traction

samples and patients in centraxx

trac = new tr.traction("num_test")
result = trac.sample(sampleids=["1449330267"], verbose=[tr.locationpath])

docs here.

on the command line:

traction num_test sample --sampleid 1449330267 --verbose-all

see traction -h.

install

download traction whl from here. install with pip:

pip install traction-<version>.whl

for database connection setup see dbcq.

run traction once:

traction

then edit ~/.traction/settings.yaml to set your default idcontainer codes for sample and patient.

.traction/settings.yaml looks like this:

# sampleid sets the idcontainertype code that is used when searching for sampleid.
# put in a code per db target.
sampleid: 
  <db target>: <an idcontainertype code, e.g. SAMPLEID>
# patientid sets the idcontainertype code that is used when searching for patientid.
# put in a code per db target.
patientid: 
  <db target>: <an idcontainertype code, e.g. LIMSPSN>

# idc holds additional idcontainertype codes that will be queryable as command line flags.
idc:
 - <an idcontainertype code>
 - <another idcontainertype code>

more usage

command line

get a sample.

traction <db> sample --sampleid abc

get samples from file.

traction <db> sample --sampleid f:mysampleids.txt

get the samples of a patient:

traction <db> sample --patientid lims_565551365

get the samples of a patient that were taken after a specific date.

traction <db> sample --patientid lims_565551365 --sampling-date ">=2025-11-24"

get all samples in a trial.

traction <db> sample --trial "NUM RAPID_REVIVE"

filter out the just the sampleids with jq.

traction <db> sample --trial "NUM RAPID_REVIVE" | jq -r '.[] | .sampleid'

get all master samples where the kitid is NULL that don't have a dot at the end of their sample id (passed as an additional where clause with --where).

traction <db> sample --cxxkitid NULL --category MASTER --where "idc_SAMPLEID.psn not like '%.'"

get all the child samples of a sample.

traction <db> sample --sampleid abc --childs

get all patients in the BSI or CNS module of SNID.

traction <db> patient --trial "NUM S-SNID" --modul "BSI: Bloodstream Infections,CNS: CNS Infections"

get the findings (messbefunde) and their values for a bunch of samples:

traction <db> finding --sampleid A0942214,A0941343,A0941344

get all methods and their labvals.

traction <db> method

get names for messparameters.

traction <db> name --table laborvalue

python

start a new traction instance.

trac = tr.traction("db_target")

get samples barebone.

res = trac.sample(sampleids=["sid1", "sid2", "sid3"])

get samples with all joined in info (slower).

res = trac.sample(sampleids=["sid1", "sid2", "sid3"], verbose_all=True)

get samples with info from idcontainers (idc).

res = trac.sample(idc={"EXTSAMPLEID": ["sid1", "sid2", "sid3"]}, verbose=[tr.locationpath])

get the samples of a patient1 in the rapid revive trial in module 1.

res = trac.sample(patientids=["patient1"], trials=["NUM RAPID_REVIVE"], idc={"MODUL": ["module 1"]}, verbose_all=True)

get all samples in a trial.

res = trac.sample(trials=["NUM RAPID_REVIVE"])

get the samples on a locationpath.

res = trac.sample(locationpaths=["my --> location --> path"])

get a patient.

res = trac.patient(patientids=["patient1"])

get the patient for a sample.

pat = trac.patient(sampleids=["sample1"])

get all patients in the revive trial that are in the BSI module.

res = trac.patient(trials=["NUM RAPID_REVIVE"], idc={"MODUL": ["BSI: Bloodstream Infections"]})

get the findings and their values for a sample.

res = trac.finding(sampleids=["sid1"])

get the display name for laborvalues (messparameters) by code.

acetone_name = trac.name("laborvalue")["NUM_NMR_ACETONE_VALUE"]["en"]

dev

edit tr/main.ct and tr/init.ct.

to generate the code from the ct files get ct.

build and install:

make install

test:

make test

generate api doc:

make doc