diff --git a/HISTORY.rst b/HISTORY.rst index 8c3a1d34..8f3cd1f4 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,44 @@ History Unreleased / master ------------------- +1.20.0 (2021-04-13) +------------------- + +* Tables, views and indices: + + * New cryoEM table `ParticleClassificationGroup`. Some columns were moved to this table from `ParticlePicker` and `ParticleClassification`. + * Add `capillary` as enum option to `BLSampleGroup_has_BLSample.type` + * XChem DB: First version of schema for production (not part of release) + * Analytics schema: Add access to all lookup tables, `RobotAction`, `ProcessingJob*`, `Protein` tables through views (not part of release) + * Drop duplicate indices, add missing indices that existed only in DLS prod + +* Data in lookup tables: + + * Add additional container types: some historical, some new + * Update `ExperimentType.proposalType`: Change scm to saxs, MX to mx + * Update `ContainerType.proposalType`: Change scm to saxs + * Add two XPDF and five MX container types + * Update `SpaceGroup` table: Remove newlines in names. Set `MX_used` = 1 for all SGs. + +* Stored procedures: + + * `retrieve_scm_*``: Preferentially get experiement type and container type+capacity from new lookup tables `ExperimentType` and `ContainerType`, otherwise fall-back to `experimentType` and `containerType`+`capacity` columns in the `Container` table. + * `upsert_sample_image`: set `BLSampleImage.modifiedTimeStamp` if the upsert is an update + +* Tools and documentation: + + * New script `bin/missed_updates.sh` to identify update .sql files that haven't been run + * `bin/backup.sh`: Use `--add-drop-trigger` flag to drop trigger if exists before creation + * `CONTRIBUTING.md`: Simplify pull request procedure for table changes + * Updated simplified MX database diagram files + * Move list + string with lookup tables to separate file so it can be reused + * All bash scripts have been given new shebang lines to run on systems where bash is not at `/bin/bash`. + +* Users, roles and grants: + + * More `INSERT` grants for `ispyb_web` role: DC, DCG, `ProcessingJob`, `ProcessingJobParameter` + * New `ispyb_ro_nopii` role (read-only-except-PII) + 1.19.0 (2021-03-05) ------------------- diff --git a/bin/add_schema_status_stmts.sh b/bin/add_schema_status_stmts.sh index b0566e96..821231ef 100755 --- a/bin/add_schema_status_stmts.sh +++ b/bin/add_schema_status_stmts.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash fname=$(basename ${1}) diff --git a/bin/backup.sh b/bin/backup.sh index 265a4156..6fe06912 100755 --- a/bin/backup.sh +++ b/bin/backup.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Usage example: # backup.sh ../dbbackups diff --git a/bin/db_procs_to_rst.sh b/bin/db_procs_to_rst.sh index f382398f..6125f54c 100755 --- a/bin/db_procs_to_rst.sh +++ b/bin/db_procs_to_rst.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash db=$1 diff --git a/bin/db_tables_to_rst.sh b/bin/db_tables_to_rst.sh index c821da45..e4e3f749 100755 --- a/bin/db_tables_to_rst.sh +++ b/bin/db_tables_to_rst.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash db=$1 mysql --defaults-file=../.my.cnf -D $db --skip-column-names --batch --raw < sql/db_tables_to_tsv.sql > /tmp/tmp1.tsv diff --git a/bin/export_session.sh b/bin/export_session.sh index bc8aa802..315038d8 100755 --- a/bin/export_session.sh +++ b/bin/export_session.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Usage: # export_session.sh <.cnf file> diff --git a/bin/forget_all_labs.sh b/bin/forget_all_labs.sh index d0f5ffd2..7134d79c 100755 --- a/bin/forget_all_labs.sh +++ b/bin/forget_all_labs.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes details about laboratories on a particular proposal # and session. diff --git a/bin/forget_all_persons.sh b/bin/forget_all_persons.sh index 8ee206dd..d82e8824 100755 --- a/bin/forget_all_persons.sh +++ b/bin/forget_all_persons.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Caution: This script attempts to remove all Personally Identifiable # Information (PII) in the given ispyb database for the given proposal diff --git a/bin/forget_lab.sh b/bin/forget_lab.sh index 45e67f79..2eda0f9c 100755 --- a/bin/forget_lab.sh +++ b/bin/forget_lab.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes details about a particular laboratory. # Usage: diff --git a/bin/forget_pdb.sh b/bin/forget_pdb.sh index 7878efcc..d6c5b2f3 100755 --- a/bin/forget_pdb.sh +++ b/bin/forget_pdb.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes information for a particular PDB. # diff --git a/bin/forget_person.sh b/bin/forget_person.sh index 37b0bc66..f5885724 100755 --- a/bin/forget_person.sh +++ b/bin/forget_person.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes Personally Identifiable Information (PII) for a particular person. # diff --git a/bin/forget_protein.sh b/bin/forget_protein.sh index 415ecc28..a40e7673 100755 --- a/bin/forget_protein.sh +++ b/bin/forget_protein.