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Commits on Source (8)
......@@ -6,6 +6,16 @@
# rel-1-7-patches
------------------------------------------------
1.7.6
FIX: application metadata files
FIX: searching across all EMRs
FIX: constrain document PRW to current patient
FIX: lab/table: exception on double-clicking empty cell in row w/o meta test type
FIX: lab/result EA: failure to show test type on edit
NEW: stub out $praxis_scan2pay$
1.7.5
FIX: exception on following vaccs reminder from provider inbox
......@@ -1987,6 +1997,12 @@ FIX: missing cast to ::text in dem.date_trunc_utc() calls
# gnumed_v22
------------------------------------------------
22.6
FIX: properly include fixups in v21-v22 upgrade
IMPROVED: database backup script
22.4
FIX: LaTeX-Template for Begleitbrief
......
......@@ -3,7 +3,8 @@
<!-- Thanks to Carsten Grohmann <mail@carstengrohmann.de> -->
<!-- Thanks to Richard Hughes (https://people.freedesktop.org/~hughsient/appdata/) -->
<component type="desktop">
<id>gnumed_client.desktop</id>
<id>de.gnumed.client</id>
<launchable type="desktop-id">gnumed_client.desktop</launchable>
<metadata_license>CC0-1.0</metadata_license>
<project_license>GPL-2.0+ and GFDL-1.3</project_license>
<name>GNUmed EMR</name>
......@@ -28,14 +29,14 @@
</p>
</description>
<screenshots>
<screenshot type="default">
<caption>http://wiki.gnumed.de</caption>
</screenshot>
<!--<screenshot type="default">
<image>https://screenshots.debian.net/screenshots/000/002/117/large.png</image>
<caption>The main window showing the application in action</caption>
<caption>http://wiki.gnumed.de</caption>
</screenshot>-->
<screenshot type="default">
<image>https://screenshots.debian.net/screenshots/000/002/117/large.png</image>
<caption>The main window showing one of the ways to enter Progress Notes during a patient encounter</caption>
</screenshot
</screenshots>
<url type="homepage">http://www.gnumed.de</url>
<url type="homepage">https://www.gnumed.de</url>
<update_contact>gnumed-devel_AT_gnu.org</update_contact>
</component>
......@@ -38,6 +38,7 @@ AMTS_BMP_DOB_FORMAT_YEAR_ONLY = '%Y'
AMTS2GMD_GENDER_MAP = {
'W': 'f',
'M': 'm',
'D': 'h',
'X': None
}
......
......@@ -498,6 +498,409 @@ def get_as_journal(since=None, until=None, encounters=None, episodes=None, issue
#============================================================
# convenience functions
#============================================================
__VIEW_DEF = """
create temporary view v_narrative4search as
select * from (
-- clin.clin_root_items
select
vpi.pk_patient as pk_patient,
vpi.soap_cat as soap_cat,
vpi.narrative as narrative,
vpi.pk_encounter as pk_encounter,
vpi.pk_episode as pk_episode,
vpi.pk_health_issue as pk_health_issue,
vpi.pk_item as src_pk,
vpi.src_table as src_table
from
clin.v_pat_items vpi
where
src_table not in (
'clin.allergy',
'clin.test_result',
'clin.procedure',
'clin.substance_intake',
'clin.family_history'
)
union all
select * from clin.v_subst_intake4narr_search
where gm.is_null_or_blank_string(narrative) is FALSE
union all
select -- clin.procedure
(select fk_patient from clin.encounter where pk = cpr.fk_encounter)
as pk_patient,
cpr.soap_cat
as soap_cat,
cpr.narrative
as narrative,
cpr.fk_encounter
as pk_encounter,
cpr.fk_episode
as pk_episode,
(select fk_health_issue from clin.episode where pk = cpr.fk_episode)
as pk_health_issue,
cpr.pk
as src_pk,
'clin.procedure'
as src_table
from
clin.procedure cpr
where
cpr.narrative is not NULL
union all
select -- test results
(select fk_patient from clin.encounter where pk = ctr.fk_encounter)
as pk_patient,
ctr.soap_cat
as soap_cat,
coalesce(ctr.narrative, '')
|| coalesce(' ' || ctr.val_alpha, '')
|| coalesce(' ' || ctr.val_unit, '')
