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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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# SENAITE.CORE is free software: you can redistribute it and/or modify it under |
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# the terms of the GNU General Public License as published by the Free Software |
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# Foundation, version 2. |
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# |
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# This program is distributed in the hope that it will be useful, but WITHOUT |
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
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# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more |
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# details. |
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# |
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# You should have received a copy of the GNU General Public License along with |
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# this program; if not, write to the Free Software Foundation, Inc., 51 |
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# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
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# |
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# Copyright 2018-2025 by it's authors. |
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# Some rights reserved, see README and LICENSE. |
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import base64 |
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import functools |
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import re |
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from collections import defaultdict |
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from datetime import datetime |
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from decimal import Decimal |
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from AccessControl import ClassSecurityInfo |
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from bika.lims import api |
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from bika.lims import bikaMessageFactory as _ |
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from bika.lims import deprecated |
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from bika.lims import logger |
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from bika.lims.api.security import check_permission |
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from bika.lims.browser.fields import ARAnalysesField |
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from bika.lims.browser.fields import DurationField |
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from bika.lims.browser.fields import EmailsField |
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from bika.lims.browser.fields import ResultsRangesField |
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from bika.lims.browser.fields import UIDReferenceField |
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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.browser.widgets import DateTimeWidget |
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from bika.lims.browser.widgets import DecimalWidget |
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from bika.lims.browser.widgets import PrioritySelectionWidget |
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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.browser.widgets import SelectionWidget as BikaSelectionWidget |
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from bika.lims.browser.widgets.durationwidget import DurationWidget |
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from bika.lims.config import PRIORITIES |
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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.content.clientawaremixin import ClientAwareMixin |
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from bika.lims.interfaces import IAnalysisRequest |
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from bika.lims.interfaces import IAnalysisRequestPartition |
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from bika.lims.interfaces import IAnalysisRequestWithPartitions |
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from bika.lims.interfaces import IBatch |
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from bika.lims.interfaces import ICancellable |
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from bika.lims.interfaces import IClient |
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from bika.lims.interfaces import ISubmitted |
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from bika.lims.utils import getUsers |
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from bika.lims.utils import tmpID |
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from bika.lims.utils.analysisrequest import apply_hidden_services |
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from bika.lims.workflow import getTransitionDate |