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes information for a particular protein. # diff --git a/bin/forget_sample.sh b/bin/forget_sample.sh index 11c6f842..b216af86 100755 --- a/bin/forget_sample.sh +++ b/bin/forget_sample.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes information for a particular sample (BLSample). # diff --git a/bin/forget_shipping.sh b/bin/forget_shipping.sh index 381edd15..72e2f3e1 100755 --- a/bin/forget_shipping.sh +++ b/bin/forget_shipping.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes information for a particular shipping. # diff --git a/bin/forget_subsample.sh b/bin/forget_subsample.sh index 0c353c3e..044f5be8 100755 --- a/bin/forget_subsample.sh +++ b/bin/forget_subsample.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes information for a particular sub-sample (BLSubSample). # diff --git a/bin/forget_unused_shipments.sh b/bin/forget_unused_shipments.sh index 87ca6aaf..2990ebfc 100755 --- a/bin/forget_unused_shipments.sh +++ b/bin/forget_unused_shipments.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script removes all descriptive information related to shipments for # a particular proposal, except that related to samples on which data was diff --git a/bin/lookup_tables.sh b/bin/lookup_tables.sh index 8a95e741..174f53d7 100644 --- a/bin/lookup_tables.sh +++ b/bin/lookup_tables.sh @@ -4,6 +4,8 @@ SchemaStatus ComponentType ComponentSubType ConcentrationType +ContainerType +ExperimentType InspectionType PlateType SessionType diff --git a/bin/mdb_cluster_backup.sh b/bin/mdb_cluster_backup.sh index 9f9592d1..c4560a89 100755 --- a/bin/mdb_cluster_backup.sh +++ b/bin/mdb_cluster_backup.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # This script assumes a MariaDB Galera Cluster with read-write split. The # script must be run locally on one of the database read nodes. diff --git a/bin/missed_updates.sh b/bin/missed_updates.sh new file mode 100755 index 00000000..8dd84e94 --- /dev/null +++ b/bin/missed_updates.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +# Get the database name +if [ -z "${DB}" ] +then + DB="ispyb_build" +fi + +# Get this scripts dir +dir=$(dirname $(realpath -e ${0})) + +# Get the project'r root dir +project_root=$(dirname "${dir}") + +# Load some function definitions in case we need them +source ${project_root}/bin/functions.sh + +# Get a list of all update files +all_sql_files=`cd ${project_root}/schemas/ispyb/updates && ls *.sql && cd ../..` + +# Get a list of all update files recorded in the SchemaStatus table +done_sql_files=`mysql --defaults-file=${project_root}/.my.cnf -D $DB --skip-column-names --silent --raw -e "SELECT scriptName FROM SchemaStatus WHERE schemaStatus = 'DONE' ORDER BY recordTimeStamp;"` + +# Make a list of all update files not recorded in the SchemaStatus table +arr=() +while read -r sql_file; do + contains "$done_sql_files" "$sql_file" + if [[ $? -ne 0 ]] + then + echo "$sql_file" + fi +done <<< "$all_sql_files" diff --git a/build.sh b/build.sh index 98598854..313ec20f 100755 --- a/build.sh +++ b/build.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Script to create the database from the schema .sql files and identify any # update .sql files that haven't been run. Also generate documentation from @@ -11,44 +11,32 @@ source bin/functions.sh -if [ -z "${db}" ] +if [ -z "${DB}" ] then - db="ispyb_build" + DB="ispyb_build" fi echo "Dropping + creating build database" -mysql --defaults-file=.my.cnf -e "DROP DATABASE IF EXISTS $db; CREATE DATABASE $db; SET GLOBAL log_bin_trust_function_creators=ON;" +mysql --defaults-file=.my.cnf -e "DROP DATABASE IF EXISTS $DB; CREATE DATABASE $DB; SET GLOBAL log_bin_trust_function_creators=ON;" if [[ $? -eq 0 ]] then - mysql --defaults-file=.my.cnf -D $db < schemas/ispyb/tables.sql - mysql --defaults-file=.my.cnf -D $db < schemas/ispyb/lookups.sql - mysql --defaults-file=.my.cnf -D $db < schemas/ispyb/data.sql - mysql --defaults-file=.my.cnf -D $db < schemas/ispyb/routines.sql - mysql --defaults-file=.my.cnf -D $db < grants/ispyb_acquisition.sql - mysql --defaults-file=.my.cnf -D $db < grants/ispyb_processing.sql - mysql --defaults-file=.my.cnf -D $db < grants/ispyb_web.sql - mysql --defaults-file=.my.cnf -D $db < grants/ispyb_import.sql + mysql --defaults-file=.my.cnf -D $DB < schemas/ispyb/tables.sql + mysql --defaults-file=.my.cnf -D $DB < schemas/ispyb/lookups.sql + mysql --defaults-file=.my.cnf -D $DB < schemas/ispyb/data.sql + mysql --defaults-file=.my.cnf -D $DB < schemas/ispyb/routines.sql + mysql --defaults-file=.my.cnf -D $DB < grants/ispyb_acquisition.sql + mysql --defaults-file=.my.cnf -D $DB < grants/ispyb_processing.sql + mysql --defaults-file=.my.cnf -D $DB < grants/ispyb_web.sql + mysql --defaults-file=.my.cnf -D $DB < grants/ispyb_import.sql - # Identify update .sql files that haven't been run, and run them - all_sql_files=`cd schemas/ispyb/updates && ls *.sql && cd ../..