Closed FilipSmith closed 4 years ago
selik
commented
6 years ago I'm in the middle of a refactor and haven't yet updated the documentation to match the code. You can read the variable metadata. Each variable is represented by a namedtuple.
https://github.com/selik/xport/blob/fafd15a24ccd102fc92d0c0123b9877a0c752182/xport/v56.py#L366:L367
selik
commented
6 years ago @FilipSmith If you'd like to email me an example XPT document and tell me what you're trying to get out of it, I'll send you back a specific code example.
<mike [at] selik [dot] org>
FilipSmith
commented
6 years ago Thanks for the fast answer.
Enclosed is a XPT file. For example, for the variable USUBJID , the label is "Unique subject identifier".
When I import the file with the command " with open(xport_file, 'rb') as f:" I cannot extract the label "Unique subject identifier" from f.
If it is possible to get also the format - type - length etc... as well I 'm interested. Cf. Picture below.
Many thanks !
sbjain
commented
5 years ago Hi following up on this comment, yes how can we retrieve a certain variable in our xpt file -- read, edit the variable value, and then save the file?
Thanks, Sagar
selik
commented
5 years ago I'm in the middle of an API revision (for a very relaxed concept of "in the middle of"), so it looks like the current code raises a NotImplementedError if you try to write/dump to XPT. I think the previous API had a working dump function. Following the pattern of the json module, this xpt module loads XPT-format files as Python objects and dumps Python objects to XPT-format. So, the answer to your question is that you load, modify, then dump.
If this task is urgent for your business, I'm happy to accept a consulting contract ;-) Otherwise, I'll get around to fixing the documentation sometime in 2019. It's on my to-do list. I'm also happy to accept help.
selik
commented
4 years ago Solved #34
selik
commented
4 years ago Doublechecked that this works.
In [1]: import xport.v56
In [3]: with open('data/adsl.xpt', 'rb') as f:
...: library = xport.v56.load(f)
...:
In [4]: library
Out[4]: <Library members=['ADSL']>
In [5]: library['ADSL']
Out[5]:
Member ADSL
Variable Type Length Format Informat Label Position
#
1 STUDYID Character 12 Study Identifier 0
2 USUBJID Character 11 Unique Subject Identifier 23
3 SUBJID Character 4 Subject Identifier for the Study 27
4 SITEID Character 3 Study Site Identifier 30
5 SITEGR1 Character 3 Pooled Site Group 1 33
6 ARM Character 20 Description of Planned Arm 53
7 TRT01P Character 20 Planned Treatment for Period 01 73
8 TRT01PN Numeric 8 Planned Treatment for Period 01 (N) 81
9 TRT01A Character 20 Actual Treatment for Period 01 101
10 TRT01AN Numeric 8 Actual Treatment for Period 01 (N) 109
11 TRTSDT Numeric 8 DATE9. Date of First Exposure to Treatment 117
12 TRTEDT Numeric 8 DATE9. Date of Last Exposure to Treatment 125
13 TRTDUR Numeric 8 Duration of Treatment (days) 133
14 AVGDD Numeric 8 Avg Daily Dose (as planned) 141
15 CUMDOSE Numeric 8 Cumulative Dose (as planned) 149
16 AGE Numeric 8 Age 157
17 AGEGR1 Character 5 Pooled Age Group 1 162
18 AGEGR1N Numeric 8 Pooled Age Group 1 (N) 170
19 AGEU Character 5 Age Units 175
20 RACE Character 32 Race 207
21 RACEN Numeric 8 Race (N) 215
22 SEX Character 1 Sex 216
23 ETHNIC Character 22 Ethnicity 238
24 SAFFL Character 1 Safety Population Flag 239
25 ITTFL Character 1 Intent-To-Treat Population Flag 240
26 EFFFL Character 1 Efficacy Population Flag 241
27 COMP8FL Character 1 Completers of Week 8 Population Flag 242
28 COMP16FL Character 1 Completers of Week 16 Population Flag 243
29 COMP24FL Character 1 Completers of Week 24 Population Flag 244
30 DISCONFL Character 1 Did the Subject Discontinue the Study? 245
31 DSRAEFL Character 1 Discontinued due to AE? 246
32 DTHFL Character 1 Subject Died? 247
33 BMIBL Numeric 8 Baseline BMI (kg/m^2) 255
34 BMIBLGR1 Character 6 Pooled Baseline BMI Group 1 261
35 HEIGHTBL Numeric 8 Baseline Height (cm) 269
36 WEIGHTBL Numeric 8 Baseline Weight (kg) 277
37 EDUCLVL Numeric 8 Years of Education 285
38 DISONSDT Numeric 8 DATE9. Date of Onset of Disease 293
39 DURDIS Numeric 8 Duration of Disease (Months) 301
40 DURDSGR1 Character 4 Pooled Disease Duration Group 1 305
41 VISIT1DT Numeric 8 DATE9. Date of Visit 1 313
42 RFSTDTC Character 20 Subject Reference Start Date/Time 333
43 RFENDTC Character 20 Subject Reference End Date/Time 353
44 VISNUMEN Numeric 8 End of Trt Visit (Vis 12 or Early Term.) 361
45 RFENDT Numeric 8 DATE9. Date of Discontinuation/Completion 369
46 DCDECOD Character 27 Standardized Disposition Term 396
47 DCREASCD Character 18 Reason for Discontinuation 414
48 MMSETOT Numeric 8 MMSE Total 422
STUDYID USUBJID SUBJID SITEID SITEGR1 ... VISNUMEN RFENDT DCDECOD DCREASCD MMSETOT
0 CDISCPILOT01 01-701-1023 1023 701 701 ... 5.0 19238.0 ADVERSE EVENT Adverse Event 23.0
1 CDISCPILOT01 01-701-1028 1028 701 701 ... 12.0 19737.0 COMPLETED Completed 23.0
2 CDISCPILOT01 01-701-1294 1294 701 701 ... 9.0 19523.0 ADVERSE EVENT Adverse Event 23.0
[3 rows x 48 columns]
name: ADSL, created: 2013-02-07 14:35:51, modified: 2013-02-07 14:35:51, sas_os: Linux, sas_version: 9.2
Hi,
It tried without any success to read metadata as label and format of the xpt variables . Such an option seems to not be available.
Many thanks !