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from bika.lims.workflow import getTransitionUsers |
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from DateTime import DateTime |
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from Products.Archetypes.atapi import BaseFolder |
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from Products.Archetypes.atapi import BooleanField |
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from Products.Archetypes.atapi import BooleanWidget |
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from Products.Archetypes.atapi import ComputedField |
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from Products.Archetypes.atapi import ComputedWidget |
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from Products.Archetypes.atapi import FileField |
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from Products.Archetypes.atapi import FileWidget |
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from Products.Archetypes.atapi import FixedPointField |
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from Products.Archetypes.atapi import StringField |
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from Products.Archetypes.atapi import StringWidget |
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from Products.Archetypes.atapi import TextField |
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from Products.Archetypes.atapi import registerType |
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from Products.Archetypes.config import UID_CATALOG |
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from Products.Archetypes.Field import IntegerField |
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from Products.Archetypes.public import Schema |
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from Products.Archetypes.Widget import IntegerWidget |
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from Products.Archetypes.Widget import RichWidget |
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from Products.CMFCore.permissions import ModifyPortalContent |
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from Products.CMFCore.permissions import View |
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from Products.CMFCore.utils import getToolByName |
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from Products.CMFPlone.utils import _createObjectByType |
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from Products.CMFPlone.utils import safe_unicode |
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from senaite.core.browser.fields.datetime import DateTimeField |
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from senaite.core.browser.fields.records import RecordsField |
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from senaite.core.browser.widgets.referencewidget import ReferenceWidget |
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from senaite.core.catalog import ANALYSIS_CATALOG |
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from senaite.core.catalog import CLIENT_CATALOG |
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from senaite.core.catalog import CONTACT_CATALOG |
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from senaite.core.catalog import SAMPLE_CATALOG |
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from senaite.core.catalog import SENAITE_CATALOG |
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from senaite.core.catalog import SETUP_CATALOG |
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from senaite.core.catalog import WORKSHEET_CATALOG |
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from senaite.core.permissions import FieldEditBatch |
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from senaite.core.permissions import FieldEditClient |
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from senaite.core.permissions import FieldEditClientOrderNumber |
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from senaite.core.permissions import FieldEditClientReference |
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from senaite.core.permissions import FieldEditClientSampleID |
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from senaite.core.permissions import FieldEditComposite |
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from senaite.core.permissions import FieldEditContact |
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from senaite.core.permissions import FieldEditContainer |
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from senaite.core.permissions import FieldEditDatePreserved |
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from senaite.core.permissions import FieldEditDateReceived |
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from senaite.core.permissions import FieldEditDateSampled |
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from senaite.core.permissions import FieldEditEnvironmentalConditions |
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from senaite.core.permissions import FieldEditInternalUse |