` - - done_sql_files=`mysql --defaults-file=.my.cnf -D $db --skip-column-names --silent --raw -e "SELECT scriptName FROM SchemaStatus WHERE schemaStatus = 'DONE' ORDER BY recordTimeStamp;"` - - arr=() - while read -r sql_file; do - contains "$done_sql_files" "$sql_file" - if [[ $? -ne 0 ]] - then - arr+=("$sql_file") - mysql --defaults-file=.my.cnf -D $db < schemas/ispyb/updates/$sql_file - fi - done <<< "$all_sql_files" + arr=$(bin/missed_updates.sh) if [ -n "$arr" ]; then - echo "The following schemas/ispyb/updates/*.sql files were sourced:" - for val in "${arr[@]}"; do - echo "$val" + echo "Running schemas/ispyb/updates/*.sql files that haven't yet been run:" + for sql_file in ${arr[@]}; do + echo "$sql_file" + mysql --defaults-file=.my.cnf -D ${DB} < "schemas/ispyb/updates/${sql_file}" done else echo "No new schemas/ispyb/updates/*.sql files." @@ -57,8 +45,8 @@ then # Generate table and sproc documentation if [ -d "bin" ] && [ -d "docs" ]; then cd bin - ./db_procs_to_rst.sh $db > ../docs/list_of_procs.rst - ./db_tables_to_rst.sh $db > ../docs/list_of_tables_and_columns.rst + ./db_procs_to_rst.sh $DB > ../docs/list_of_procs.rst + ./db_tables_to_rst.sh $DB > ../docs/list_of_tables_and_columns.rst cd .. fi diff --git a/docs/list_of_tables_and_columns.rst b/docs/list_of_tables_and_columns.rst index 60af81fa..d7efa316 100644 --- a/docs/list_of_tables_and_columns.rst +++ b/docs/list_of_tables_and_columns.rst @@ -1317,26 +1317,29 @@ ``y``,float,"" **ParticleClassification**,table,"Results of 2D or 2D classification" ``particleClassificationId``,int,"" - ``particlePickerId``,int,"" - ``type``,enum,"Indicates the type of particle classification" - ``batchNumber``,int,"Corresponding to batch number" ``classNumber``,int,"Identified of the class. A unique ID given by Relion" ``classImageFullPath``,varchar,"The PNG of the class" - ``numberOfParticlesPerBatch``,int,"total number of particles per batch (a large integer)" - ``numberOfClassesPerBatch``,int,"" ``particlesPerClass``,int,"Number of particles within the selected class, can then be used together with the total number above to calculate the percentage" ``rotationAccuracy``,int,"???" ``translationAccuracy``,float,"Unit: Angstroms" ``estimatedResolution``,float,"???, Unit: Angstroms" ``overallFourierCompleteness``,float,"" + ``particleClassificationGroupId``,int,"" + **ParticleClassificationGroup**,table,"" + ``particleClassificationGroupId``,int,"" + ``particlePickerId``,int,"" + ``programId``,int,"" + ``type``,enum,"Indicates the type of particle classification" + ``batchNumber``,int,"Corresponding to batch number" + ``numberOfParticlesPerBatch``,int,"total number of particles per batch (a large integer)" + ``numberOfClassesPerBatch``,int,"" ``symmetry``,varchar,"" **ParticleClassification_has_CryoemInitialModel**,table,"" ``particleClassificationId``,int,"" ``cryoemInitialModelId``,int,"" **ParticlePicker**,table,"An instance of a particle picker program that was run" ``particlePickerId``,int,"" - ``particlePickerProgramId``,int,"" - ``particleClassificationProgramId``,int,"" + ``programId``,int,"" ``firstMotionCorrectionId``,int,"" ``particlePickingTemplate``,varchar,"Cryolo model" ``particleDiameter``,float,"Unit: nm" diff --git a/release.sh b/release.sh index 2505192c..c417d4ad 100755 --- a/release.sh +++ b/release.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Script to make a release from code currently in the repo if none exists for # the current schema version. diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index 6d4e1e19..12d5b0c9 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -422,14 +422,6 @@ INSERT INTO `ContainerRegistry` (`containerRegistryId`, `barcode`, `comments`, ` /*!40000 ALTER TABLE `ContainerReport` DISABLE KEYS */; /*!40000 ALTER TABLE `ContainerReport` ENABLE KEYS */; --- --- Dumping data for table `ContainerType` --- - -/*!40000 ALTER TABLE `ContainerType` DISABLE KEYS */; -INSERT INTO `ContainerType` (`containerTypeId`, `name`, `proposalType`, `active`, `capacity`, `wellPerRow`, `dropPerWellX`, `dropPerWellY`, `dropHeight`, `dropWidth`, `dropOffsetX`, `dropOffsetY`, `wellDrop`) VALUES (1,'B21_8+1','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(2,'B21_96','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(3,'B21_1tube','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(4,'I22_Capillary_Rack_20','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(5,'I22_Grid_100','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(6,'I22_Grid_45','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(7,'P38_Capillary_Rack_27','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(8,'P38_Solids','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(9,'P38_Powder','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(10,'B22_6','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(11,'I11_Capillary_Rack_6','scm',1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(12,'Puck','mx',1,16,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(13,'ReferencePlate','mx',1,16,2,1,1,1,1,0,0,-1),(14,'CrystalQuickX','mx',1,192,12,2,1,0.5,1,0,0,-1),(15,'MitegenInSitu','mx',1,192,12,2,1,0.5,1,0,0,-1),(16,'FilmBatch','mx',1,96,12,1,1,1,1,0,0,-1),(17,'MitegenInSitu_3_Drop','mx',1,288,12,3,1,0.5,1,0,0,-1),(18,'Greiner 