|| coalesce(' ' || ctr.val_normal_range, '')
|| coalesce(' ' || ctr.val_target_range, '')
|| coalesce(' ' || ctr.norm_ref_group, '')
|| coalesce(' ' || ctr.note_test_org, '')
|| coalesce(' ' || ctr.material, '')
|| coalesce(' ' || ctr.material_detail, '')
as narrative,
ctr.fk_encounter
as pk_encounter,
ctr.fk_episode
as pk_episode,
(select fk_health_issue from clin.episode where pk = ctr.fk_episode)
as pk_health_issue,
ctr.pk
as src_pk,
'clin.test_result'
as src_table
from
clin.test_result ctr
union all -- test result reviews
select
(select fk_patient from clin.encounter where pk =
(select fk_encounter from clin.test_result where clin.test_result.pk = crtr.fk_reviewed_row)
)
as pk_patient,
'o'::text
as soap_cat,
crtr.comment
as narrative,
(select fk_encounter from clin.test_result where clin.test_result.pk = crtr.fk_reviewed_row)
as pk_encounter,
(select fk_episode from clin.test_result where clin.test_result.pk = crtr.fk_reviewed_row)
as pk_episode,
(select fk_health_issue from clin.episode where pk =
(select fk_episode from clin.test_result where clin.test_result.pk = crtr.fk_reviewed_row)
)
as pk_health_issue,
crtr.pk
as src_pk,
'clin.reviewed_test_results'
as src_table
from
clin.reviewed_test_results crtr
union all
select -- allergy state
(select fk_patient from clin.encounter where pk = cas.fk_encounter)
as pk_patient,
'o'::text
as soap_cat,
cas.comment
as narrative,
cas.fk_encounter
as pk_encounter,
null
as pk_episode,
null
as pk_health_issue,
cas.pk
as src_pk,
'clin.allergy_state'
as src_table
from
clin.allergy_state cas
where
cas.comment is not NULL
union all
select -- allergies
(select fk_patient from clin.encounter where pk = ca.fk_encounter)
as pk_patient,
ca.soap_cat
as soap_cat,
coalesce(narrative, '')
|| coalesce(' ' || substance, '')
|| coalesce(' ' || substance_code, '')
|| coalesce(' ' || generics, '')
|| coalesce(' ' || allergene, '')
|| coalesce(' ' || atc_code, '')
as narrative,
ca.fk_encounter
as pk_encounter,
ca.fk_episode
as pk_episode,
(select fk_health_issue from clin.episode where pk = ca.fk_episode)
as pk_health_issue,
ca.pk
as src_pk,
'clin.allergy'
as src_table
from
clin.allergy ca
union all -- health issues
select
(select fk_patient from clin.encounter where pk = chi.fk_encounter)
as pk_patient,
'a' as soap_cat,
chi.description
|| coalesce(' ' || chi.summary, '')
as narrative,
chi.fk_encounter
as pk_encounter,
null
as pk_episode,
chi.pk
as pk_health_issue,
chi.pk
as src_pk,
'clin.health_issue'
as src_table
from
clin.health_issue chi
union all -- encounters
select
cenc.fk_patient as pk_patient,
's' as soap_cat,
coalesce(cenc.reason_for_encounter, '')
|| coalesce(' ' || cenc.assessment_of_encounter, '')
as narrative,
cenc.pk as pk_encounter,
null as pk_episode,
null as pk_health_issue,
cenc.pk as src_pk,
'clin.encounter' as src_table
from
clin.encounter cenc
union all -- episodes
select
(select fk_patient from clin.encounter where pk = cep.fk_encounter)
as pk_patient,
's' as soap_cat,
cep.description
|| coalesce(' ' || cep.summary, '')
as narrative,
cep.fk_encounter
as pk_encounter,
cep.pk
as pk_episode,
cep.fk_health_issue
as pk_health_issue,
cep.pk
as src_pk,
'clin.episode'
as src_table
from
clin.episode cep
union all -- family history
select
c_vfhx.pk_patient,
c_vfhx.soap_cat,
(c_vfhx.relation || ' / ' || c_vfhx.l10n_relation || ' '
|| c_vfhx.name_relative || ': '
|| c_vfhx.condition
) as narrative,
c_vfhx.pk_encounter,
c_vfhx.pk_episode,
c_vfhx.pk_health_issue,
c_vfhx.pk_family_history as src_pk,
'clin.family_history' as src_table
from
clin.v_family_history c_vfhx
union all -- documents
select
vdm.pk_patient as pk_patient,
'o' as soap_cat,
(vdm.l10n_type || ' ' ||
coalesce(vdm.ext_ref, '') || ' ' ||
coalesce(vdm.comment, '')
) as narrative,
vdm.pk_encounter as pk_encounter,
