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<article id="content">
<header>
<h1 class="title">Module <code>Gnumed.business.gmSOAPimporter</code></h1>
</header>
<section id="section-intro">
<p>GNUmed SOAP importer</p>
<p>(specification by Karsten Hilbert <a href="mailto:Karsten.Hilbert@gmx.net">Karsten.Hilbert@gmx.net</a>)</p>
<p>This script is designed for importing GNUmed SOAP input "bundles".</p>
<pre><code> - "bundle" is list of dicts
- each "bundle" is processed dict by dict
- the dicts in the list are INDEPENDENT of each other
- each dict contains information for one new clin_narrative row
- each dict has the keys: 'soap', 'types', 'text', 'clin_context'
- 'soap':
- relates to clin_narrative.soap_cat
- 'types':
- a list of strings
- the strings must be found in clin_item_type.type
- strings not found in clin_item_type.type are ignored during
import and the user is warned about that
- 'text':
- the narrative for clin_narrative.narrative, imported as is
- 'clin_context':
- 'clin_context' is a dictionary containing clinical
context information, required to properly create clinical items.
Its 'episode_id' must always be supplied.
</code></pre>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">"""GNUmed SOAP importer
(specification by Karsten Hilbert <Karsten.Hilbert@gmx.net>)
This script is designed for importing GNUmed SOAP input "bundles".
- "bundle" is list of dicts
- each "bundle" is processed dict by dict
- the dicts in the list are INDEPENDENT of each other
- each dict contains information for one new clin_narrative row
- each dict has the keys: 'soap', 'types', 'text', 'clin_context'
- 'soap':
- relates to clin_narrative.soap_cat
- 'types':
- a list of strings
- the strings must be found in clin_item_type.type
- strings not found in clin_item_type.type are ignored during
import and the user is warned about that
- 'text':
- the narrative for clin_narrative.narrative, imported as is
- 'clin_context':
- 'clin_context' is a dictionary containing clinical
context information, required to properly create clinical items.
Its 'episode_id' must always be supplied.
"""
#===============================================================
__author__ = "Carlos Moro <cfmoro1976@yahoo.es>"
__license__ = "GPL v2 or later (details at https://www.gnu.org)"
# stdlib
import sys, logging
# GNUmed
from Gnumed.pycommon import gmDispatcher
from Gnumed.business import gmClinNarrative, gmPerson, gmPersonSearch
_log = logging.getLogger('gm.soap')
# module level constants
soap_bundle_SOAP_CAT_KEY = "soap"
soap_bundle_TYPES_KEY = "types"
soap_bundle_TEXT_KEY = "text"
soap_bundle_CLIN_CTX_KEY = "clin_context"
soap_bundle_TYPE_KEY = "type"
soap_bundle_EPISODE_ID_KEY = "episode_id"
soap_bundle_ENCOUNTER_ID_KEY = "encounter_id"
soap_bundle_STAFF_ID_KEY = "staff_id"
soap_bundle_SOAP_CATS = ['s','o','a','p'] # these are pretty much fixed
#===============================================================
class cSOAPImporter:
"""
Main SOAP importer class
"""
#-----------------------------------------------------------
def __init__(self):
pass
#-----------------------------------------------------------
# external API
#-----------------------------------------------------------
def import_soap(self, bundle=None):
"""
Import supplied GNUmed SOAP input "bundle". For details consult current
module's description information.
@param bundle: GNUmed SOAP input data (as described in module's information)
@type bundle: list of dicts
"""
# process each entry in soap bundle independently
for soap_entry in bundle:
if not self.__import_narrative(soap_entry):
_log.error('skipping soap entry')
continue
gmDispatcher.send(signal = 'clin_item_updated')
return True
#-----------------------------------------------------------
# internal helpers
#-----------------------------------------------------------
def __import_narrative(self, soap_entry):
"""Import soap entry into GNUmed backend.
@param soap_entry: dictionary containing information related
to one SOAP input line
@type soap_entry: dictionary with keys 'soap', 'types', 'text'
FIXME: Later we may want to allow for explicitly setting a staff ID to be
FIXME: used for import. This would allow to import data "on behalf of" someone.
"""
if not self.__verify_soap_entry(soap_entry=soap_entry):
_log.error('cannot verify soap entry')
return False
# obtain clinical context information
emr = gmPerson.gmCurrentPatient().emr
epi_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
try:
enc_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_ENCOUNTER_ID_KEY]
except KeyError:
enc = emr.active_encounter
enc_id = enc['pk_encounter']
# create narrative row
narr = gmClinNarrative.create_narrative_item (
narrative = soap_entry[soap_bundle_TEXT_KEY],
soap_cat = soap_entry[soap_bundle_SOAP_CAT_KEY],
episode_id = epi_id,
encounter_id = enc_id
)
# # attach types
# if soap_bundle_TYPES_KEY in soap_entry:
# print "code missing to attach types to imported narrative"
return (narr is not None)
#-----------------------------------------------------------
def __verify_soap_entry(self, soap_entry):
"""Perform basic integrity check of a supplied SOAP entry.