3 Drop','mx',1,288,12,3,1,0.5,1,0,0,-1),(19,'MRC Maxi','mx',1,48,6,1,1,1,0.5,0,0,-1),(20,'MRC 2 Drop','mx',1,192,12,1,2,1,0.5,0.5,0,-1),(21,'Griener 1536','mx',1,1536,12,4,4,1,1,0,0,-1),(22,'3 Drop Square','mx',1,288,12,2,2,1,1,0,0,3),(23,'SWISSCI 3 Drop','mx',1,288,12,2,2,1,1,0,0,1),(24,'1 drop','mx',1,96,12,1,1,0.5,0.5,0,0,-1),(25,'LCP Glass','mx',1,96,12,1,1,1,1,0,0,-1),(26,'PCRStrip','scm',1,9,9,1,1,1,1,0,0,-1); -/*!40000 ALTER TABLE `ContainerType` ENABLE KEYS */; - -- -- Dumping data for table `CourierTermsAccepted` -- @@ -591,14 +583,6 @@ INSERT INTO `EnergyScan` (`energyScanId`, `sessionId`, `blSampleId`, `fluorescen /*!40000 ALTER TABLE `ExperimentKindDetails` DISABLE KEYS */; /*!40000 ALTER TABLE `ExperimentKindDetails` ENABLE KEYS */; --- --- Dumping data for table `ExperimentType` --- - -/*!40000 ALTER TABLE `ExperimentType` DISABLE KEYS */; -INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `active`) VALUES (1,'Default',NULL,1),(2,'MXPressE','mx',1),(3,'MXPressO','mx',1),(4,'MXPressE_SAD','mx',1),(5,'MXScore','mx',1),(6,'MXPressM','mx',1),(7,'MAD','mx',1),(8,'SAD','mx',1),(9,'Fixed','mx',1),(10,'Ligand binding','mx',1),(11,'Refinement','mx',1),(12,'OSC','MX',1),(13,'MAD - Inverse Beam','mx',1),(14,'SAD - Inverse Beam','mx',1),(15,'MESH','mx',1),(16,'XFE','mx',1),(17,'Stepped transmission','mx',1),(18,'XChem High Symmetry','mx',1),(19,'XChem Low Symmetry','mx',1),(20,'Commissioning','mx',1),(21,'HPLC','scm',1),(22,'Robot','scm',1),(23,'Rack','scm',1),(24,'Grid','scm',1),(25,'Solids','scm',1),(26,'Powder','scm',1),(27,'Peltier','scm',1),(28,'Spectroscopy','scm',1),(29,'CD Spectroscopy','scm',1),(30,'Microscopy','scm',1),(31,'Imaging','scm',1),(32,'CD Thermal Melt','scm',1),(33,'Fixed Energy At Ambient With Robot','scm',1); -/*!40000 ALTER TABLE `ExperimentType` ENABLE KEYS */; - -- -- Dumping data for table `Frame` -- @@ -870,6 +854,13 @@ INSERT INTO `PDB` (`pdbId`, `name`, `contents`, `code`) VALUES (6,'ceo2','\r\nda /*!40000 ALTER TABLE `ParticleClassification` DISABLE KEYS */; /*!40000 ALTER TABLE `ParticleClassification` ENABLE KEYS */; +-- +-- Dumping data for table `ParticleClassificationGroup` +-- + +/*!40000 ALTER TABLE `ParticleClassificationGroup` DISABLE KEYS */; +/*!40000 ALTER TABLE `ParticleClassificationGroup` ENABLE KEYS */; + -- -- Dumping data for table `ParticleClassification_has_CryoemInitialModel` -- @@ -1457,4 +1448,4 @@ INSERT INTO `v_run` (`runId`, `run`, `startDate`, `endDate`) VALUES (1,'2008-01' /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-03-05 16:12:02 +-- Dump completed on 2021-04-13 17:47:06 diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 1841cba9..f06807c6 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -19,7 +19,7 @@ -- /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.19.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.20.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; -- @@ -27,7 +27,7 @@ INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.1 -- /*!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 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16:17:12'),(173,'2021_04_13_ContainerType_update.sql','DONE','2021-04-13 16:42:57'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; -- @@ -54,6 +54,22 @@ INSERT INTO `ComponentSubType` (`componentSubTypeId`, `name`, `hasPh`, `proposal INSERT INTO `ConcentrationType` (`concentrationTypeId`, `name`, `symbol`, `proposalType`, `active`) VALUES (1,'Molar','M',NULL,1),(2,'Percentage Weight / Volume','%(w/v)',NULL,1),(3,'Percentage Volume / Volume','%(v/v)',NULL,1),(4,'Milligrams / Millilitre','mg/ml',NULL,1),(5,'Grams','g',NULL,1),(6,'Microlitre','uL','scm',1),(7,'Millilitre','ml','scm',1); /*!40000 ALTER TABLE `ConcentrationType` ENABLE KEYS */; +-- +-- Dumping data for table `ContainerType` +-- + +/*!40000 ALTER TABLE `ContainerType` DISABLE KEYS */; +INSERT INTO `ContainerType` (`containerTypeId`, `name`, `proposalType`, `active`, `capacity`, `wellPerRow`, `dropPerWellX`, `dropPerWellY`, `dropHeight`, `dropWidth`, `dropOffsetX`, `dropOffsetY`, `wellDrop`) VALUES 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ALTER TABLE `ExperimentType` DISABLE KEYS */; +INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `active`) VALUES (1,'Default',NULL,1),(2,'MXPressE','mx',1),(3,'MXPressO','mx',1),(4,'MXPressE_SAD','mx',1),(5,'MXScore','mx',1),(6,'MXPressM','mx',1),(7,'MAD','mx',1),(8,'SAD','mx',1),(9,'Fixed','mx',1),(10,'Ligand binding','mx',1),(11,'Refinement','mx',1),(12,'OSC','mx',1),(13,'MAD - Inverse Beam','mx',1),(14,'SAD - Inverse Beam','mx',1),(15,'MESH','mx',1),(16,'XFE','mx',1),(17,'Stepped transmission','mx',1),(18,'XChem High Symmetry','mx',1),(19,'XChem Low Symmetry','mx',1),(20,'Commissioning','mx',1),(21,'HPLC','saxs',1),(22,'Robot','saxs',1),(23,'Rack','saxs',1),(24,'Grid','saxs',1),(25,'Solids','saxs',1),(26,'Powder','saxs',1),(27,'Peltier','saxs',1),(28,'Spectroscopy','saxs',1),(29,'CD