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# -*- coding: utf-8 -*- |
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# |
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# This file is part of SENAITE.CORE |
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# |
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# Copyright 2018 by it's authors. |
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# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst. |
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"""Sample represents a physical sample submitted for testing |
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""" |
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from datetime import timedelta |
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from AccessControl import ClassSecurityInfo |
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from bika.lims import bikaMessageFactory as _ |
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from bika.lims.api import get_object_by_uid |
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from bika.lims.browser.fields.remarksfield import RemarksField |
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from bika.lims.browser.fields.uidreferencefield import get_backreferences |
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from bika.lims.utils import t, getUsers |
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from Products.ATExtensions.field import RecordsField |
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from bika.lims.browser.widgets.datetimewidget import DateTimeWidget |
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from bika.lims.browser.widgets import RejectionWidget |
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from bika.lims.browser.widgets import RemarksWidget |
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from bika.lims.config import PROJECTNAME |
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from bika.lims.content.bikaschema import BikaSchema |
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from bika.lims.interfaces import ISample |
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from bika.lims.permissions import SampleSample |
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from bika.lims.permissions import ScheduleSampling |
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from Products.Archetypes import atapi |
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from Products.Archetypes.public import * |
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from Products.Archetypes.references import HoldingReference |
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from Products.ATContentTypes.lib.historyaware import HistoryAwareMixin |
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from Products.ATContentTypes.utils import DT2dt, dt2DT |
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from Products.CMFCore import permissions |
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from Products.CMFCore.utils import getToolByName |
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from Products.CMFPlone.utils import safe_unicode |
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from zope.interface import implements |
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from bika.lims.browser.fields import DateTimeField |
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from bika.lims.browser.widgets import ReferenceWidget |
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from bika.lims.browser.widgets import SelectionWidget as BikaSelectionWidget |
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import sys |
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from bika.lims.utils import to_unicode |
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schema = BikaSchema.copy() + Schema(( |
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# TODO This field is only for v1.3.0 migration purposes |
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# bika_catalog contains an "isValid" index. We will take advantage of this |
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# index to keep track of the Samples that have been migrated already in |
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# order to prevent an unnecessary reimport when v1.3.0 is rerun. |
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# This field is used by `isValid` function |
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BooleanField('Migrated', |
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default = False, |
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), |
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StringField('SampleID', |
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required=1, |
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searchable=True, |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=StringWidget( |
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label=_("Sample ID"), |
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description=_("The ID assigned to the client's sample by the lab"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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StringField('ClientReference', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=StringWidget( |
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label=_("Client Reference"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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StringField('ClientSampleID', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=StringWidget( |
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label=_("Client SID"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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ReferenceField('SampleType', |
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required=1, |
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vocabulary_display_path_bound=sys.maxsize, |
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allowed_types=('SampleType',), |
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relationship='SampleSampleType', |
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referenceClass=HoldingReference, |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=ReferenceWidget( |
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label=_("Sample Type"), |
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render_own_label=True, |
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visible=False, |