@param soap_entry: dictionary containing information related to one
SOAP input
@type soap_entry: dictionary with keys 'soap', 'types', 'text'
"""
required_keys = [
soap_bundle_SOAP_CAT_KEY,
soap_bundle_CLIN_CTX_KEY,
soap_bundle_TEXT_KEY
]
# verify key existence
for a_key in required_keys:
try:
soap_entry[a_key]
except KeyError:
_log.error('key [%s] is missing from soap entry' % a_key)
_log.error('%s' % soap_entry)
return False
# verify key *values*
if not soap_entry[soap_bundle_SOAP_CAT_KEY] in soap_bundle_SOAP_CATS:
_log.error('invalid soap category [%s]' % soap_entry[soap_bundle_SOAP_CAT_KEY])
_log.error('%s' % soap_entry)
return False
try:
soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
except KeyError:
_log.error('SOAP entry does not provide mandatory episode ID')
_log.error('%s' % soap_entry)
return False
return True
#-----------------------------------------------------------
# def _verify_types(self, soap_entry):
# """
# Perform types key check of a supplied SOAP entry
#
# @param soap_entry: dictionary containing information related to one
# SOAP input
# @type soap_entry: dictionary with keys 'soap', 'types', 'text'
# """
#
# # FIXME fetch from backend
# allowed_types = ['Hx']
# for input_type in soap_entry[soap_bundle_TYPES_KEY]:
# if not input_type in allowed_types:
# _log.error('bad clin_item_type.type in supplied soap entry [%s]' %
# soap_entry)
# return False
# return True
#================================================================
# MAIN
#----------------------------------------------------------------
if __name__ == '__main__':
_log.info("starting SOAP importer...")
# obtain patient
patient = gmPersonSearch.ask_for_patient()
if patient is None:
print("No patient. Exiting gracefully...")
sys.exit(0)
gmPerson.set_active_patient(patient=patient)
# now import
importer = cSOAPImporter()
bundle = [
{soap_bundle_SOAP_CAT_KEY: 's',
soap_bundle_TYPES_KEY: ['Hx'],
soap_bundle_TEXT_KEY: 'Test subjective narrative',
soap_bundle_CLIN_CTX_KEY: {soap_bundle_EPISODE_ID_KEY: '1'}
},
{soap_bundle_SOAP_CAT_KEY: 'o',
soap_bundle_TYPES_KEY: ['Hx'],
soap_bundle_TEXT_KEY: 'Test objective narrative',
soap_bundle_CLIN_CTX_KEY: {soap_bundle_EPISODE_ID_KEY: '1'}
},
{soap_bundle_SOAP_CAT_KEY: 'a',
soap_bundle_TYPES_KEY: ['Hx'],
soap_bundle_TEXT_KEY: 'Test assesment narrative',
soap_bundle_CLIN_CTX_KEY: {soap_bundle_EPISODE_ID_KEY: '1'}
},
{soap_bundle_SOAP_CAT_KEY: 'p',
soap_bundle_TYPES_KEY: ['Hx'],
soap_bundle_TEXT_KEY: 'Test plan narrative. [:tetanus:]. [:pneumoniae:].',
soap_bundle_CLIN_CTX_KEY: {
soap_bundle_EPISODE_ID_KEY: '1',
soap_bundle_ENCOUNTER_ID_KEY: '1',
soap_bundle_STAFF_ID_KEY: '1'
},
}
]
importer.import_soap(bundle)
# clean up
if patient is not None:
try:
patient.cleanup()
except Exception:
print("error cleaning up patient")
_log.info("closing SOAP importer...")
#================================================================</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-classes">Classes</h2>
<dl>
<dt id="Gnumed.business.gmSOAPimporter.cSOAPImporter"><code class="flex name class">
<span>class <span class="ident">cSOAPImporter</span></span>
</code></dt>
<dd>
<div class="desc"><p>Main SOAP importer class</p></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">class cSOAPImporter:
"""
Main SOAP importer class
"""
#-----------------------------------------------------------
def __init__(self):
pass
#-----------------------------------------------------------
# external API
#-----------------------------------------------------------
def import_soap(self, bundle=None):
"""
Import supplied GNUmed SOAP input "bundle". For details consult current
module's description information.
