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#Visualization logic

Map-reduce views

The visualizations depend on a number of statusdb Couchdb map-reduce views from in the form of json strings accessible through a url on the form:

http://<user>:<password>@tools.scilifelab.se:5984/<database>/_design/<design>/_view/<view>?[group_level=<n>][reduce=false]

KPI_applications

parameter value
database project
design process_flow
view KPI_applications (sofa view)
group_level 3 (json)

####Map function simplified pseudo code For each project of type "Production" For each sample For each lib prep

		Emit:
		[
			application,  // reduce group level 1
			project_name, // reduce group level 2
			project_id,   // reduce group level 3
			sample,       // reduce group level 4
			lib_prep      // reduce group level 5
		]:
		{
			Arrival date: open_date
			Queue date: queued
			QC library finished: last of library_validation->finish_date
			All samples sequenced: last of sample_run_metrics->sequencing_finish_date

		   /** 
		     These dates are in the form YYYY-MM-DD. 
		     If absent a date is set to 0000-00-00) 
		    */
		}

####Reduce function simplified pseudo code For each line return the latest date of each result date as the reduced value for a particular level unless there is a 0000-00-00 date return 0000-00-00

KPI

parameter value
database project
design process_flow
view KPI (sofa view)
group_level 3 (json)

####Map function simplified pseudo code For each project of type "Production" For each sample For each lib prep

		Emit:
		[
			sequencing_platform,  // reduce group level 1
			project_name, // reduce group level 2
			project_id,   // reduce group level 3
			sample,       // reduce group level 4
			lib_prep      // reduce group level 5
		]:
		{
			Arrival date: open_date
			Queue date: queued
			QC library finished: last of library_validation->finish_date
			All samples sequenced: last of sample_run_metrics->sequencing_finish_date

		   /** 
		     These dates are in the form YYYY-MM-DD. 
		     If absent a date is set to 0000-00-00) 
		    */
		}

####Reduce function simplified pseudo code For each line return the latest date of each result date as the reduced value for a particular level unless there is a 0000-00-00 date return 0000-00-00

###KPI1

parameter value
database project
design kpi_external
view KPI1 (sofa view)
reduce false (json)

####Map function simplified pseudo code For each project of type "Production" For each sample For each lib prep if sample_run_metrics && dillution_and_pooling_start_date

	    	Emit:
			[
				dillution_and_pooling_start_date,  
				application, 
				sample
			]:
			incoming_QC_status /** True || False */

###KPI2

parameter value
database project
design kpi_external
view KPI2 (sofa view)
reduce false (json)

####Map function simplified pseudo code For each project of type "Production" For each sample For each lib prep

			if workset_setup
		
	    	Emit:
			[
				workset_setup, 
				application, 
				"library validation"->start_date, 
				sample
			]:
			prep_status /** PASSED || FAILED */

###KPI3_1

parameter value
database project
design kpi_external
view KPI3_1 (sofa view)
reduce false (json)

####Map function simplified pseudo code For each project of type "Production" ordered = sequencing_platform * sequence_units_ordered_(lanes) * "platform amount factor" delivered = Sum of m_reads_sequenced For each sample

	Emit:
	[
		sequencing_finished, // date 
		project_name, 
	]:
	[
		sequencing_platform,
		sequence_units_ordered_(lanes),
		ordered, // amount
		samples, // no. of
		delivered,
		delivered/ordered
	]

Dataset generation

Ongoing projects today

This section needs at complete re-write for the stacked load barcharts

Total delivery times runchart & boxplot

Function runchart: generateRunchartDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection)

Calculates the time difference in days between dateFromKey and dateToKey for projects active between dateRangeStart and dateRangeEnd [that has [the inverse of] filter as the first value in the json key].

Returns a list of [time diff, project name, done date, project id]

Function boxplot: generateBoxDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection)

Calculates the time difference in days between dateFromKey and dateToKey for projects active between dateRangeStart and dateRangeEnd [that has [the inverseSelection of] filter as the first value in the json key].

Returns a list of time diff

Stratifications

All projects

View: KPI_applications

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
Library prep projects

View: KPI_applications

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
filter: Finished library
inverseSelection: true
Finished library project

View: KPI_applications

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
filter: Finished library
inverseSelection: false
HiSeq projects

View: KPI

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
filter: HiSeq
MiSeq projects

View: KPI

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
filter: MiSeq

Rec control delivery times runchart & boxplot

Function runchart: generateRunchartDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection). See Total delivery times above

Function boxplot: generateBoxDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection) See Total delivery times above

View: KPI_applications

dateRangeStart: Arrival date
dateRangeEnd: Queue date

Lib prep delivery times runchart & boxplot

Function runchart: generateRunchartDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection). See Total delivery times above

Function boxplot: generateBoxDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection) See Total delivery times above

View: KPI_applications

dateRangeStart: Queue date
dateRangeEnd: QC library finished

Sequencing delivery times runchart & boxplot

Function runchart: generateRunchartDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection). See Total delivery times above

Function boxplot: generateBoxDataset (jsonview, dateRangeStart, dateRangeEnd, dateFromKey, dateToKey, filter, inverseSelection) See Total delivery times above

Stratifications

All projects

View: KPI

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
HiSeq projects

View: KPI

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
filter: HiSeq
MiSeq projects

View: KPI

dateRangeStart: Arrival date
dateRangeEnd: All samples sequenced
filter: MiSeq

Reception control - number of failed samples that are progressed barchart

View: KPI1

Function: generateFailedProgressedDataset(data, cmpDate)

Bins samples on sequencing_start date in three 4-week bins until cpmDate. Returns (#samples failed in rec ctrl that has a sequencing start date)/(all samples with sequencing start date) for each bin

Library prep - fraction failed samples/workset runchart & boxplot

View: KPI2

Function: generateWorksetFailureDataset (jsonview, dateRangeStart, dateRangeEnd, filter)

Calculates the fraction of failed samples for worksets active between dateRangeStart and dateRangeEnd [that has filter as the first value in the json key].

Returns list of [fraction failed, workset, date, total number of samples]

Function: generateGenericBoxDataset (dataset, index) Returns a list of values that has index in the specified dataset (a list of lists)

Seq - data delivered / data ordered runchart & boxplot

View: KPI3_1

Function: generateDeliveredDataDataset (jsonview, dateRangeStart, dateRangeEnd)

Selects data for projects active between dateRangeStart and dateRangeEnd.

Returns list of [fraction delivered, project name, date, platform, ordered lanes, # samples, data amount delivered]

Function: generateGenericBoxDataset (dataset, index) See Library prep - fraction failed samples/workset above