DELIMITER ;;
+CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `retrieve_sample`(p_id int unsigned, p_useContainerSession boolean, p_authLogin varchar(45)) 
+READS SQL DATA
+COMMENT 'Returns a single-row result-set with the sample for the given ID'
+BEGIN
+ IF p_id IS NOT NULL THEN
+
+ IF p_useContainerSession = True THEN
+
+ IF p_authLogin IS NOT NULL THEN
+ -- Authorise only if the person (p_authLogin) is a member of a session on the proposal.
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ bs.sessionId "sessionId",
+ bs.visit_number "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN BLSession bs ON c.sessionId = bs.sessionId
+ INNER JOIN Proposal p ON p.proposalId = bs.proposalId
+ INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId
+ INNER JOIN Person pe ON pe.personId = shp.personId
+ WHERE pe.login = p_authLogin AND bls.blSampleId = p_id;
+
+ ELSE
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ bs.sessionId "sessionId",
+ bs.visit_number "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN BLSession bs ON c.sessionId = bs.sessionId
+ INNER JOIN Proposal p ON p.proposalId = bs.proposalId
+ WHERE bls.blSampleId = p_id;
+
+ END IF;
+
+ ELSE
+
+ IF p_authLogin IS NOT NULL THEN
+ -- Authorise only if the person (p_authLogin) is a member of a session on the proposal.
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ NULL "sessionId",
+ NULL "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN Dewar d ON d.dewarId = c.dewarId
+ INNER JOIN Shipping s ON s.shippingId = d.shippingId
+ INNER JOIN Proposal p ON p.proposalId = s.proposalId
+ INNER JOIN BLSession bs ON bs.proposalId = p.proposalId
+ INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId
+ INNER JOIN Person pe ON pe.personId = shp.personId
+ WHERE pe.login = p_authLogin AND bls.blSampleId = p_id;
+
+ ELSE
+
+ SELECT bls.blSampleId "sampleId",
+ bls.containerId "containerId",
+ bls.diffractionPlanId "dataCollectionPlanId",
+ bls.name "sampleName",
+ bls.code "sampleCode",
+ bls.comments "sampleComments",
+ bls.location "sampleLocation",
+ bls.subLocation "sampleSubLocation",
+ bls.blSampleStatus "sampleStatus",
+ p.proposalId "proposalId",
+ p.proposalCode "proposalCode",
+ p.proposalNumber "proposalNumber",
+ NULL "sessionId",
+ NULL "sessionNumber"
+ FROM BLSample bls
+ INNER JOIN Container c ON c.containerId = bls.containerId
+ INNER JOIN Dewar d ON d.dewarId = c.dewarId
+ INNER JOIN Shipping s ON s.shippingId = d.shippingId
+ INNER JOIN Proposal p ON p.proposalId = s.proposalId
+ WHERE bls.blSampleId = p_id;
+
+ END IF;
+
+ END IF;
+
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_id can not be NULL';
+ END IF;
+END;;
+DELIMITER ;
+