@param bundle: GNUmed SOAP input data (as described in module's information)
@type bundle: list of dicts
"""
# process each entry in soap bundle independently
for soap_entry in bundle:
if not self.__import_narrative(soap_entry):
_log.error('skipping soap entry')
continue
gmDispatcher.send(signal = 'clin_item_updated')
return True
#-----------------------------------------------------------
# internal helpers
#-----------------------------------------------------------
def __import_narrative(self, soap_entry):
"""Import soap entry into GNUmed backend.
@param soap_entry: dictionary containing information related
to one SOAP input line
@type soap_entry: dictionary with keys 'soap', 'types', 'text'
FIXME: Later we may want to allow for explicitly setting a staff ID to be
FIXME: used for import. This would allow to import data "on behalf of" someone.
"""
if not self.__verify_soap_entry(soap_entry=soap_entry):
_log.error('cannot verify soap entry')
return False
# obtain clinical context information
emr = gmPerson.gmCurrentPatient().emr
epi_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
try:
enc_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_ENCOUNTER_ID_KEY]
except KeyError:
enc = emr.active_encounter
enc_id = enc['pk_encounter']
# create narrative row
narr = gmClinNarrative.create_narrative_item (
narrative = soap_entry[soap_bundle_TEXT_KEY],
soap_cat = soap_entry[soap_bundle_SOAP_CAT_KEY],
episode_id = epi_id,
encounter_id = enc_id
)
# # attach types
# if soap_bundle_TYPES_KEY in soap_entry:
# print "code missing to attach types to imported narrative"
return (narr is not None)
#-----------------------------------------------------------
def __verify_soap_entry(self, soap_entry):
"""Perform basic integrity check of a supplied SOAP entry.
@param soap_entry: dictionary containing information related to one
SOAP input
@type soap_entry: dictionary with keys 'soap', 'types', 'text'
"""
required_keys = [
soap_bundle_SOAP_CAT_KEY,
soap_bundle_CLIN_CTX_KEY,
soap_bundle_TEXT_KEY
]
# verify key existence
for a_key in required_keys:
try:
soap_entry[a_key]
except KeyError:
_log.error('key [%s] is missing from soap entry' % a_key)
_log.error('%s' % soap_entry)
return False
# verify key *values*
if not soap_entry[soap_bundle_SOAP_CAT_KEY] in soap_bundle_SOAP_CATS:
_log.error('invalid soap category [%s]' % soap_entry[soap_bundle_SOAP_CAT_KEY])
_log.error('%s' % soap_entry)
return False
try:
soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
except KeyError:
_log.error('SOAP entry does not provide mandatory episode ID')
_log.error('%s' % soap_entry)
return False
return True
#-----------------------------------------------------------</code></pre>
</details>
<h3>Methods</h3>
<dl>
<dt id="Gnumed.business.gmSOAPimporter.cSOAPImporter.import_soap"><code class="name flex">
<span>def <span class="ident">import_soap</span></span>(<span>self, bundle=None)</span>
</code></dt>
<dd>
<div class="desc"><p>Import supplied GNUmed SOAP input "bundle". For details consult current
module's description information.</p>
<p>@param bundle: GNUmed SOAP input data (as described in module's information)
@type bundle: list of dicts</p></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def import_soap(self, bundle=None):
"""
Import supplied GNUmed SOAP input "bundle". For details consult current
module's description information.
@param bundle: GNUmed SOAP input data (as described in module's information)
@type bundle: list of dicts
"""
# process each entry in soap bundle independently
for soap_entry in bundle:
if not self.__import_narrative(soap_entry):
_log.error('skipping soap entry')
continue
gmDispatcher.send(signal = 'clin_item_updated')
return True</code></pre>
</details>
</dd>
</dl>
</dd>
</dl>
</section>
</article>
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<h1>Index</h1>
<div class="toc">
<ul></ul>
</div>
<ul id="index">
<li><h3>Super-module</h3>
<ul>
<li><code><a title="Gnumed.business" href="http://www.gnumed.de/downloads/docs/api/business/index.html">Gnumed.business</a></code></li>
</ul>
</li>
<li><h3><a href="gmSOAPimporter.html#header-classes">Classes</a></h3>
<ul>
<li>
<h4><code><a title="Gnumed.business.gmSOAPimporter.cSOAPImporter" href="gmSOAPimporter.html#Gnumed.business.gmSOAPimporter.cSOAPImporter">cSOAPImporter</a></code></h4>
<ul class="">
<li><code><a title="Gnumed.business.gmSOAPimporter.cSOAPImporter.import_soap" href="gmSOAPimporter.html#Gnumed.business.gmSOAPimporter.cSOAPImporter.import_soap">import_soap</a></code></li>
</ul>
</li>
</ul>
</li>
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