vdm.pk_episode as pk_episode,
vdm.pk_health_issue as pk_health_issue,
vdm.pk_doc as src_pk,
'blobs.doc_med' as src_table
from
blobs.v_doc_med vdm
union all -- document objects
select
vo4d.pk_patient as pk_patient,
'o' as soap_cat,
vo4d.obj_comment as narrative,
vo4d.pk_encounter as pk_encounter,
vo4d.pk_episode as pk_episode,
vo4d.pk_health_issue as pk_health_issue,
vo4d.pk_obj as src_pk,
'blobs.doc_obj' as src_table
from
blobs.v_obj4doc_no_data vo4d
union all -- document descriptions
select
vdd.pk_patient as pk_patient,
'o' as soap_cat,
vdd.description as narrative,
vdd.pk_encounter as pk_encounter,
vdd.pk_episode as pk_episode,
vdd.pk_health_issue as pk_health_issue,
vdd.pk_doc_desc as src_pk,
'blobs.doc_desc' as src_table
from
blobs.v_doc_desc vdd
union all -- reviewed documents
select
vrdo.pk_patient as pk_patient,
's' as soap_cat,
vrdo.comment as narrative,
null as pk_encounter,
vrdo.pk_episode as pk_episode,
vrdo.pk_health_issue as pk_health_issue,
vrdo.pk_review_root as src_pk,
'blobs.v_reviewed_doc_objects' as src_table
from
blobs.v_reviewed_doc_objects vrdo
union all -- patient tags
select
d_vit.pk_identity
as pk_patient,
's' as soap_cat,
d_vit.l10n_description
|| coalesce(' ' || d_vit.comment, '')
as narrative,
null
as pk_encounter,
null
as pk_episode,
null
as pk_health_issue,
d_vit.pk_identity_tag
as src_pk,
'dem.v_identity_tags'
as src_table
from
dem.v_identity_tags d_vit
union all -- external care
select
c_vec.pk_identity
as pk_patient,
's' as soap_cat,
case
when c_vec.pk_health_issue is null then
coalesce(c_vec.issue, '')
|| coalesce(' / ' || c_vec.provider, '')
|| coalesce(' / ' || c_vec.comment, '')
else
coalesce(c_vec.provider, '')
|| coalesce(' / ' || c_vec.comment, '')
end as narrative,
c_vec.pk_encounter
as pk_encounter,
null
as pk_episode,
c_vec.pk_health_issue
as pk_health_issue,
c_vec.pk_external_care
as src_pk,
'clin.v_external_care'
as src_table
from
clin.v_external_care c_vec
union all -- export items
select
c_vei.pk_identity
as pk_patient,
's' as soap_cat,
case
when c_vei.pk_doc_obj is null then
coalesce(c_vei.description, '')
|| coalesce(' / ' || c_vei.filename, '')
else
coalesce(c_vei.description, '')
end as narrative,
null
as pk_encounter,
null
as pk_episode,
null
as pk_health_issue,
c_vei.pk_export_item
as src_pk,
'clin.v_export_items'
as src_table
from
clin.v_export_items c_vei
union all -- hint suppression rationale
select
(select fk_patient from clin.encounter where pk = c_sh.fk_encounter)
as pk_patient,
'p' as soap_cat,
c_sh.rationale
as narrative,
c_sh.fk_encounter
as pk_encounter,
null
as pk_episode,
null
as pk_health_issue,
c_sh.pk
as src_pk,
'clin.suppressed_hint'
as src_table
from
clin.suppressed_hint c_sh
) as union_table
where
trim(coalesce(union_table.narrative, '')) != ''
;
"""
def search_text_across_emrs(search_term=None):
if search_term is None:
......@@ -506,9 +909,14 @@ def search_text_across_emrs(search_term=None):
if search_term.strip() == u'':
return []
cmd = u'select * from clin.v_narrative4search where narrative ~* %(term)s order by pk_patient limit 1000'
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'term': search_term}}], get_col_idx = False)
#cmd = u'select * from clin.v_narrative4search where narrative ~* %(term)s order by pk_patient limit 1000'
#rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'term': search_term}}], get_col_idx = False)
cmd = u'select * from v_narrative4search where narrative ~* %(term)s order by pk_patient limit 1000'
queries = [
{'cmd': __VIEW_DEF},
{'cmd': cmd, 'args': {'term': search_term}}
]
rows, idx = gmPG2.run_rw_queries(queries = queries, get_col_idx = True, return_data = True)
return rows
#============================================================
......
