Updated schema files, history, docs for version 1.19.0

HISTORY.rst

@@ -5,6 +5,19 @@ History
 Unreleased / master
 -------------------
 
+1.19.0 (2021-03-05)
+-------------------
+
+* Add new tables for CryoEM - note that these are still subject to potentially significant change:
+ * ``ParticlePicker``
+ * ``ParticleClassification``: Results of 2D or 2D classification
+ * ``CryoemInitialModel``: Initial cryo-EM model generation results
+ * ``ParticleClassification_has_CryoemInitialModel``
+* Add old tables that exist in prod database, but not yet in repo:
+ * ``BF_automationFault``: Software faults, stacktrace, severity etc.
+ * ``BF_automationError``: Lookup table used by ``BF_automationFault``
+* Add ``ContainerType`` table and foreign key referencing it in ``Container`` table
+
 1.18.0 (2021-02-22)
 -------------------
 

docs/list_of_procs.rst

@@ -163,12 +163,15 @@
  Returns: Record ID in p_id."
  "**upsert_energy_scan**", "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_startEnergy float, p_endEnergy float, p_detector varchar(40), p_element varchar(10), p_edgeEnergy varchar(10), p_synchrotronCurrent float, p_temperature float, p_peakEnergy float, p_peakFPrime float, p_peakFDoublePrime float, p_inflectionEnergy float, p_inflectionFPrime float, p_inflectionFDoublePrime float, p_choochFileFullPath varchar(255), p_jpegChoochFileFullPath 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 an energy scan (p_id).
  Mandatory c"
- "**upsert_fluo_mapping**", "INOUT p_id int(11) unsigned, p_roiId int(11) unsigned, p_roiStartEnergy float, p_roiEndEnergy float, p_dcId int(11) unsigned, p_imgNumber int(10) unsigned, p_counts int(10) unsigned", "Inserts or updates info about a fluorescence spectrum mapping (p_id).
+ "**upsert_fluo_mapping**", "INOUT p_id int(11) unsigned, p_xrfFluorescenceMappingROIId int(11), p_gridInfoId int(11) unsigned, p_dataFormat varchar(15), p_data longblob, p_points int(11), p_opacity float, p_colourMap varchar(20), p_min int(3), p_max int(3), p_autoProcProgramId int(10) unsigned", "Inserts or updates info about a fluorescence spectrum mapping (p_id).
+ Mandatory columns:
+ For insert:
+ For update: p_id
+ Returns: Record ID in p_id."
+ "**upsert_fluo_mapping_roi**", "INOUT p_id int(11) unsigned, p_startEnergy float, p_endEnergy float, p_element varchar(2), p_edge varchar(15), p_r tinyint(3) unsigned, p_g tinyint(3) unsigned, p_b tinyint(3) unsigned, p_blSampleId int(10) unsigned, p_scalar varchar(50)", "Inserts or updates info about a fluorescence spectrum mapping region of interest (p_id).
  Mandatory columns:
- For insert: (p_roiId OR (p_roiStartEnergy AND p_roiEndEnergy)) AND p_dcId
  For update: p_id
  Returns: Record ID in p_id."
- "**upsert_fluo_mapping_roi**", "INOUT p_id int(11) unsigned, p_startEnergy float, p_endEnergy float, p_element varchar(2), p_edge varchar(2), p_r tinyint unsigned, p_g tinyint unsigned, p_b tinyint unsigned", "Inserts or updates info about a fluorescence spectrum mapping re"
  "**upsert_motion_correction**", "INOUT p_motionCorrectionId int(11) unsigned, p_movieId int(11) unsigned, p_autoProcProgramId int(11) unsigned, p_imageNumber smallint unsigned, p_firstFrame smallint unsigned, p_lastFrame smallint unsigned, p_dosePerFrame float, p_totalMotion float, p_averageMotionPerFrame float, p_driftPlotFullPath varchar(255), p_micrographFullPath varchar(255), p_micrographSnapshotFullPath varchar(255), p_fftFullPath varchar(255), p_fftCorrectedFullPath varchar(255), p_patchesUsedX mediumint unsigned, p_patchesUsedY mediumint unsigned, p_comments varchar(255)", ""
  "**upsert_motion_correction_drift**", "INOUT p_id int(11) unsigned, p_motionCorrectionId int(11) unsigned, p_frameNumber smallint unsigned, p_deltaX float, p_deltaY float", "If p_id is not provided, inserts new row. Otherwise updates exis"
  "**upsert_movie**", "INOUT p_movieId int(11) unsigned, p_dataCollectionId int(11) unsigned, p_movieNumber mediumint unsigned, p_movieFullPath varchar(255), p_createdTimeStamp timestamp, p_positionX float, p_positionY float, p_nominalDefocus float unsigned", ""
@@ -201,7 +204,7 @@
  For insert: p_proposalId, p_personId
  For update: p_id
  Returns: Record ID in p_id."
- "**upsert_quality_indicators**", "OUT p_id int(11) unsigned, p_dataCollectionId int(11) unsigned, p_autoProcProgramId int(10) unsigned, p_imageNumber mediumint(8) unsigned, p_spotTotal int(10), p_inResTotal int(10), p_goodBraggCandidates int(10), p_iceRings int(10), p_method1Res float, p_method2Res float, p_maxUnitCell float, p_pctSaturationTop50Peaks float, p_inResolutionOvrlSpots int(10), p_binPopCutOffMethod2Res float, p_totalIntegratedSignal double, p_dozorScore double, p_driftFactor float", "Inserts into or updates a row in the image quality indicators table"
+ "**upsert_quality_indicators**", "OUT p_id int(11) unsigned, p_dataCollectionId int(11) unsigned,  p_autoProcProgramId int(10) unsigned,  p_imageNumber mediumint(8) unsigned, p_spotTotal int(10), p_inResTotal int(10), p_goodBraggCandidates int(10), p_iceRings int(10), p_method1Res float, p_method2Res float, p_maxUnitCell float, p_pctSaturationTop50Peaks float, p_inResolutionOvrlSpots int(10), p_binPopCutOffMethod2Res float, p_totalIntegratedSignal double, p_dozorScore double, p_driftFactor float", "Inserts into or updates a row in the image quality indicators table"
  "**upsert_quality_indicators_dozor_score**", "OUT p_id int(11) unsigned, p_dataCollectionId int(11) unsigned, p_imageNumber mediumint(8) unsigned, p_dozorScore double", "Inserts into or updates a row in the image quality indicators table"
  "**upsert_robot_action**", "INOUT p_id int(11) unsigned, p_sessionId int(11) unsigned, p_sampleId int(11) unsigned, p_actionType varchar(15), p_startTimestamp timestamp, p_endTimestamp timestamp, p_status varchar(24), p_message varchar(255), p_containerLocation smallint, p_dewarLocation smallint, p_sampleBarcode varchar(45), p_snapshotBefore varchar(255), p_snapshotAfter varchar(255)", "Inserts or updates info about a robot action (p_id).
  Mandatory c"