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from senaite.core.permissions import FieldEditInvoiceExclude |
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from senaite.core.permissions import FieldEditMemberDiscount |
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from senaite.core.permissions import FieldEditPreservation |
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from senaite.core.permissions import FieldEditPreserver |
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from senaite.core.permissions import FieldEditPriority |
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from senaite.core.permissions import FieldEditProfiles |
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from senaite.core.permissions import FieldEditPublicationSpecifications |
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from senaite.core.permissions import FieldEditRejectionReasons |
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from senaite.core.permissions import FieldEditRemarks |
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from senaite.core.permissions import FieldEditResultsInterpretation |
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from senaite.core.permissions import FieldEditSampleCondition |
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from senaite.core.permissions import FieldEditSamplePoint |
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from senaite.core.permissions import FieldEditSampler |
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from senaite.core.permissions import FieldEditSampleType |
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from senaite.core.permissions import FieldEditSamplingDate |
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from senaite.core.permissions import FieldEditSamplingDeviation |
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from senaite.core.permissions import FieldEditScheduledSampler |
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from senaite.core.permissions import FieldEditSpecification |
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from senaite.core.permissions import FieldEditStorageLocation |
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from senaite.core.permissions import FieldEditTemplate |
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from senaite.core.permissions import ManageInvoices |
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from six.moves.urllib.parse import urljoin |
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from zope.interface import alsoProvides |
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from zope.interface import implements |
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from zope.interface import noLongerProvides |
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IMG_SRC_RX = re.compile(r'<img.*?src="(.*?)"') |
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IMG_DATA_SRC_RX = re.compile(r'<img.*?src="(data:image/.*?;base64,)(.*?)"') |
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FINAL_STATES = ["published", "retracted", "rejected", "cancelled"] |
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DETACHED_STATES = ["retracted", "rejected"] |
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# SCHEMA DEFINITION |
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schema = BikaSchema.copy() + Schema(( |
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UIDReferenceField( |
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"Contact", |
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required=1, |
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allowed_types=("Contact",), |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditContact, |
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widget=ReferenceWidget( |
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label=_( |
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"label_sample_contact", |
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default="Contact"), |
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description=_( |
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"description_sample_contact", |
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default="Select the primary contact for this sample"), |
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render_own_label=True, |
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visible={ |
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"add": "edit", |
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"header_table": "prominent", |
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}, |
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ui_item="Title", |
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catalog=CONTACT_CATALOG, |
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# TODO: Make custom query to handle parent client UID |
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query={ |
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"getParentUID": "", |
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"is_active": True, |