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catalog_name='bika_setup_catalog', |
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base_query={'inactive_state': 'active'}, |
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showOn=True, |
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), |
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), |
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ComputedField('SampleTypeTitle', |
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expression="here.getSampleType() and here.getSampleType().Title() or ''", |
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widget=ComputedWidget( |
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visible=False, |
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), |
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), |
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ReferenceField('SamplePoint', |
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vocabulary_display_path_bound=sys.maxsize, |
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allowed_types=('SamplePoint',), |
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relationship = 'SampleSamplePoint', |
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referenceClass = HoldingReference, |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=ReferenceWidget( |
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label=_("Sample Point"), |
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render_own_label=True, |
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visible=False, |
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catalog_name='bika_setup_catalog', |
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base_query={'inactive_state': 'active'}, |
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showOn=True, |
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), |
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), |
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ComputedField('SamplePointTitle', |
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expression = "here.getSamplePoint() and here.getSamplePoint().Title() or ''", |
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widget = ComputedWidget( |
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visible=False, |
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), |
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), |
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ReferenceField( |
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'StorageLocation', |
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allowed_types='StorageLocation', |
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relationship='AnalysisRequestStorageLocation', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=ReferenceWidget( |
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label=_("Storage Location"), |
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description=_("Location where sample is kept"), |
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size=20, |
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render_own_label=True, |
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visible=False, |
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catalog_name='bika_setup_catalog', |
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base_query={'inactive_state': 'active'}, |
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showOn=True, |
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), |
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), |
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BooleanField('SamplingWorkflowEnabled', |
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default_method='getSamplingWorkflowEnabledDefault' |
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), |
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DateTimeField('DateSampled', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=SampleSample, |
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widget = DateTimeWidget( |
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label=_("Date Sampled"), |
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show_time=True, |
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size=20, |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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StringField('Sampler', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=SampleSample, |
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vocabulary='getSamplers', |
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widget=BikaSelectionWidget( |
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format='select', |
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label=_("Sampler"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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StringField('ScheduledSamplingSampler', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=ScheduleSampling, |
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vocabulary='getSamplers', |
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widget=BikaSelectionWidget( |
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description=_("Define the sampler supposed to do the sample in " |
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"the scheduled date"), |
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format='select', |
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label=_("Sampler for scheduled sampling"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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DateTimeField('SamplingDate', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget = DateTimeWidget( |
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label=_("Expected Sampling Date"), |
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description=_("Define when the sampler has to take the samples"), |
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show_time=True, |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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ReferenceField('SamplingDeviation', |
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vocabulary_display_path_bound = sys.maxsize, |
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allowed_types = ('SamplingDeviation',), |
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relationship = 'SampleSamplingDeviation', |
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referenceClass = HoldingReference, |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=ReferenceWidget( |