docs/list_of_tables_and_columns.rst

@@ -234,6 +234,18 @@
  ``flux``,double,""
  ``scanFileW``,varchar,""
  ``scanFileH``,varchar,""
+ **BF_automationError**,table,""
+ ``automationErrorId``,int,""
+ ``errorType``,varchar,""
+ ``solution``,text,""
+ **BF_automationFault**,table,""
+ ``automationFaultId``,int,""
+ ``automationErrorId``,int,""
+ ``containerId``,int,""
+ ``severity``,enum,""
+ ``stacktrace``,text,""
+ ``resolved``,tinyint,""
+ ``faultTimeStamp``,timestamp,""
  **BF_component**,table,""
  ``componentId``,int,""
  ``systemId``,int,""
@@ -512,11 +524,12 @@
  ``requestedReturn``,tinyint,"True for requesting return, False means container will be disposed"
  ``comments``,varchar,""
  ``experimentType``,varchar,""
- ``storageTemperature``,float,""
+ ``storageTemperature``,float,"NULL=ambient"
  ``containerRegistryId``,int,""
  ``scLocationUpdated``,datetime,""
  ``priorityPipelineId``,int,""
  ``experimentTypeId``,int,""
+ ``containerTypeId``,int,""
  **ContainerHistory**,table,""
  ``containerHistoryId``,int,""
  ``containerId``,int,""
@@ -565,13 +578,31 @@
  ``report``,text,""
  ``attachmentFilePath``,varchar,""
  ``recordTimestamp``,datetime,""
+ **ContainerType**,table,"A lookup table for different types of containers"
+ ``containerTypeId``,int,""
+ ``name``,varchar,""
+ ``proposalType``,varchar,""
+ ``active``,tinyint,"1=active, 0=inactive"
+ ``capacity``,int,""
+ ``wellPerRow``,smallint,""
+ ``dropPerWellX``,smallint,""
+ ``dropPerWellY``,smallint,""
+ ``dropHeight``,float,""
+ ``dropWidth``,float,""
+ ``dropOffsetX``,float,""
+ ``dropOffsetY``,float,""
+ ``wellDrop``,smallint,""
  **CourierTermsAccepted**,table,"Records acceptances of the courier T and C"
  ``courierTermsAcceptedId``,int,""
  ``proposalId``,int,""
  ``personId``,int,""
  ``shippingName``,varchar,""
  ``timestamp``,datetime,""
  ``shippingId``,int,""
+ **CryoemInitialModel**,table,"Initial cryo-EM model generation results"
+ ``cryoemInitialModelId``,int,""
+ ``resolution``,float,"Unit: Angstroms"
+ ``numberOfParticles``,int,""
  **Crystal**,table,""
  ``crystalId``,int,""
  ``diffractionPlanId``,int,""
@@ -1284,6 +1315,32 @@
  ``dataCollectionId``,int,""
  ``x``,float,""
  ``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,""
+ ``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,""
+ ``firstMotionCorrectionId``,int,""
+ ``particlePickingTemplate``,varchar,"Cryolo model"
+ ``particleDiameter``,float,"Unit: nm"
+ ``numberOfParticles``,int,""
  **PDB**,table,""
  ``pdbId``,int,""
  ``name``,varchar,""