Below is an example of a "complex" result delivered by a lab in HL7 format, where that result was not provided in the form
numeric value | units | reference range
but instead all-in-a-single-field, characterized by:
- a variation of the test (assay) name
- a series of 'breaks" denoted by \.br\
- each of which informs a "fraction" or "component"
- each with its own quasi reference range
of which I offer below its 148 lines (broken out), after which I append the original HL7 fields. A more common example might be the result of a urine culture, with antibiogram (sensitivities).
My questions:
1. Assuming that "breaks" can be translated by the importer script, informed for example by
so that the breaks are incorporated and stored in the text string in the row's GNUmed column
clin.test_result.val_alpha
--> what value should be stored in val_alpha to enable GNUmed (in wx) to display those intentional "breaks"? A unicode character 'LINE FEED (LF)' (U+000A)?
2. Currently, the "Editing measurement" dialog appears to interpret and store values as appropriate in val_num or val_alpha, and for example storing a combined blood pressure (140/90) as val_alpha.
To see what would happen, I opened a value for Spock's previously-entered Sp02 (which had contained a numeric value of 96) and pasted in the ~ 2700 characters from the alpha result below. My python quit on me, with the terminal reporting
gm-from-vcs.sh: line 51: 1611 Segmentation fault: 11 python gnumed.py ${LOG} ${CONF} ${DEV_OPTS} $@
--> is this most likely any memory or buffer problem
--> a consequence of GNUmed trying to cope with changing a val_num to NULL and a val_alpha to 2700 characters?
--> anything to test?
Interestingly, despite Python crashing on me, postgres did save the result, as shown in the screenshot, but neither the 'Edit result' dialog nor the tooltip permit adequate visualization (review) of lengthy val_alpha results.
Currently (1.3.7) the GNUmed GUI is smart enough -- in the case of a multi-value cell -- to intercept the user, and to prompt them with a different screen asking which among the multiple values to work on.
Would it be feasible for GNUmed to detect whether a val_alpha contains a single line, such as in the case of
160 / 80
Positive
etc.
vs multi-line, and in the case of a multi-line display provide a window that auto-opens larger, and with scrollbars to assist viewing of a large text area?
-- Jim
============================================
Bloodspot, Acylcarnitine, (umol/L);
Date of Assay:14Jul2010
Carnitine:24.9
Reference Range (umol/L): 10.9 - 29.8
C2:18.6
Reference Range (umol/L): 7.1 - 28.0
C3:1.58
Reference Range (umol/L): 0.60 - 2.87
C4:0.32
Reference Range (umol/L): 0.12 - 0.47
C5:1:0.02
Reference Range (umol/L): less than 0.08
C5:0.14
Reference Range (umol/L): 0.05 - 0.24
C4 OH:0.12
Reference Range (umol/L): 0.05 - 0.27
C6:0.04
Reference Range (umol/L): 0.02 - 0.12
