Bump to v1.23.0, update schema files + documentation

HISTORY.rst

@@ -4,6 +4,28 @@ History
 
 Unreleased / master
 -------------------
+
+1.23.0 (2021-07-07)
+-------------------
+
+New columns:
+
+* ``DiffractionPlan``: ``qMin``, ``qMax``, ``reductionParametersAveraging``
+* ``ParticleClassification``: ``classDistribution``
+* ``ParticlePicker``: ``summaryImageFullPath``
+* ``BLSampleGroup``: ``proposalId`` (and populate it based on ``BLSampleGroup_has_BLSample -> BLSample -> Crystal -> Protein.proposalId``)
+
+New tables:
+
+* ``zc_ZocaloBuffer``: A table for temporary Zocalo data. 
+
+Lookup table data changes:
+
+* ``SpaceGroup``: Changed a few ``spaceGroupShortName`` values for common spacegroups, and set ``MX_used = 0`` for less commonly used spacegroups. 
+* ``UserGroup``: Add groups ``detector_admin``, ``prop_admin``, ``goods_handling``, ``imaging_admin``, ``spectroscopy_admin``, ``mm_admin``.
+
+Additionally, new enum options have been added to DataCollectionGroup.experimentType: Mesh3D, Screening.
+
 1.22.0 (2021-05-28)
 -------------------
 

docs/list_of_procs.rst

@@ -196,6 +196,7 @@
  "**upsert_mrrun**", "INOUT p_id integer, p_parentId integer, p_success boolean, p_message varchar(255), p_pipeline varchar(50), p_inputCoordFile varchar(255), p_outputCoordFile varchar(255), p_inputMTZFile varchar(255), p_outputMTZFile varchar(255), p_runDirectory varchar(255), p_logFile varchar(255), p_commandLine varchar(255), p_rValueStart float , p_rValueEnd float , p_rFreeValueStart float , p_rFreeValueEnd float , p_starttime datetime, p_endtime datetime", "Update or insert new entry with info about a MX molecular replacements run, e.g. Dimple"
  "**upsert_mrrun_blob**", "p_Id integer, p_parentId integer, p_view1 varchar(255), p_view2 varchar(255), p_view3 varchar(255)", "Update or insert new entry with info about views (image paths) for an MX molecular replacement run, e.g. Dimple."
  "**upsert_mrrun_blob**", "INOUT p_id integer, p_parentId integer, p_view1 varchar(255), p_view2 varchar(255), p_view3 varchar(255)", "Update or insert new entry with info about views (image paths) for an MX molecular replacement run, e.g. Dimple."
+ "**upsert_mx_sample**", "INOUT p_sampleId int(10) unsigned, p_authLogin varchar(45), p_containerId int(10) unsigned, p_dataCollectionPlanId int(10) unsigned, p_crystalId int(10) unsigned, p_positionId int(10) unsigned, p_sampleName varchar(45), p_sampleCode varchar(45), p_sampleComments varchar(1024), p_publicationComments varchar(255), p_sampleLocation varchar(45), p_sampleSubLocation smallint(5) unsigned, p_isInSampleChanger tinyint(1), p_lastKnownCenteringPosition varchar(255), p_holderLength double, p_loopLength double, p_loopType varchar(45), p_wireWidth double, p_sampleStatus varchar(20), p_completionStage varchar(45), p_structureStage varchar(45), p_publicationStage varchar(45)", "Inserts or updates info about a sample."
  "**upsert_particle_classification**", "INOUT p_id int unsigned, p_particleClassificationGroupId int unsigned, p_classNumber int unsigned, p_classImageFullPath varchar(255), p_particlesPerClass int unsigned, p_rotationAccuracy float, p_translationAccuracy float, p_estimatedResolution float, p_overallFourierCompleteness float", "Inserts or updates info about a particle classification (p_id).
  Mandatory columns:
  For insert: p_particleClassificationGroupId

docs/list_of_tables_and_columns.rst

@@ -334,6 +334,7 @@
  **BLSampleGroup**,table,""
  ``blSampleGroupId``,int,""
  ``name``,varchar,"Human-readable name"
+ ``proposalId``,int,""
  **BLSampleGroup_has_BLSample**,table,""
  ``blSampleGroupId``,int,""
  ``blSampleId``,int,""
@@ -953,6 +954,9 @@
  ``purificationColumnId``,int,""
  ``collectionMode``,enum,"The requested collection mode, possible values are auto, manual"
  ``priority``,int,"The priority of this sample relative to others in the shipment"
+ ``qMin``,float,"minimum in qRange, unit: nm^-1, needed for SAXS"
+ ``qMax``,float,"maximum in qRange, unit: nm^-1, needed for SAXS"
+ ``reductionParametersAveraging``,enum,"Post processing params for SAXS"
  **EMMicroscope**,table,""
  ``emMicroscopeId``,int,""
  ``instrumentName``,varchar,""
@@ -1331,6 +1335,7 @@
  ``estimatedResolution``,float,"???, Unit: Angstroms"
  ``overallFourierCompleteness``,float,""
  ``particleClassificationGroupId``,int,""
+ ``classDistribution``,float,"Provides a figure of merit for the class, higher number is better"
  **ParticleClassificationGroup**,table,""
  ``particleClassificationGroupId``,int,""
  ``particlePickerId``,int,""
@@ -1350,6 +1355,7 @@
  ``particlePickingTemplate``,varchar,"Cryolo model"
  ``particleDiameter``,float,"Unit: nm"
  ``numberOfParticles``,int,""
+ ``summaryImageFullPath``,varchar,"Generated summary micrograph image with highlighted particles"
  **PDB**,table,""
  ``pdbId``,int,""
  ``name``,varchar,""
@@ -2243,3 +2249,7 @@
  ``b``,tinyint,"B colour component"
  ``blSampleId``,int,"ROIs can be created within the context of a sample"
  ``scalar``,varchar,"For ROIs that are not an element, i.e. could be a scan counter instead"
+ **zc_ZocaloBuffer**,table,""
+ ``AutoProcProgramID``,int,"Reference to an existing AutoProcProgram"
+ ``UUID``,int,"AutoProcProgram-specific unique identifier"
+ ``Reference``,int,"Context-dependent reference to primary key IDs in other ISPyB tables"