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"sort_on": "sortable_title", |
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"sort_order": "ascending" |
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}, |
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columns=[ |
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{"name": "Title", "label": _("Name")}, |
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{"name": "getEmailAddress", "label": _("Email")}, |
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], |
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), |
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), |
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UIDReferenceField( |
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"CCContact", |
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multiValued=1, |
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allowed_types=("Contact",), |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditContact, |
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widget=ReferenceWidget( |
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label=_( |
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"label_sample_cccontact", |
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default="CC Contact"), |
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description=_( |
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"description_sample_cccontact", |
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default="The contacts used in CC for email notifications"), |
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render_own_label=True, |
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visible={ |
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"add": "edit", |
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"header_table": "prominent", |
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}, |
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ui_item="Title", |
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catalog=CONTACT_CATALOG, |
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# TODO: Make custom query to handle parent client UID |
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query={ |
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"getParentUID": "", |
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"is_active": True, |
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"sort_on": "sortable_title", |
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"sort_order": "ascending" |
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}, |
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columns=[ |
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{"name": "Title", "label": _("Name")}, |
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{"name": "getEmailAddress", "label": _("Email")}, |
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], |
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), |
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), |
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EmailsField( |
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'CCEmails', |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditContact, |
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widget=StringWidget( |
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label=_("CC Emails"), |
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description=_("Additional email addresses to be notified"), |
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visible={ |
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'add': 'edit', |
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'header_table': 'prominent', |
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}, |
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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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UIDReferenceField( |
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"Client", |
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required=1, |
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allowed_types=("Client",), |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditClient, |
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widget=ReferenceWidget( |
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label=_( |
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"label_sample_client", |
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default="Client"), |
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description=_( |
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"description_sample_client", |
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default="Select the client for this sample"), |
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render_own_label=True, |
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visible={ |
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"add": "edit", |
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"header_table": "prominent", |
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}, |