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label=_("Sampling Deviation"), |
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render_own_label=True, |
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visible=False, |
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catalog_name='bika_setup_catalog', |
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base_query={'inactive_state': 'active'}, |
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showOn=True, |
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), |
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), |
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ReferenceField('SampleCondition', |
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vocabulary_display_path_bound = sys.maxsize, |
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allowed_types = ('SampleCondition',), |
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relationship = 'SampleSampleCondition', |
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referenceClass = HoldingReference, |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=ReferenceWidget( |
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label=_("Sample Condition"), |
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render_own_label=True, |
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visible=False, |
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catalog_name='bika_setup_catalog', |
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base_query={'inactive_state': 'active'}, |
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showOn=True, |
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), |
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), |
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StringField( |
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'EnvironmentalConditions', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget=StringWidget( |
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label=_("Environmental Conditions"), |
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visible=False, |
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render_own_label=True, |
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size=20, |
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), |
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), |
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# Another way to obtain a transition date is using getTransitionDate |
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# function. We are using a DateTimeField/Widget here because in some |
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# cases the user may want to change the Received Date. |
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# AnalysisRequest and Sample's DateReceived fields needn't to have |
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# the same value. |
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# This field is updated in workflow_script_receive method. |
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DateTimeField('DateReceived', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget = DateTimeWidget( |
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label=_("Date Received"), |
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show_time=True, |
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datepicker_nofuture=1, |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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ComputedField('ClientUID', |
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expression = 'context.aq_parent.UID()', |
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widget = ComputedWidget( |
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visible=False, |
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), |
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), |
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ComputedField('SampleTypeUID', |
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expression='context.getSampleType() and \ |
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context.getSampleType().UID() or None', |
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widget=ComputedWidget( |
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visible=False, |
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), |
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), |
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ComputedField('SamplePointUID', |
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expression = 'context.getSamplePoint() and context.getSamplePoint().UID() or None', |
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widget = ComputedWidget( |
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visible=False, |
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), |
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), |
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BooleanField('Composite', |
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default = False, |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget = BooleanWidget( |
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label=_("Composite"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
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DateTimeField('DateExpired', |
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mode="rw", |
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read_permission=permissions.View, |
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write_permission=permissions.ModifyPortalContent, |
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widget = DateTimeWidget( |
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label=_("Date Expired"), |
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visible=False, |
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render_own_label=True, |
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), |
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), |
|
308
|
|
|
ComputedField('DisposalDate', |
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|
|
|
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|
309
|
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expression = 'context.disposal_date()', |
|
310
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|
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widget=DateTimeWidget( |
|
311
|
|
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visible=False, |
|
312
|
|
|
render_own_label=True, |
|
313