......@@ -97,6 +97,7 @@
<li> <strong class="uidlink"><a href="Gnumed.business.gmExternalCare-module.html">Gnumed.business.gmExternalCare</a></strong>: <em class="summary">GNUmed external care classes.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmFamilyHistory-module.html">Gnumed.business.gmFamilyHistory</a></strong>: <em class="summary">GNUmed family history handling middleware</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmForms-module.html">Gnumed.business.gmForms</a></strong>: <em class="summary">GNUmed forms classes</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmGenericEMRItem-module.html">Gnumed.business.gmGenericEMRItem</a></strong>: <em class="summary">GNUmed clinical business object in generic form.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmHL7-module.html">Gnumed.business.gmHL7</a></strong>: <em class="summary">Some HL7 handling.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmIncomingData-module.html">Gnumed.business.gmIncomingData</a></strong>: <em class="summary">Handling of &lt;INCOMING&gt; area.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmKVK-module.html">Gnumed.business.gmKVK</a></strong>: <em class="summary">GNUmed German KVK/eGK objects.</em> </li>
......@@ -705,7 +706,6 @@
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgBillingPluginPnl-module.html">Gnumed.wxGladeWidgets.wxgBillingPluginPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgCardiacDevicePluginPnl-module.html">Gnumed.wxGladeWidgets.wxgCardiacDevicePluginPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgCommChannelEditAreaPnl-module.html">Gnumed.wxGladeWidgets.wxgCommChannelEditAreaPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgCreatePatientMediaDlg-module.html">Gnumed.wxGladeWidgets.wxgCreatePatientMediaDlg</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgCurrentMedicationEAPnl-module.html">Gnumed.wxGladeWidgets.wxgCurrentMedicationEAPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgCurrentSubstancesPnl-module.html">Gnumed.wxGladeWidgets.wxgCurrentSubstancesPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgDataMiningPnl-module.html">Gnumed.wxGladeWidgets.wxgDataMiningPnl</a></strong> </li>
......@@ -726,7 +726,9 @@
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgEncounterTypeEditAreaPnl-module.html">Gnumed.wxGladeWidgets.wxgEncounterTypeEditAreaPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgEpisodeEditAreaPnl-module.html">Gnumed.wxGladeWidgets.wxgEpisodeEditAreaPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgExamplePluginPnl-module.html">Gnumed.wxGladeWidgets.wxgExamplePluginPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgExportAreaExportToMediaDlg-module.html">Gnumed.wxGladeWidgets.wxgExportAreaExportToMediaDlg</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgExportAreaPluginPnl-module.html">Gnumed.wxGladeWidgets.wxgExportAreaPluginPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgExportAreaSaveAsDlg-module.html">Gnumed.wxGladeWidgets.wxgExportAreaSaveAsDlg</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgExternalCareEAPnl-module.html">Gnumed.wxGladeWidgets.wxgExternalCareEAPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgExternalIDEditAreaPnl-module.html">Gnumed.wxGladeWidgets.wxgExternalIDEditAreaPnl</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxGladeWidgets.wxgFamilyHistoryEAPnl-module.html">Gnumed.wxGladeWidgets.wxgFamilyHistoryEAPnl</a></strong> </li>
......@@ -811,6 +813,7 @@
</li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython-module.html">Gnumed.wxpython</a></strong>
<ul>
<li> <strong class="uidlink">Gnumed.wxpython.gmAMTS_BMPWidgets</strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmATCWidgets-module.html">Gnumed.wxpython.gmATCWidgets</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmAU_VaccV01-module.html">Gnumed.wxpython.gmAU_VaccV01</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmAbout-module.html">Gnumed.wxpython.gmAbout</a></strong> </li>
......@@ -847,6 +850,7 @@