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ui_item="getName", |
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catalog=CLIENT_CATALOG, |
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search_index="client_searchable_text", |
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query={ |
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"is_active": True, |
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"sort_on": "sortable_title", |
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"sort_order": "ascending" |
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}, |
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columns=[ |
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{"name": "getName", "label": _("Name")}, |
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{"name": "getClientID", "label": _("Client ID")}, |
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], |
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), |
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), |
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# Field for the creation of Secondary Analysis Requests. |
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# This field is meant to be displayed in AR Add form only. A viewlet exists |
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# to inform the user this Analysis Request is secondary |
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UIDReferenceField( |
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"PrimaryAnalysisRequest", |
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allowed_types=("AnalysisRequest",), |
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relationship='AnalysisRequestPrimaryAnalysisRequest', |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditClient, |
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widget=ReferenceWidget( |
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label=_( |
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"label_sample_primary", |
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default="Primary Sample"), |
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description=_( |
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"description_sample_primary", |
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default="Select a sample to create a secondary Sample"), |
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render_own_label=True, |
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visible={ |
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"add": "edit", |
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"header_table": "prominent", |
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}, |
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catalog_name=SAMPLE_CATALOG, |
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search_index="listing_searchable_text", |
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query={ |
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"is_active": True, |
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"is_received": True, |
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"sort_on": "sortable_title", |
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"sort_order": "ascending" |
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}, |
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columns=[ |
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{"name": "getId", "label": _("Sample ID")}, |
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{"name": "getClientSampleID", "label": _("Client SID")}, |
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{"name": "getSampleTypeTitle", "label": _("Sample Type")}, |
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{"name": "getClientTitle", "label": _("Client")}, |
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], |
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ui_item="getId", |
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) |
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), |
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UIDReferenceField( |
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"Batch", |
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allowed_types=("Batch",), |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditBatch, |
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widget=ReferenceWidget( |
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label=_( |
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"label_sample_batch", |
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default="Batch"), |
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description=_( |
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"description_sample_batch", |
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default="Assign sample to a batch"), |
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render_own_label=True, |
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visible={ |
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"add": "edit", |