|
|
|
), |
|
314
|
|
|
), |
|
315
|
|
|
DateTimeField('DateDisposed', |
|
316
|
|
|
mode="rw", |
|
317
|
|
|
read_permission=permissions.View, |
|
318
|
|
|
write_permission=permissions.ModifyPortalContent, |
|
319
|
|
|
widget = DateTimeWidget( |
|
320
|
|
|
label=_("Date Disposed"), |
|
321
|
|
|
visible=False, |
|
322
|
|
|
render_own_label=True, |
|
323
|
|
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), |
|
324
|
|
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), |
|
325
|
|
|
BooleanField('AdHoc', |
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|
|
|
|
|
326
|
|
|
default=False, |
|
327
|
|
|
mode="rw", |
|
328
|
|
|
read_permission=permissions.View, |
|
329
|
|
|
write_permission=permissions.ModifyPortalContent, |
|
330
|
|
|
widget=BooleanWidget( |
|
|
|
|
|
|
331
|
|
|
label=_("Ad-Hoc"), |
|
332
|
|
|
visible=False, |
|
333
|
|
|
render_own_label=True, |
|
334
|
|
|
), |
|
335
|
|
|
), |
|
336
|
|
|
RemarksField( |
|
337
|
|
|
'Remarks', |
|
338
|
|
|
searchable=True, |
|
339
|
|
|
widget=RemarksWidget( |
|
340
|
|
|
label=_("Remarks"), |
|
341
|
|
|
), |
|
342
|
|
|
), |
|
343
|
|
|
RecordsField( |
|
344
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|
|
'RejectionReasons', |
|
345
|
|
|
widget = RejectionWidget( |
|
346
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|
|
label=_("Sample Rejection"), |
|
347
|
|
|
description = _("Set the Sample Rejection workflow and the reasons"), |
|
348
|
|
|
render_own_label=False, |
|
349
|
|
|
visible=False, |
|
350
|
|
|
), |
|
351
|
|
|
), |
|
352
|
|
|
)) |
|
353
|
|
|
|
|
354
|
|
|
|
|
355
|
|
|
schema['title'].required = False |
|
356
|
|
|
|
|
357
|
|
|
|
|
358
|
|
|
class Sample(BaseFolder, HistoryAwareMixin): |
|
|
|
|
|
|
359
|
|
|
implements(ISample) |
|
360
|
|
|
security = ClassSecurityInfo() |
|
361
|
|
|
displayContentsTab = False |
|
362
|
|
|
schema = schema |
|
|
|
|
|
|
363
|
|
|
|
|
364
|
|
|
_at_rename_after_creation = True |
|
365
|
|
|
|
|
366
|
|
|
def _renameAfterCreation(self, check_auto_id=False): |
|
367
|
|
|
from bika.lims.idserver import renameAfterCreation |
|
368
|
|
|
renameAfterCreation(self) |
|
369
|
|
|
|
|
370
|
|
|
def _getCatalogTool(self): |
|
371
|
|
|
from bika.lims.catalog import getCatalog |
|
372
|
|
|
return getCatalog(self) |
|
373
|
|
|
|
|
374
|
|
|
def getSampleID(self): |
|
375
|
|
|
""" Return the Sample ID as title """ |
|
376
|
|
|
return safe_unicode(self.getId()).encode('utf-8') |
|
377
|
|
|
|
|
378
|
|
|
def Title(self): |
|
379
|
|
|
""" Return the Sample ID as title """ |
|
380
|
|
|
return self.getSampleID() |
|
381
|
|
|
|
|
382
|
|
|
def getSamplingWorkflowEnabledDefault(self): |
|
383
|
|
|
return self.bika_setup.getSamplingWorkflowEnabled() |
|
384
|
|
|
|
|
385
|
|
|
def getContactTitle(self): |
|
386
|
|
|
return "" |
|
387
|
|
|
|
|
388
|
|
|
def getClientTitle(self): |
|
389
|
|
|
proxies = self.getAnalysisRequests() |
|
390
|
|
|
if not proxies: |
|
391
|
|
|
return "" |
|
392
|
|
|
value = proxies[0].aq_parent.Title() |
|
393
|
|
|
return value |
|
394
|
|
|
|
|
395
|
|
|
def getProfilesTitle(self): |
|
396
|
|
|
return "" |
|
397
|
|
|
|
|
398
|
|
|
def getAnalysisService(self): |
|
399
|
|
|
analyses = [] |
|
400
|
|
|
for ar in self.getAnalysisRequests(): |
|
401
|
|
|
analyses += list(ar.getAnalyses(full_objects=True)) |
|
402
|
|
|
value = [] |
|
403
|
|
|
for analysis in analyses: |
|
404
|
|
|
val = analysis.Title() |
|
405
|
|
|
if val not in value: |
|
406
|
|
|
value.append(val) |
|
407
|
|
|
return value |
|
408
|
|
|
|
|
409
|
|
View Code Duplication |
def getAnalysts(self): |
|
|
|
|
|
|
410
|
|
|
analyses = [] |
|
411
|
|
|
for ar in self.getAnalysisRequests(): |
|
412
|
|
|
analyses += list(ar.getAnalyses(full_objects=True)) |
|
413
|
|
|
value = [] |
|
414
|
|
|
for analysis in analyses: |
|
415
|
|
|
val = analysis.getAnalyst() |
|
416
|
|
|
if val not in value: |
|
417
|
|
|
value.append(val) |
|
418
|
|
|
return value |
|
419
|
|
|
|
|
420
|
|
|
security.declarePublic('getAnalysisRequests') |
|
421
|
|
|
|
|
422
|
|
|
def getAnalysisRequests(self): |
|
423
|
|
|
backrefs = get_backreferences(self, 'AnalysisRequestSample') |
|
424
|
|
|
ars = map(get_object_by_uid, backrefs) |
|
425
|
|
|
return ars |
|
426
|
|
|
|
|
427
|
|
|
security.declarePublic('getAnalyses') |
|
428
|
|
|
|
|
429
|
|
|
def getAnalyses(self, contentFilter=None, **kwargs): |
|
430
|
|
|
""" return list of all analyses against this sample |
|
431
|
|
|
""" |
|
432
|
|
|
# contentFilter and kwargs are combined. They both exist for |
|
433
|
|
|
# compatibility between the two signatures; kwargs has been added |
|
434
|
|
|
# to be compatible with how getAnalyses() is used everywhere else. |
|
435
|
|
|
cf = contentFilter if contentFilter else {} |
|
436
|
|
|
cf.update(kwargs) |
|
437
|
|
|
analyses = [] |
|
438
|
|
|
for ar in self.getAnalysisRequests(): |
|
439
|
|
|
analyses.extend(ar.getAnalyses(**cf)) |
|
440
|
|
|
return analyses |
|
441
|
|
|
|
|
442
|
|
|
def getSamplers(self): |
|
443
|
|
|
return getUsers(self, ['Sampler', ]) |
|
444
|
|
|
|
|
445
|
|
|
def disposal_date(self): |
|
446
|
|
|
"""Returns the date the retention period ends for this sample based on |
|
447
|
|
|
the retention period from the Sample Type. If the sample hasn't been |
|
448
|
|
|
collected yet, returns None |
|
449
|
|
|
""" |
|
450
|
|
|
date_sampled = self.getDateSampled() |
|
451
|
|
|
if not date_sampled: |
|
452
|
|
|
return None |
|
453
|
|
|
|
|
454
|
|
|
# TODO Preservation - preservation's retention period has priority over |
|
455
|
|
|
# sample type's preservation period |
|
456
|
|
|
|
|
457
|
|
|
retention_period = self.getSampleType().getRetentionPeriod() or {} |
|
458
|
|
|
retention_period_delta = timedelta( |
|
459
|
|
|
days=int(retention_period.get("days", 0)), |
|
460
|
|
|
hours=int(retention_period.get("hours", 0)), |
|
461
|
|
|
minutes=int(retention_period.get("minutes", 0)) |
|
462
|
|
|
) |
|
463
|
|
|
return dt2DT(DT2dt(date_sampled) + retention_period_delta) |
|
464
|
|
|
|
|
465
|
|
|
|
|
466
|
|
|
# TODO This method is only for v1.3.0 migration purposes |
|
467
|
|
|
# bika_catalog contains an "isValid" index. We will take advantage of this |
|
468
|
|
|
# index to keep track of the Samples that have been migrated already in |
|
469
|
|
|
# order to prevent an unnecessary reimport when v1.3.0 is rerun. |
|
470
|
|
|
def isValid(self): |
|
471
|
|
|
return self.getMigrated() |
|
472
|
|
|
|
|
473
|
|
|
|
|
474
|
|
|
atapi.registerType(Sample, PROJECTNAME) |
|
475
|
|
|
|
senaite /
senaite.core
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