Spectroscopy','saxs',1),(30,'Microscopy','saxs',1),(31,'Imaging','saxs',1),(32,'CD Thermal Melt','saxs',1),(33,'Fixed Energy At Ambient With Robot','saxs',1); +/*!40000 ALTER 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-3 c1',NULL,NULL,NULL,NULL,1),(229,229,'Im-3m','Im -3 m',NULL,NULL,NULL,NULL,1),(230,230,'Ia-3d1','Ia -3 d1',NULL,NULL,NULL,NULL,1); /*!40000 ALTER TABLE `SpaceGroup` ENABLE KEYS */; -- @@ -215,4 +231,4 @@ INSERT INTO `PurificationColumn` (`purificationColumnId`, `name`, `active`) VALU /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-03-05 16:12:02 +-- Dump completed on 2021-04-13 17:47:06 diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index d1f04592..06f07b93 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -1,4 +1,4 @@ --- MariaDB dump 10.18 Distrib 10.5.8-MariaDB, for Linux (x86_64) +-- MariaDB dump 10.19 Distrib 10.5.9-MariaDB, for Linux (x86_64) -- -- Host: 10.88.0.5 Database: ispyb_build -- ------------------------------------------------------ @@ -4629,7 +4629,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4642,13 +4642,14 @@ BEGIN bs.visit_number "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN BLSession bs ON bs.sessionId = c.sessionId JOIN Proposal p ON p.proposalId = bs.proposalId JOIN BLSession bs2 ON bs2.proposalId = p.proposalId JOIN Session_has_Person shp ON shp.sessionId = bs2.sessionId JOIN Person per on per.personId = shp.personId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.containerId = p_id AND per.login = p_authLogin; @@ -4662,7 +4663,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4675,10 +4676,11 @@ BEGIN bs.visit_number "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN BLSession bs ON bs.sessionId = c.sessionId JOIN Proposal p ON p.proposalId = bs.proposalId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.containerId = p_id; @@ -4698,7 +4700,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4711,7 +4713,7 @@ BEGIN NULL "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN Dewar d ON c.dewarId = d.dewarId JOIN Shipping s ON s.shippingId = d.shippingId @@ -4719,6 +4721,7 @@ BEGIN JOIN BLSession bs2 ON bs2.proposalId = p.proposalId JOIN Session_has_Person shp ON shp.sessionId = bs2.sessionId JOIN Person per on per.personId = shp.personId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.containerId = p_id AND per.login = p_authLogin; @@ -4732,7 +4735,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4745,11 +4748,12 @@ BEGIN NULL "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN Dewar d ON c.dewarId = d.dewarId JOIN Shipping s ON s.shippingId = d.shippingId JOIN Proposal p ON p.proposalId = s.proposalId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.containerId = p_id; @@ -4803,7 +4807,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4816,13 +4820,14 @@ BEGIN bs.visit_number "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN BLSession bs ON bs.sessionId = c.sessionId JOIN Proposal p ON p.proposalId = bs.proposalId JOIN BLSession bs2 ON bs2.proposalId = p.proposalId JOIN Session_has_Person shp ON shp.sessionId = bs2.sessionId JOIN Person per on per.personId = shp.personId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber AND bs.visit_number = p_sessionNumber AND c.containerStatus = p_status AND per.login = p_authLogin; @@ -4836,7 +4841,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4849,10 +4854,11 @@ BEGIN bs.visit_number "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN BLSession bs ON bs.sessionId = c.sessionId JOIN Proposal p ON p.proposalId = bs.proposalId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber AND bs.visit_number = p_sessionNumber AND c.containerStatus = p_status; @@ -4872,7 +4878,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4885,7 +4891,7 @@ BEGIN NULL "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN Dewar d ON c.dewarId = d.dewarId JOIN Shipping s ON s.shippingId = d.shippingId @@ -4893,6 +4899,7 @@ BEGIN JOIN BLSession bs2 ON bs2.proposalId = p.proposalId JOIN Session_has_Person shp ON shp.sessionId = bs2.sessionId JOIN Person per on per.personId = shp.personId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber AND c.containerStatus = p_status AND per.login = p_authLogin; @@ -4906,7 +4913,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4919,11 +4926,12 @@ BEGIN NULL "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN Dewar d ON c.dewarId = d.dewarId JOIN Shipping s ON s.shippingId = d.shippingId JOIN Proposal p ON p.proposalId = s.proposalId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber AND c.containerStatus = p_status; @@ -4971,7 +4979,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -4984,13 +4992,14 @@ BEGIN bs.visit_number "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN BLSession bs ON bs.sessionId = c.sessionId JOIN Proposal p ON p.proposalId = bs.proposalId JOIN BLSession bs2 ON bs2.proposalId = p.proposalId JOIN Session_has_Person shp ON shp.sessionId = bs2.sessionId JOIN Person per on per.personId = shp.personId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.barcode = p_barcode AND per.login = p_authLogin; @@ -5004,7 +5013,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -5017,10 +5026,11 @@ BEGIN bs.visit_number "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN BLSession bs ON bs.sessionId = c.sessionId JOIN Proposal p ON p.proposalId = bs.proposalId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.barcode = p_barcode; @@ -5039,7 +5049,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -5052,7 +5062,7 @@ BEGIN NULL "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN Dewar d ON c.dewarId = d.dewarId JOIN Shipping s ON s.shippingId = d.shippingId @@ -5060,6 +5070,7 @@ BEGIN JOIN BLSession bs2 ON bs2.proposalId = p.proposalId JOIN Session_has_Person shp ON shp.sessionId = bs2.sessionId JOIN Person per on per.personId = shp.personId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.barcode = p_barcode AND per.login = p_authLogin; @@ -5073,7 +5084,7 @@ BEGIN c.ownerId "ownerId", per2.login "ownerUsername", c.code "name", - c.containerType "type", + IFNULL(ct.name, c.containerType) "type", c.barcode "barcode", c.beamlineLocation "beamline", c.sampleChangerLocation "location", @@ -5086,11 +5097,12 @@ BEGIN NULL "sessionNumber", c.comments "comments", - et.name "experimentType" + IFNULL(et.name, c.experimentType) "experimentType" FROM Container c JOIN Dewar d ON c.dewarId = d.dewarId JOIN Shipping s ON s.shippingId = d.shippingId JOIN Proposal p ON p.proposalId = s.proposalId + LEFT JOIN ContainerType ct ON ct.containerTypeId = c.containerTypeId LEFT JOIN Person per2 ON per2.personId = c.ownerId LEFT JOIN ExperimentType et ON et.experimentTypeId = c.experimentTypeId WHERE c.barcode = p_barcode; @@ -5158,7 +5170,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5212,7 +5224,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5268,7 +5280,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5323,7 +5335,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5409,7 +5421,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5463,7 +5475,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5519,7 +5531,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5574,7 +5586,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5660,7 +5672,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5714,7 +5726,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5770,7 +5782,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -5825,7 +5837,7 @@ BEGIN conct.name "materialConcentrationType", pr.isotropy "materialIsotropy", - et.name "planExperimentType", + IFNULL(et.name, c.experimentType) "planExperimentType", pc.name "planPurificationColumn", plan.robotPlateTemperature "planRobotPlateTemperature", plan.exposureTemperature "planExposureTemperature", @@ -9304,7 +9316,8 @@ BEGIN micronsPerPixelX = IFNULL(p_micronsPerPixelX, micronsPerPixelX), micronsPerPixelY = IFNULL(p_micronsPerPixelY, micronsPerPixelY), imageFullPath = IFNULL(p_imageFullPath, imageFullPath), - comments = IFNULL(p_comments, comments) + comments = IFNULL(p_comments, comments), + modifiedTimeStamp = current_timestamp WHERE blSampleImageId = p_id; END IF; END ;; @@ -9706,8 +9719,8 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-02-22 15:32:37 --- MariaDB dump 10.18 Distrib 10.5.8-MariaDB, for Linux (x86_64) +-- Dump completed on 2021-04-13 17:10:05 +-- MariaDB dump 10.19 Distrib 10.5.9-MariaDB, for Linux (x86_64) -- -- Host: 10.88.0.5 Database: ispyb_build -- ------------------------------------------------------ @@ -9730,6 +9743,7 @@ DELIMITER ; /*!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' */ ; +/*!50032 DROP TRIGGER IF EXISTS Container_sc_loc_update */; DELIMITER ;; /*!50003 CREATE*/ /*!50017 */ /*!50003 TRIGGER Container_sc_loc_update BEFORE UPDATE ON Container FOR EACH ROW @@ -9752,4 +9766,4 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-02-22 15:32:39 +-- Dump completed on 2021-04-13 17:10:05 diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index fcbb9ce4..2db4f0ea 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -366,7 +366,6 @@ CREATE TABLE `AutoProcScaling_has_Int` ( PRIMARY KEY (`autoProcScaling_has_IntId`), KEY `AutoProcScalingHasInt_FKIndex3` (`autoProcScalingId`,`autoProcIntegrationId`), KEY `AutoProcScal_has_IntIdx2` (`autoProcIntegrationId`), - KEY `AutoProcScl_has_IntIdx1` (`autoProcScalingId`), CONSTRAINT `AutoProcScaling_has_IntFk1` FOREIGN KEY (`autoProcScalingId`) REFERENCES `AutoProcScaling` (`autoProcScalingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `AutoProcScaling_has_IntFk2` FOREIGN KEY (`autoProcIntegrationId`) REFERENCES `AutoProcIntegration` (`autoProcIntegrationId`) ON DELETE CASCADE ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; @@ -619,7 +618,6 @@ CREATE TABLE `BLSample` ( `staffComments` varchar(255) DEFAULT NULL COMMENT 'Any staff comments on the sample', PRIMARY KEY (`blSampleId`), KEY `BLSample_FKIndex1` (`containerId`), - KEY `BLSample_FKIndex2` (`crystalId`), KEY `BLSample_FKIndex3` (`diffractionPlanId`), KEY `BLSample_FKIndex_Status` (`blSampleStatus`), KEY `BLSample_Index1` (`name`), @@ -659,7 +657,7 @@ CREATE TABLE `BLSampleGroup_has_BLSample` ( `blSampleGroupId` int(11) unsigned NOT NULL, `blSampleId` int(11) unsigned NOT NULL, `groupOrder` mediumint(9) DEFAULT NULL, - `type` enum('background','container','sample','calibrant') DEFAULT NULL, + `type` enum('background','container','sample','calibrant','capillary') DEFAULT NULL, `blSampleTypeId` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`blSampleGroupId`,`blSampleId`), KEY `BLSampleGroup_has_BLSample_ibfk2` (`blSampleId`), @@ -921,8 +919,8 @@ CREATE TABLE `BLSession` ( `externalId` binary(16) DEFAULT NULL, `archived` tinyint(1) DEFAULT 0 COMMENT 'The data for the session is archived and no longer available on disk', PRIMARY KEY (`sessionId`), + UNIQUE KEY `proposalId` (`proposalId`,`visit_number`), KEY `BLSession_FKIndexOperatorSiteNumber` (`operatorSiteNumber`), - KEY `Session_FKIndex1` (`proposalId`), KEY `Session_FKIndex2` (`beamLineSetupId`), KEY `Session_FKIndexBeamLineName` (`beamLineName`), KEY `Session_FKIndexEndDate` (`endDate`), @@ -1440,10 +1438,10 @@ CREATE TABLE `ContainerInspection` ( `scheduledTimeStamp` datetime DEFAULT NULL, `completedTimeStamp` datetime DEFAULT NULL, PRIMARY KEY (`containerInspectionId`), - KEY `ContainerInspection_idx1` (`containerId`), KEY `ContainerInspection_idx2` (`inspectionTypeId`), KEY `ContainerInspection_idx3` (`imagerId`), KEY `ContainerInspection_fk4` (`scheduleComponentid`), + KEY `ContainerInspection_idx4` (`containerId`,`scheduleComponentid`,`state`,`manual`), CONSTRAINT `ContainerInspection_fk1` FOREIGN KEY (`containerId`) REFERENCES `Container` (`containerId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ContainerInspection_fk2` FOREIGN KEY (`inspectionTypeId`) REFERENCES `InspectionType` (`inspectionTypeId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `ContainerInspection_fk3` FOREIGN KEY (`imagerId`) REFERENCES `Imager` (`imagerId`) ON DELETE NO ACTION ON UPDATE NO ACTION, @@ -3198,25 +3196,44 @@ DROP TABLE IF EXISTS `ParticleClassification`; /*!40101 SET character_set_client = utf8 */; CREATE TABLE `ParticleClassification` ( `particleClassificationId` int(10) unsigned NOT NULL AUTO_INCREMENT, - `particlePickerId` int(10) unsigned DEFAULT NULL, - `type` enum('2D','3D') DEFAULT NULL COMMENT 'Indicates the type of particle classification', - `batchNumber` int(10) unsigned DEFAULT NULL COMMENT 'Corresponding to batch number', `classNumber` int(10) unsigned DEFAULT NULL COMMENT 'Identified of the class. A unique ID given by Relion', `classImageFullPath` varchar(255) DEFAULT NULL COMMENT 'The PNG of the class', - `numberOfParticlesPerBatch` int(10) unsigned DEFAULT NULL COMMENT 'total number of particles per batch (a large integer)', - `numberOfClassesPerBatch` int(10) unsigned DEFAULT NULL, `particlesPerClass` int(10) unsigned DEFAULT NULL COMMENT 'Number of particles within the selected class, can then be used together with the total number above to calculate the percentage', `rotationAccuracy` int(10) unsigned DEFAULT NULL COMMENT '???', `translationAccuracy` float DEFAULT NULL COMMENT 'Unit: Angstroms', `estimatedResolution` float DEFAULT NULL COMMENT '???, Unit: Angstroms', `overallFourierCompleteness` float DEFAULT NULL, - `symmetry` varchar(20) DEFAULT NULL, + `particleClassificationGroupId` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`particleClassificationId`), - KEY `ParticleClassification_fk_particlePickerId` (`particlePickerId`), - CONSTRAINT `ParticleClassification_fk_particlePickerId` FOREIGN KEY (`particlePickerId`) REFERENCES `ParticlePicker` (`particlePickerId`) ON DELETE CASCADE ON UPDATE CASCADE + KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`), + CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Results of 2D or 2D classification'; /*!40101 SET character_set_client = @saved_cs_client */; +-- +-- Table structure for table `ParticleClassificationGroup` +-- + +DROP TABLE IF EXISTS `ParticleClassificationGroup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `ParticleClassificationGroup` ( + `particleClassificationGroupId` int(10) unsigned NOT NULL AUTO_INCREMENT, + `particlePickerId` int(10) unsigned DEFAULT NULL, + `programId` int(10) unsigned DEFAULT NULL, + `type` enum('2D','3D') DEFAULT NULL COMMENT 'Indicates the type of particle classification', + `batchNumber` int(10) unsigned DEFAULT NULL COMMENT 'Corresponding to batch number', + `numberOfParticlesPerBatch` int(10) unsigned DEFAULT NULL COMMENT 'total number of particles per batch (a large integer)', + `numberOfClassesPerBatch` int(10) unsigned DEFAULT NULL, + `symmetry` varchar(20) DEFAULT NULL, + PRIMARY KEY (`particleClassificationGroupId`), + KEY `ParticleClassificationGroup_fk_particlePickerId` (`particlePickerId`), + KEY `ParticleClassificationGroup_fk_programId` (`programId`), + CONSTRAINT `ParticleClassificationGroup_fk_particlePickerId` FOREIGN KEY (`particlePickerId`) REFERENCES `ParticlePicker` (`particlePickerId`) ON