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}, |
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catalog_name=SENAITE_CATALOG, |
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search_index="listing_searchable_text", |
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query={ |
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"is_active": True, |
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"sort_on": "sortable_title", |
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"sort_order": "ascending" |
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}, |
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columns=[ |
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{"name": "getId", "label": _("Batch ID")}, |
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{"name": "Title", "label": _("Title")}, |
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{"name": "getClientBatchID", "label": _("CBID")}, |
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{"name": "getClientTitle", "label": _("Client")}, |
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], |
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ui_item="Title", |
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) |
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), |
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UIDReferenceField( |
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"SubGroup", |
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required=False, |
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allowed_types=("SubGroup",), |
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mode="rw", |
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read_permission=View, |
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write_permission=FieldEditBatch, |
347
|
|
|
widget=ReferenceWidget( |
348
|
|
|
label=_( |
349
|
|
|
"label_sample_subgroup", |
350
|
|
|
default="Batch Sub-group"), |
351
|
|
|
description=_( |
352
|
|
|
"description_sample_subgroup", |
353
|
|
|
default="The assigned batch sub group of this request"), |
354
|
|
|
render_own_label=True, |
355
|
|
|
visible={ |
356
|
|
|
"add": "edit", |
357
|
|
|
}, |
358
|
|
|
catalog_name=SETUP_CATALOG, |
359
|
|
|
query={ |
360
|
|
|
"is_active": True, |
361
|
|
|
"sort_on": "sortable_title", |
362
|
|
|
"sort_order": "ascending" |
363
|
|
|
}, |
364
|
|
|
ui_item="Title", |
365
|
|
|
) |
366
|
|
|
), |
367
|
|
|
|
368
|
|
|
UIDReferenceField( |
369
|
|
|
"Template", |
370
|
|
|
allowed_types=("SampleTemplate",), |
371
|
|
|
mode="rw", |
372
|
|
|
read_permission=View, |
373
|
|
|
write_permission=FieldEditTemplate, |
374
|
|
|
widget=ReferenceWidget( |
375
|
|
|
label=_( |
376
|
|
|
"label_sample_template", |
377
|
|
|
default="Sample Template"), |
378
|
|
|
description=_( |
379
|
|
|
"description_sample_template", |
380
|
|
|
default="Select an analysis template for this sample"), |
381
|
|
|
render_own_label=True, |
382
|
|
|
visible={ |
383
|
|
|
"add": "edit", |
384
|
|
|
"secondary": "disabled", |
385
|
|
|
}, |
386
|
|
|
catalog=SETUP_CATALOG, |
387
|
|
|
query={ |
388
|
|
|
"is_active": True, |
389
|
|
|
"sort_on": "sortable_title", |
390
|
|
|
"sort_order": "ascending" |
391
|
|
|
}, |
392
|
|
|
), |
393
|
|
|
), |
394
|
|
|
|
395
|
|
|
UIDReferenceField( |
396
|
|
|
"Profiles", |
397
|
|
|
multiValued=1, |
398
|
|
|
allowed_types=("AnalysisProfile",), |
399
|
|
|
mode="rw", |
400
|
|
|
read_permission=View, |
401
|
|
|
write_permission=FieldEditProfiles, |
402
|
|
|
widget=ReferenceWidget( |
403
|
|
|
label=_( |
404
|
|
|
"label_sample_profiles", |
405
|
|
|
default="Analysis Profiles"), |
406
|
|
|
description=_( |
407
|
|
|
"description_sample_profiles", |
408
|
|
|
default="Select an analysis profile for this sample"), |
409
|
|
|
render_own_label=True, |
410
|
|
|
visible={ |
411
|
|
|
"add": "edit", |
412
|
|
|
}, |
413
|
|
|
catalog_name=SETUP_CATALOG, |
414
|
|
|
query="get_profiles_query", |
415
|
|
|
columns=[ |
416
|
|
|
{"name": "Title", "label": _("Profile Name")}, |
417
|
|
|
{"name": "getProfileKey", "label": _("Profile Key")}, |
418
|
|
|
], |
419
|
|
|
) |
420
|
|
|
), |
421
|
|
|
|
422
|
|
|
# TODO Workflow - Request - Fix DateSampled inconsistencies. At the moment, |
423
|
|
|
# one can create an AR (with code) with DateSampled set when sampling_wf at |
424
|
|
|
# the same time sampling workflow is active. This might cause |
425
|
|
|
# inconsistencies: AR still in `to_be_sampled`, but getDateSampled returns |
426
|
|
|
# a valid date! |
427
|
|
|
DateTimeField( |
428
|
|
|
'DateSampled', |
429
|
|
|
mode="rw", |
430
|
|
|
max="getMaxDateSampled", |
431
|
|
|
read_permission=View, |
432
|
|
|
write_permission=FieldEditDateSampled, |
433
|
|
|
widget=DateTimeWidget( |
434
|
|
|
label=_( |
435
|
|
|
"label_sample_datesampled", |
436
|
|
|
default="Date Sampled" |
437
|
|
|
), |
438
|
|
|
description=_( |
439
|
|
|
"description_sample_datesampled", |
440
|
|
|
default="The date when the sample was taken" |
441
|
|
|
), |
442
|
|
|
size=20, |
443
|
|
|
show_time=True, |
444
|
|
|
visible={ |
445
|
|
|
'add': 'edit', |