C5 OH:0.29
Reference Range (umol/L): 0.05 - 0.40
C8:1:0.23 H
Reference Range (umol/L): less than 0.22
C8:0.05
Reference Range (umol/L):0.01 - 0.12
Malonyl:0.10 H
Reference Range (umol/L): less than 0.06
C10:1:0.05
Reference Range (umol/L): less than 0.12
C10:0.05
Reference Range (umol/L): 0.03 - 0.17
C4DC:0.19
Reference Range (umol/L): 0.07 - 0.30
Glutaryl DC:0.05
Reference Range (umol/L): less than 0.07
C12:1:0.04
Reference Range (umol/L): less than 0.16
C12:0.15
Reference Range (umol/L): 0.04 - 0.42
C6DC:0.01
Reference Range (umol/L): less than 0.05
C12:1OH:0.02
Reference Range (umol/L): less than 0.08
C12 OH:0.02
Reference Range (umol/L): less than 0.07
C14:2:0.08
Reference Range (umol/L): 0.02 - 0.16
C14:1:0.23
Reference Range (umol/L): 0.08 - 0.81
C14:0.19
Reference Range (umol/L): 0.06 - 0.41
C8DC:0.01
Reference Range (umol/L): less than 0.05
C14:1 OH:0.04
Reference Range (umol/L): less than 0.08
C14 OH:0.03
Reference Range (umol/L): less than 0.05
C16:0.77
Reference Range (umol/L): 0.33 - 1.52
C16:1 OH0.06
Reference Range (umol/L): less than 0.11
C16 OH:0.02
Reference Range (umol/L): less than 0.06
C18:2:0.41
Reference Range (umol/L):0.13 - 0.50
C18:1:1.06
Reference Range (umol/L): 0.57 - 2.04
C18:0.60
Reference Range (umol/L): 0.23 - 1.00
C18:2 OH:0.01
Reference Range (umol/L): less than 0.03
C18:1 OH:0.02
Reference Range (umol/L): less than 0.04
C16DC:None Detected
Reference Range (umol/L): less than 0.03
C18:1 DC:0.01
Reference Range (umol/L): less than 0.04
Total Acyl Carnitines:23.7
Reference Range (umol/L): 9.8 - 34.4
Total Carnitine:48.5
Reference Range (umol/L): 21.8 - 62.5
Fraction:0.49
Reference Range (umol/L): 0.38 - 0.62
C8/C10 Ratio:0.97
Reference Range (umol/L): 0.31 - 1.11
C3/C2 Ratio:0.09
Reference Range (umol/L): 0.04 - 0.18
C3/C16 Ratio:2.10
Reference Range (umol/L): 0.53 - 3.36
C8/C2 Ratio:None Detected
Reference Range (umol/L): less than 0.02
C0/(C16+C18) Ratio:18.10
Reference Range (umol/L): 6.86 - 27.26
(C16+C18:1)/C2 Ratio:0.10
Reference Range (umol/L): 0.09 - 0.25
C14:1/C12:1 Ratio:5.70
Reference Range (umol/L): less than 16.39
C16 OH/C16 Ratio:0.03
Reference Range (umol/L): less than 0.07|||N|||F|||20100808112546
============================================
original:
OBR|1||10-999-001666-ACARN-0|ACARN^Acyl Carnitine|RT|20100713081500|20100713074200|||||||20100713081500||90909^MDCARE^BOB||||||20100808112546||REFER1|F||^^^^^RT|90909^MDCARE^BOB~00000^B.C. Childrens' Hospital^Health Records Dept.
