Home : Using Generic LIMS Interface with Matrix Gemini LIMS
Q14174 - HOWTO: Using Generic LIMS Interface with Matrix Gemini LIMS

Matrix Gemini LIMS by Autoscribe Informatics (www.autoscribeinformatics.com/lims)

Uses the SAMPLE and Custom_SAMPLERESULTS Tables (linked on SAMPLECODE).

NOTE:  The Date fields in the tables are integers in the form of YYYYMMDD and the Time fields are the number of minutes since midnight.  Therefore to calculate a time you need the following syntax:

DATEADD(mi,SampleTime1,CAST(SUBSTRING(CAST(SampleDate1 AS VARCHAR),5,2) + '/' + RIGHT(CAST(SampleDate1 AS VARCHAR),2) + '/' + LEFT(CAST(SampleDate1 AS VARCHAR),4) AS DATETIME)) AS SAMPDATE

 

EXAMPLE 1: Directly query the Samples and Custom_SAMPLERESULTS Tables.

SELECT * FROM (Select SAMPLES.SampleCode AS SAMPLENUM, Units,ComponentCode AS ANALYTE,ReportedResult AS FINAL, SampleText2 as SAMPLOC, DATEADD(mi,SampleTime1,CAST(SUBSTRING(CAST(SampleDate1 AS VARCHAR),5,2) + '/' + RIGHT(CAST(SampleDate1 AS VARCHAR),2) + '/' + LEFT(CAST(SampleDate1 AS VARCHAR),4)  AS DATETIME)) AS SAMPDATE, DATEADD(mi,ModifyTime,CAST(SUBSTRING(CAST(ModifyDate AS VARCHAR),5,2) + '/' + RIGHT(CAST(ModifyDate AS VARCHAR),2) + '/' + LEFT(CAST(ModifyDate AS VARCHAR),4)  AS DATETIME)) AS MODIFY_DATE
from Samples,Custom_SAMPLERESULTS Where Samples.SAMPLECODE =Custom_SAMPLERESULTS.SAMPLECODE AND SAMPLES.AuditFlag=0 AND RECORDSTATUS=1 AND ReportedResult IS NOT NULL AND SAMPLETEXT15 IS NULL) AS S
WHERE MODIFY_DATE>'2013-06-20' AND Modify_DATE < '2013-06-26'

NOTE: SampleText15 IS NULL removes QC samples.

 

EXAMPLE #2: Create a View

The following is a second example of a query that was used.  This paticular query was used to create a view and the Interface used the view (view_WIMS)

SELECT SAMPNUM, Units, ANALYTE, ReportedResult, SAMPLOC, SAMPDATE, SampleDate1, MODIFYDATE
FROM (SELECT dbo.Samples.SampleCode AS SAMPNUM, dbo.Custom_SampleResults.Units, dbo.Custom_SampleResults.ComponentCode AS ANALYTE,
dbo.Custom_SampleResults.ReportedResult, dbo.Samples.SampleText2 AS SAMPLOC,
DATEADD(mi, dbo.Samples.SampleTime1, CAST(SUBSTRING(CAST(dbo.Samples.SampleDate1 AS VARCHAR), 5, 2) + '/' + RIGHT(CAST(dbo.Samples.SampleDate1 AS VARCHAR), 2) + '/' + LEFT(CAST(dbo.Samples.SampleDate1 AS VARCHAR), 4) AS DATETIME)) AS SAMPDATE,
DATEADD(mi,dbo.Custom_SampleResults.ModifyTime, CAST(SUBSTRING(CAST(dbo.Custom_SampleResults.ModifyDate AS VARCHAR), 5, 2)
+ '/' + RIGHT(CAST(dbo.Custom_SampleResults.ModifyDate AS VARCHAR), 2) + '/' + LEFT(CAST(dbo.Custom_SampleResults.ModifyDate AS VARCHAR), 4) AS DATETIME)) AS MODIFYDATE
FROM dbo.SampleNotes RIGHT OUTER JOIN dbo.Custom_SampleResultNotes RIGHT OUTER JOIN dbo.Custom_SampleResults INNER JOIN dbo.Samples INNER JOIN dbo.SampleTests ON dbo.Samples.SampleCode = dbo.SampleTests.SampleCode AND dbo.Samples.AuditFlag = dbo.SampleTests.AuditFlag ON dbo.Custom_SampleResults.TestPosition = dbo.SampleTests.TestPosition AND dbo.Custom_SampleResults.SampleCode = dbo.SampleTests.SampleCode AND dbo.Custom_SampleResults.TestCode = dbo.SampleTests.TestCode ON dbo.Custom_SampleResultNotes.SampleCode = dbo.Custom_SampleResults.SampleCode AND dbo.Custom_SampleResultNotes.RecordStatus = dbo.Custom_SampleResults.RecordStatus ON dbo.SampleNotes.SampleCode = dbo.Samples.SampleCode AND dbo.SampleNotes.AuditFlag = dbo.Samples.AuditFlagWHERE (dbo.Samples.SampleText14 IS NULL) AND (dbo.Samples.AuditFlag = 0) AND (dbo.Custom_SampleResults.RecordStatus = 1) AND (dbo.SampleTests.TestStatus = 40) AND (dbo.Samples.SampleDate1 IS NOT NULL) AND (LEN(dbo.Samples.SampleDate1) = 8) AND (LEN(dbo.Custom_SampleResults.ModifyDate) = 8)) AS S

 

EXAMPLE 3: View with Dates as integers

A view was setup (View_WIMSData) with the SampDate and ValidateDate brought in as integers:

Select SampLoc, Analyte, Final, ComponentValue, Units,

left(cast(SampDate as varchar),4)+'-'+substring(cast(SampDate as varchar),5,2)+'-'+SUBSTRING(cast(SampDate as varchar),7,2) as SampDATE

from View_WIMSData

where cast(left(cast(validateDate as varchar),4)+'-'+substring(cast(ValidateDate as varchar),5,2)+'-'+SUBSTRING(cast(validateDate as varchar),7,2) as DATETIME) >= #SD#

and cast(left(cast(validateDate as varchar),4)+'-'+substring(cast(ValidateDate as varchar),5,2)+'-'+SUBSTRING(cast(validateDate as varchar),7,2) as DATETIME) <= #ED#

 

EXAMPLE 4: View with the ability to import A and P for Total Coliform and E.coli

SELECT        dbo.Samples.SampleCode AS Lab#, dbo.Samples.SubmitterCode AS Client, dbo.Samples.SampleText10 AS SampLoc, dbo.Samples.SampleText2 AS Project, REPLACE(dbo.SampleResults.ComponentName,

                         ' Reported Result', '') AS Analyte, dbo.SampleResults.EnteredValue AS Final, dbo.SampleResults.ComponentValue, ISNULL(dbo.SampleResults.ComponentUnits, '') AS Units,

                         dbo.Samples.SampleDate2 AS SampDate, dbo.Samples.SampleTime2 AS SampTime, dbo.SampleResults.EnterDate AS [Modified Date], dbo.SampleTests.ValidateDate

FROM            dbo.Samples INNER JOIN

                         dbo.SampleTests ON dbo.Samples.SampleCode = dbo.SampleTests.SampleCode AND dbo.Samples.AuditFlag = dbo.SampleTests.AuditFlag INNER JOIN

                         dbo.SampleResults ON dbo.SampleTests.SampleCode = dbo.SampleResults.SampleCode AND dbo.SampleTests.AuditFlag = dbo.SampleResults.AuditFlag AND

                         dbo.SampleTests.TestPosition = dbo.SampleResults.TestPosition

WHERE        (dbo.Samples.AuditFlag = 0) AND (dbo.SampleTests.TestStatus = 40) AND (dbo.Samples.SampleStatus <> 900) AND (dbo.SampleResults.ResultStatus <> 0) AND (dbo.SampleResults.ComponentRow > 0) AND

                         (dbo.SampleResults.ComponentColumn IN (7, 13))

 

QUERY to use in Source Configuration

 

SELECT CASE WHEN tmp.SampleNote LIKE '%U%'  --convert U qualifier to <

                                                THEN '<' + cast(ComponentValue AS VARCHAR) WHEN FinalValue = 'A'  --LIMS records total coliform and e. coli as A if both are absent

                                                THEN 'A' WHEN FinalValue LIKE '%P%'  --LIMS records total coliform and e. coli as P/A (total present) or P/P (both present)

                                                THEN 'P' ELSE cast(ComponentValue AS VARCHAR) END AS Final, ComponentValue, SampNum, SampLoc, tmp.Analyte, Units, SampleNote, SampDate, convert(VARCHAR(5), dateadd(minute, SampTime, 0), 114) AS UD1, ApprovedDate FROM (SELECT cast(left(cast(validateDate AS VARCHAR), 4) + '-' + substring(cast(ValidateDate AS VARCHAR), 5, 2) + '-' + SUBSTRING(cast(validateDate AS VARCHAR), 7, 2) AS DATE) AS ApprovedDate, d.Lab# AS SampNum, Client + ' : ' + SampLoc + ' : ' + coalesce(rtrim(Project), '') AS SampLoc, d.Analyte, ComponentValue, Final AS FinalValue, Units, SampleNote, left(cast(SampDate AS VARCHAR), 4) + '-' + substring(cast(SampDate AS VARCHAR), 5, 2) + '-' + SUBSTRING(cast(SampDate AS VARCHAR), 7, 2) AS SampDate, SampTime --inculdes sample time for import as additional data field FROM View_WIMSData d LEFT JOIN (SELECT Lab#, Analyte, left(Analyte, (len(Analyte) - 19)) AS ACode, Final AS SampleNote    --qualifiers are stored on additional lines in view

                                               FROM View_WIMSData WHERE Analyte LIKE '%Reported Qualifier' AND len(Analyte) > 19) Q ON d.Lab# = Q.Lab# AND d.Analyte = Q.ACode WHERE SampDate IS NOT NULL AND SampLoc NOT LIKE '%testing'  AND d.Analyte NOT LIKE '%Reported Qualifier' AND ((cast(left(cast([Modified Date] AS VARCHAR), 4) + '-' + substring(cast([Modified Date] AS VARCHAR), 5, 2) + '-' + SUBSTRING(cast([Modified Date] AS VARCHAR), 7, 2) AS DATE) >= convert(DATE, #SD#) AND cast(left(cast([Modified Date] AS VARCHAR), 4) + '-' + substring(cast([Modified Date] AS VARCHAR), 5, 2) + '-' + SUBSTRING(cast([Modified Date] AS VARCHAR), 7, 2) AS DATE) <= #ED# ) OR (cast(left(cast(ValidateDate AS VARCHAR), 4) + '-' + substring(cast(ValidateDate AS VARCHAR), 5, 2) + '-' + SUBSTRING(cast(ValidateDate AS VARCHAR), 7, 2) AS DATE) >= convert(DATE, #SD#)AND cast(left(cast(ValidateDate AS VARCHAR), 4) + '-' + substring(cast(ValidateDate AS VARCHAR), 5, 2) + '-' + SUBSTRING(cast(ValidateDate AS VARCHAR), 7, 2) AS DATE) <= #ED#))) tmp ORDER BY SampDate

 

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Created on 12/18/2013 5:00 PM.
Last Modified on 3/30/2020 7:30 AM.
Last Modified by Ryan Rhoten.
Article has been viewed 4402 times.
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