446
|
|
|
'secondary': 'disabled', |
447
|
|
|
'header_table': 'prominent', |
448
|
|
|
}, |
449
|
|
|
render_own_label=True, |
450
|
|
|
), |
451
|
|
|
), |
452
|
|
|
|
453
|
|
|
StringField( |
454
|
|
|
'Sampler', |
455
|
|
|
mode="rw", |
456
|
|
|
read_permission=View, |
457
|
|
|
write_permission=FieldEditSampler, |
458
|
|
|
vocabulary='getSamplers', |
459
|
|
|
widget=BikaSelectionWidget( |
460
|
|
|
format='select', |
461
|
|
|
label=_("Sampler"), |
462
|
|
|
description=_("The person who took the sample"), |
463
|
|
|
# see SamplingWOrkflowWidgetVisibility |
464
|
|
|
visible={ |
465
|
|
|
'add': 'edit', |
466
|
|
|
'header_table': 'prominent', |
467
|
|
|
}, |
468
|
|
|
render_own_label=True, |
469
|
|
|
), |
470
|
|
|
), |
471
|
|
|
|
472
|
|
|
StringField( |
473
|
|
|
'ScheduledSamplingSampler', |
474
|
|
|
mode="rw", |
475
|
|
|
read_permission=View, |
476
|
|
|
write_permission=FieldEditScheduledSampler, |
477
|
|
|
vocabulary='getSamplers', |
478
|
|
|
widget=BikaSelectionWidget( |
479
|
|
|
description=_("Define the sampler supposed to do the sample in " |
480
|
|
|
"the scheduled date"), |
481
|
|
|
format='select', |
482
|
|
|
label=_("Sampler for scheduled sampling"), |
483
|
|
|
visible={ |
484
|
|
|
'add': 'edit', |
485
|
|
|
}, |
486
|
|
|
render_own_label=True, |
487
|
|
|
), |
488
|
|
|
), |
489
|
|
|
|
490
|
|
|
DateTimeField( |
491
|
|
|
'SamplingDate', |
492
|
|
|
mode="rw", |
493
|
|
|
min="created", |
494
|
|
|
read_permission=View, |
495
|
|
|
write_permission=FieldEditSamplingDate, |
496
|
|
|
widget=DateTimeWidget( |
497
|
|
|
label=_( |
498
|
|
|
"label_sample_samplingdate", |
499
|
|
|
default="Expected Sampling Date" |
500
|
|
|
), |
501
|
|
|
description=_( |
502
|
|
|
"description_sample_samplingdate", |
503
|
|
|
default="The date when the sample will be taken" |
504
|
|
|
), |
505
|
|
|
size=20, |
506
|
|
|
show_time=True, |
507
|
|
|
render_own_label=True, |
508
|
|
|
visible={ |
509
|
|
|
'add': 'edit', |
510
|
|
|
'secondary': 'disabled', |
511
|
|
|
}, |
512
|
|
|
), |
513
|
|
|
), |
514
|
|
|
|
515
|
|
|
UIDReferenceField( |
516
|
|
|
"SampleType", |
517
|
|
|
required=1, |
518
|
|
|
allowed_types=("SampleType",), |
519
|
|
|
mode="rw", |
520
|
|
|
read_permission=View, |
521
|
|
|
write_permission=FieldEditSampleType, |
522
|
|
|
widget=ReferenceWidget( |
523
|
|
|
label=_( |
524
|
|
|
"label_sample_sampletype", |
525
|
|
|
default="Sample Type"), |
526
|
|
|
description=_( |
527
|
|
|
"description_sample_sampletype", |
528
|
|
|
default="Select the sample type of this sample"), |
529
|
|
|
render_own_label=True, |
530
|
|
|
visible={ |
531
|
|
|
"add": "edit", |
532
|
|
|
"secondary": "disabled", |
533
|
|
|
}, |
534
|
|
|
catalog=SETUP_CATALOG, |
535
|
|
|
query={ |
536
|
|
|
"is_active": True, |
537
|
|
|
"sort_on": "sortable_title", |
538
|
|
|
"sort_order": "ascending" |
539
|
|
|
}, |
540
|
|
|
), |
541
|
|
|
), |
542
|
|
|
|
543
|
|
|
UIDReferenceField( |
544
|
|
|
"Container", |
545
|
|
|
required=0, |
546
|
|
|
allowed_types=("SampleContainer",), |
547
|
|
|
mode="rw", |
548
|
|
|
read_permission=View, |
549
|
|
|
write_permission=FieldEditContainer, |
550
|
|
|
widget=ReferenceWidget( |
551
|
|
|
label=_( |
552
|
|
|
"label_sample_container", |
553
|
|
|
default="Container"), |
554
|
|
|
description=_( |
555
|
|
|
"description_sample_container", |
556
|
|
|
default="Select a container for this sample"), |
557
|
|
|
render_own_label=True, |
558
|
|
|
visible={ |
559
|
|
|
"add": "edit", |
560
|
|
|
}, |
561
|
|
|
catalog_name=SETUP_CATALOG, |
562
|
|
|
query={ |
563
|
|
|
"is_active": True, |
564
|
|
|
"sort_on": "sortable_title", |
565
|
|
|
"sort_order": "ascending" |
566
|
|
|
}, |
567
|
|
|
columns=[ |
568
|
|
|
{"name": "Title", "label": _("Container")}, |
569
|
|
|
{"name": "getCapacity", "label": _("Capacity")}, |
570
|
|
|
], |
571
|
|
|
) |
572
|
|
|
), |
573
|
|
|
|
574
|
|
|
UIDReferenceField( |
575
|
|
|
"Preservation", |
576
|
|
|
required=0, |
577
|
|
|
allowed_types=("SamplePreservation",), |
578
|
|
|
mode="rw", |
579
|
|
|
read_permission=View, |
580
|
|
|
write_permission=FieldEditPreservation, |
581
|
|
|
widget=ReferenceWidget( |
582
|
|
|
label=_( |
583
|
|
|
"label_sample_preservation", |
584
|
|
|
default="Preservation"), |
585
|
|
|
description=_( |
586
|
|
|
"description_sample_preservation", |
587
|
|
|
default="Select the needed preservation for this sample"), |
588
|
|
|
render_own_label=True, |
589
|
|
|
visible={ |
590
|
|
|
"add": "edit", |
591
|
|
|
}, |
592
|
|
|
catalog_name=SETUP_CATALOG, |
593
|
|
|
query={ |
594
|
|
|
"is_active": True, |
595
|
|
|
"sort_on": "sortable_title", |
596
|
|
|
"sort_order": "ascending" |
597
|
|
|
}, |
598
|
|
|
) |
599
|
|
|
), |
600
|
|
|
|
601
|
|
|
DateTimeField( |
602
|
|
|
"DatePreserved", |
603
|
|
|
mode="rw", |
604
|
|
|
read_permission=View, |
605
|
|
|
write_permission=FieldEditDatePreserved, |
606
|
|
|
widget=DateTimeWidget( |
607
|
|
|
label=_("Date Preserved"), |
608
|
|
|
description=_("The date when the sample was preserved"), |
609
|
|
|
size=20, |
610
|
|
|
show_time=True, |
611
|
|
|
render_own_label=True, |
612
|
|