OBX|1|FT|X50335^Acyl Carnitine Blood Dot||Bloodspot, Acylcarnitine, (umol/L); \.br\\.br\Date of Assay:14Jul2010 \.br\\.br\Carnitine:24.9\.br\Reference Range (umol/L): 10.9 - 29.8\.br\\.br\\.br\C2:18.6\.br\Reference Range (umol/L): 7.1 - 28.0\.br\\.br\C3:1.58\.br\Reference Range (umol/L): 0.60 - 2.87\.br\\.br\C4:0.32\.br\Reference Range (umol/L): 0.12 - 0.47\.br\\.br\C5:1:0.02 \.br\Reference Range (umol/L): less than 0.08\.br\\.br\C5:0.14\.br\Reference Range (umol/L): 0.05 - 0.24\.br\\.br\C4 OH:0.12\.br\Reference Range (umol/L): 0.05 - 0.27\.br\\.br\C6:0.04\.br\Reference Range (umol/L): 0.02 - 0.12\.br\\.br\C5 OH:0.29\.br\Reference Range (umol/L): 0.05 - 0.40\.br\\.br\C8:1:0.23 H\.br\Reference Range (umol/L): less than 0.22\.br\\.br\C8:0.05\.br\Reference Range (umol/L):0.01 - 0.12\.br\\.br\Malonyl:0.10 H\.br\Reference Range (umol/L): less than 0.06\.br\\.br\C10:1:0.05\.br\Reference Range (umol/L): less than 0.12\.br\\.br\C10:0.05\.br\Reference Range (umol/L): 0.03 - 0.17\.br\\.br\C4DC:0.19\.br\Reference Range (umol/L): 0.07 - 0.30\.br\\.br\Glutaryl DC:0.05\.br\Reference Range (umol/L): less than 0.07\.br\\.br\C12:1:0.04\.br\Reference Range (umol/L): less than 0.16\.br\\.br\C12:0.15\.br\Reference Range (umol/L): 0.04 - 0.42\.br\\.br\C6DC:0.01\.br\Reference Range (umol/L): less than 0.05\.br\\.br\C12:1OH:0.02\.br\Reference Range (umol/L): less than 0.08\.br\\.br\C12 OH:0.02\.br\Reference Range (umol/L): less than 0.07\.br\\.br\C14:2:0.08\.br\Reference Range (umol/L): 0.02 - 0.16\.br\\.br\C14:1:0.23\.br\Reference Range (umol/L): 0.08 - 0.81\.br\\.br\C14:0.19\.br\Reference Range (umol/L): 0.06 - 0.41\.br\\.br\C8DC:0.01\.br\Reference Range (umol/L): less than 0.05\.br\\.br\C14:1 OH:0.04\.br\Reference Range (umol/L): less than 0.08\.br\\.br\C14 OH:0.03\.br\Reference Range (umol/L): less than 0.05\.br\\.br\C16:0.77\.br\Reference Range (umol/L): 0.33 - 1.52\.br\\.br\C16:1 OH0.06\.br\Reference Range (umol/L): less than 0.11\.br\\.br\C16 OH:0.02\.br\Reference Range (umol/L): less than 0.06\.br\\.br\C18:2:0.41\.br\Reference Range (umol/L):0.13 - 0.50\.br\\.br\C18:1:1.06\.br\Reference Range (umol/L): 0.57 - 2.04\.br\\.br\C18:0.60\.br\Reference Range (umol/L): 0.23 - 1.00\.br\\.br\C18:2 OH:0.01\.br\Reference Range (umol/L): less than 0.03\.br\\.br\C18:1 OH:0.02\.br\Reference Range (umol/L): less than 0.04\.br\\.br\C16DC:None Detected\.br\Reference Range (umol/L): less than 0.03\.br\\.br\C18:1 DC:0.01\.br\Reference Range (umol/L): less than 0.04\.br\\.br\Total Acyl Carnitines:23.7\.br\Reference Range (umol/L): 9.8 - 34.4\.br\\.br\Total Carnitine:48.5\.br\Reference Range (umol/L): 21.8 - 62.5\.br\\.br\Fraction:0.49\.br\Reference Range (umol/L): 0.38 - 0.62\.br\\.br\C8/C10 Ratio:0.97\.br\Reference Range (umol/L): 0.31 - 1.11\.br\\.br\C3/C2 Ratio:0.09\.br\Reference Range (umol/L): 0.04 - 0.18\.br\\.br\C3/C16 Ratio:2.10\.br\Reference Range (umol/L): 0.53 - 3.36\.br\\.br\C8/C2 Ratio:None Detected\.br\Reference Range (umol/L): less than 0.02\.br\\.br\C0/(C16+C18) Ratio:18.10\.br\Reference Range (umol/L): 6.86 - 27.26\.br\\.br\(C16+C18:1)/C2 Ratio:0.10\.br\Reference Range (umol/L): 0.09 - 0.25\.br\\.br\C14:1/C12:1 Ratio:5.70\.br\Reference Range (umol/L): less than 16.39\.br\\.br\C16 OH/C16 Ratio:0.03\.br\Reference Range (umol/L): less than 0.07|||N|||F|||20100808112546
-- Jim
