samples and patients in centraxx
trac = new tr.traction("num_test")
pat = trac.patient(sampleids=["abc"])
on the command line:
traction num_test sample --sampleid 1449330267 --verbose-all
see traction -h.
download traction whl from here. install with pip:
pip install traction-<version>.whl
for database connection setup see dbcq.
after the first traction run set your default idcontainer codes for
sample and patient in ~/.traction/settings.yaml.
command line
get the samples of a patient:
traction <db> sample --patientid lims_565551365
get all samples in a study.
traction <db> sample --study "NUM RAPID_REVIVE"
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 --dtype MASTER --where "sidc.psn not like '%.'"
get the findings (messbefunde) and their values for a bunch of samples:
traction <db> finding --sampleid A0942214,A0941343,A0941344
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 study in module 1.
res = trac.sample(patientids=["patient1"], study=["NUM RAPID_REVIVE"], idc={"module": ["module 1"]}, verbose_all=True)
get all samples in a study.
res = trac.sample(studies=["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"])
TODO get all patients in a study.
res = trac.patient(studies=["NUM RAPID_REVIVE"])
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"]
get codetext for assembling init.ct and main.ct.
build and install:
make install