DELETE CASCADE ON UPDATE CASCADE, + CONSTRAINT `ParticleClassificationGroup_fk_programId` FOREIGN KEY (`programId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE NO ACTION ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + -- -- Table structure for table `ParticleClassification_has_CryoemInitialModel` -- @@ -3243,19 +3260,16 @@ DROP TABLE IF EXISTS `ParticlePicker`; /*!40101 SET character_set_client = utf8 */; CREATE TABLE `ParticlePicker` ( `particlePickerId` int(10) unsigned NOT NULL AUTO_INCREMENT, - `particlePickerProgramId` int(10) unsigned DEFAULT NULL, - `particleClassificationProgramId` int(10) unsigned DEFAULT NULL, + `programId` int(10) unsigned DEFAULT NULL, `firstMotionCorrectionId` int(10) unsigned DEFAULT NULL, `particlePickingTemplate` varchar(255) DEFAULT NULL COMMENT 'Cryolo model', `particleDiameter` float DEFAULT NULL COMMENT 'Unit: nm', `numberOfParticles` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`particlePickerId`), - KEY `ParticlePicker_fk_particlePickerProgramId` (`particlePickerProgramId`), - KEY `ParticlePicker_fk_particleClassificationProgramId` (`particleClassificationProgramId`), + KEY `ParticlePicker_fk_particlePickerProgramId` (`programId`), KEY `ParticlePicker_fk_motionCorrectionId` (`firstMotionCorrectionId`), CONSTRAINT `ParticlePicker_fk_motionCorrectionId` FOREIGN KEY (`firstMotionCorrectionId`) REFERENCES `MotionCorrection` (`motionCorrectionId`) ON DELETE NO ACTION ON UPDATE CASCADE, - CONSTRAINT `ParticlePicker_fk_particleClassificationProgramId` FOREIGN KEY (`particleClassificationProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE NO ACTION ON UPDATE CASCADE, - CONSTRAINT `ParticlePicker_fk_particlePickerProgramId` FOREIGN KEY (`particlePickerProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE NO ACTION ON UPDATE CASCADE + CONSTRAINT `ParticlePicker_fk_programId` FOREIGN KEY (`programId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE NO ACTION ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='An instance of a particle picker program that was run'; /*!40101 SET character_set_client = @saved_cs_client */; @@ -3897,7 +3911,6 @@ CREATE TABLE `Protein` ( `isotropy` enum('isotropic','anisotropic') DEFAULT NULL, PRIMARY KEY (`proteinId`), KEY `ProteinAcronym_Index` (`proposalId`,`acronym`), - KEY `Protein_FKIndex1` (`proposalId`), KEY `Protein_FKIndex2` (`personId`), KEY `Protein_Index2` (`acronym`), KEY `protein_fk3` (`componentTypeId`), @@ -4599,7 +4612,6 @@ CREATE TABLE `Session_has_Person` ( `role` enum('Local Contact','Local Contact 2','Staff','Team Leader','Co-Investigator','Principal Investigator','Alternate Contact','Data Access','Team Member','ERA Admin') DEFAULT NULL, `remote` tinyint(1) DEFAULT 0, PRIMARY KEY (`sessionId`,`personId`), - KEY `Session_has_Person_FKIndex1` (`sessionId`), KEY `Session_has_Person_FKIndex2` (`personId`), CONSTRAINT `Session_has_Person_ibfk_1` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Session_has_Person_ibfk_2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE ON UPDATE CASCADE @@ -4672,7 +4684,6 @@ CREATE TABLE `ShippingHasSession` ( `shippingId` int(10) unsigned NOT NULL, `sessionId` int(10) unsigned NOT NULL, PRIMARY KEY (`shippingId`,`sessionId`), - KEY `ShippingHasSession_FKIndex1` (`shippingId`), KEY `ShippingHasSession_FKIndex2` (`sessionId`), CONSTRAINT `ShippingHasSession_ibfk_1` FOREIGN KEY (`shippingId`) REFERENCES `Shipping` (`shippingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ShippingHasSession_ibfk_2` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE @@ -6026,4 +6037,4 @@ SET character_set_client = @saved_cs_client; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-03-05 16:06:13 +-- Dump completed on 2021-04-13 17:10:05 diff --git a/schemas/ispyb/updates/2021_04_13_AdminVar_bump_version.sql b/schemas/ispyb/updates/2021_04_13_AdminVar_bump_version.sql new file mode 100644 index 00000000..2d22632f --- /dev/null +++ b/schemas/ispyb/updates/2021_04_13_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2021_04_13_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '1.20.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2021_04_13_AdminVar_bump_version.sql'; diff --git a/schemas/ispyb/updates/2021_04_13_ContainerType_update.sql b/schemas/ispyb/updates/2021_04_13_ContainerType_update.sql new file mode 100644 index 00000000..8de0e7f5 --- /dev/null +++ b/schemas/ispyb/updates/2021_04_13_ContainerType_update.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2021_04_13_ContainerType_update.sql', 'ONGOING'); + +UPDATE ContainerType SET name = 'Puck-22' WHERE proposalType = 'xpdf' AND name = 'Puck'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2021_04_13_ContainerType_update.sql'; diff --git a/schemas/ispyb_analytics/build.sh b/schemas/ispyb_analytics/build.sh index be0adf30..6e3464a3 100755 --- a/schemas/ispyb_analytics/build.sh +++ b/schemas/ispyb_analytics/build.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Exit on first error incl. pipeline errors set -eo pipefail