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmFormWidgets-module.html">Gnumed.wxpython.gmFormWidgets</a></strong>: <em class="summary">GNUmed form/letter handling widgets.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmGP_HabitsRiskFactors-module.html">Gnumed.wxpython.gmGP_HabitsRiskFactors</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmGP_SocialHistory-module.html">Gnumed.wxpython.gmGP_SocialHistory</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmGenericEMRItemWorkflows-module.html">Gnumed.wxpython.gmGenericEMRItemWorkflows</a></strong>: <em class="summary">GNUmed generic clinical item business object workflows.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmGuiHelpers-module.html">Gnumed.wxpython.gmGuiHelpers</a></strong>: <em class="summary">GNUmed GUI helper classes and functions.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmGuiMain-module.html">Gnumed.wxpython.gmGuiMain</a></strong> </li>
<li> <strong class="uidlink"><a href="Gnumed.wxpython.gmHabitWidgets-module.html">Gnumed.wxpython.gmHabitWidgets</a></strong>: <em class="summary">GNUmed habits widgets.</em> </li>
......@@ -1014,7 +1018,7 @@
<tr>
<td align="left" class="footer">
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on Fri Jan 25 02:55:27 2019
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</td>
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<a target="mainFrame" href="http://epydoc.sourceforge.net"
......
......@@ -98,7 +98,7 @@ expandto(location.href);
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......
......@@ -123,7 +123,7 @@
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......
......@@ -99,7 +99,7 @@ expandto(location.href);
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......@@ -154,7 +154,7 @@
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......@@ -125,7 +125,7 @@ expandto(location.href);
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......@@ -154,7 +154,7 @@
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......@@ -131,7 +131,7 @@ expandto(location.href);
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......@@ -90,6 +90,7 @@
<li> <strong class="uidlink"><a href="Gnumed.business.gmExternalCare-module.html">Gnumed.business.gmExternalCare</a></strong>: <em class="summary">GNUmed external care classes.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmFamilyHistory-module.html">Gnumed.business.gmFamilyHistory</a></strong>: <em class="summary">GNUmed family history handling middleware</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmForms-module.html">Gnumed.business.gmForms</a></strong>: <em class="summary">GNUmed forms classes</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmGenericEMRItem-module.html">Gnumed.business.gmGenericEMRItem</a></strong>: <em class="summary">GNUmed clinical business object in generic form.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmHL7-module.html">Gnumed.business.gmHL7</a></strong>: <em class="summary">Some HL7 handling.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmIncomingData-module.html">Gnumed.business.gmIncomingData</a></strong>: <em class="summary">Handling of &lt;INCOMING&gt; area.</em> </li>
<li> <strong class="uidlink"><a href="Gnumed.business.gmKVK-module.html">Gnumed.business.gmKVK</a></strong>: <em class="summary">GNUmed German KVK/eGK objects.</em> </li>
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<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#refetch_payload">refetch_payload</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#same_payload">same_payload</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#save">save</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#save_payload">save_payload</a></code>
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#save_payload">save_payload</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#staff_id">staff_id</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
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<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#refetch_payload">refetch_payload</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#same_payload">same_payload</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#save">save</a></code>,
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<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#save_payload">save_payload</a></code>,
<code><a href="Gnumed.pycommon.gmBusinessDBObject.cBusinessDBObject-class.html#staff_id">staff_id</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
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