|
visible={ |
613
|
|
|
'add': 'edit', |
614
|
|
|
'header_table': 'prominent', |
615
|
|
|
}, |
616
|
|
|
), |
617
|
|
|
), |
618
|
|
|
|
619
|
|
|
StringField( |
620
|
|
|
"Preserver", |
621
|
|
|
required=0, |
622
|
|
|
mode="rw", |
623
|
|
|
read_permission=View, |
624
|
|
|
write_permission=FieldEditPreserver, |
625
|
|
|
vocabulary='getPreservers', |
626
|
|
|
widget=BikaSelectionWidget( |
627
|
|
|
format='select', |
628
|
|
|
label=_("Preserver"), |
629
|
|
|
description=_("The person who preserved the sample"), |
630
|
|
|
visible={ |
631
|
|
|
'add': 'edit', |
632
|
|
|
'header_table': 'prominent', |
633
|
|
|
}, |
634
|
|
|
render_own_label=True, |
635
|
|
|
), |
636
|
|
|
), |
637
|
|
|
|
638
|
|
|
# TODO Sample cleanup - This comes from partition |
639
|
|
|
DurationField( |
640
|
|
|
"RetentionPeriod", |
641
|
|
|
required=0, |
642
|
|
|
mode="r", |
643
|
|
|
read_permission=View, |
644
|
|
|
widget=DurationWidget( |
645
|
|
|
label=_("Retention Period"), |
646
|
|
|
visible=False, |
647
|
|
|
), |
648
|
|
|
), |
649
|
|
|
|
650
|
|
|
RecordsField( |
651
|
|
|
'RejectionReasons', |
652
|
|
|
mode="rw", |
653
|
|
|
read_permission=View, |
654
|
|
|
write_permission=FieldEditRejectionReasons, |
655
|
|
|
widget=RejectionWidget( |
656
|
|
|
label=_("Sample Rejection"), |
657
|
|
|
description=_("Set the Sample Rejection workflow and the reasons"), |
658
|
|
|
render_own_label=False, |
659
|
|
|
visible={ |
660
|
|
|
'add': 'edit', |
661
|
|
|
'secondary': 'disabled', |
662
|
|
|
}, |
663
|
|
|
), |
664
|
|
|
), |
665
|
|
|
|
666
|
|
|
UIDReferenceField( |
667
|
|
|
"Specification", |
668
|
|
|
required=0, |
669
|
|
|
primary_bound=True, # field changes propagate to partitions |
670
|
|
|
allowed_types=("AnalysisSpec",), |
671
|
|
|
mode="rw", |
672
|
|
|
read_permission=View, |
673
|
|
|
write_permission=FieldEditSpecification, |
674
|
|
|
widget=ReferenceWidget( |
675
|
|
|
label=_( |
676
|
|
|
"label_sample_specification", |
677
|
|
|
default="Analysis Specification"), |
678
|
|
|
description=_( |
679
|
|
|
"description_sample_specification", |
680
|
|
|
default="Select an analysis specification for this sample"), |
681
|
|
|
render_own_label=True, |
682
|
|
|
visible={ |
683
|
|
|
"add": "edit", |
684
|
|
|
}, |
685
|
|
|
catalog_name=SETUP_CATALOG, |
686
|
|
|
query={ |
687
|
|
|
"is_active": True, |
688
|
|
|
"sort_on": "sortable_title", |
689
|
|
|
"sort_order": "ascending" |
690
|
|
|
}, |
691
|
|
|
columns=[ |
692
|
|
|
{"name": "Title", "label": _("Specification Name")}, |
693
|
|
|
{"name": "getSampleTypeTitle", "label": _("Sample Type")}, |
694
|
|
|
], |
695
|
|
|
) |
696
|
|
|
), |
697
|
|
|
|
698
|
|
|
# Field to keep the result ranges from the specification initially set |
699
|
|
|
# through "Specifications" field. This guarantees that the result ranges |
700
|
|
|
# set by default to this Sample won't change even if the Specifications |
701
|
|
|
# object referenced gets modified thereafter. |
702
|
|
|
# This field does not consider result ranges manually set to analyses. |
703
|
|
|
# Therefore, is also used to "detect" changes between the result ranges |
704
|
|
|
# specifically set to analyses and the results ranges set to the sample |
705
|
|
|
ResultsRangesField( |
706
|
|
|
"ResultsRange", |
707
|
|
|
write_permission=FieldEditSpecification, |
708
|
|
|
widget=ComputedWidget(visible=False), |
709
|
|
|
), |
710
|
|
|
|
711
|
|
|
UIDReferenceField( |
712
|
|
|
"PublicationSpecification", |
713
|
|
|
required=0, |
714
|
|
|
allowed_types=("AnalysisSpec",), |
715
|
|
|
mode="rw", |
716
|
|
|
read_permission=View, |
717
|
|
|
write_permission=FieldEditPublicationSpecifications, |
718
|
|
|
widget=ReferenceWidget( |
719
|
|
|
label=_( |
720
|
|
|
"label_sample_publicationspecification", |
721
|
|
|
default="Publication Specification"), |
722
|
|
|
description=_( |
723
|
|
|
"description_sample_publicationspecification", |
724
|
|
|
default="Select an analysis specification that should be used " |
725
|
|
|
"in the sample publication report"), |
726
|
|
|
render_own_label=True, |
727
|
|
|
visible={ |
728
|
|
|
"add": "invisible", |
729
|
|
|
"secondary": "disabled", |
730
|
|
|
}, |
731
|
|
|
catalog_name=SETUP_CATALOG, |
732
|
|
|
query={ |
733
|
|
|
"is_active": True, |
734
|
|
|
"sort_on": "sortable_title", |
735
|
|
|
"sort_order": "ascending" |
736
|
|
|
}, |
737
|
|
|
columns=[ |
738
|
|
|
{"name": "Title", "label": _("Specification Name")}, |
739
|
|
|
{"name": "getSampleTypeTitle", "label": _("Sample Type")}, |
740
|
|
|
], |
741
|
|
|
) |
742
|
|
|
), |
743
|
|
|
|
744
|
|
|
# Sample field |
745
|
|
|
UIDReferenceField( |
746
|
|
|
"SamplePoint", |
747
|
|
|
allowed_types=("SamplePoint",), |
748
|
|
|
mode="rw", |
749
|
|
|
read_permission=View, |
750
|
|
|
write_permission=FieldEditSamplePoint, |
751
|
|
|
widget=ReferenceWidget( |
752
|
|
|
label=_( |
753
|
|
|
"label_sample_samplepoint", |
754
|
|
|
default="Sample Point"), |
755
|
|
|
description=_( |
756
|
|
|
"description_sample_samplepoint", |
757
|
|
|
default="Location where the sample was taken"), |
758
|
|
|
render_own_label=True, |
759
|
|
|
visible={ |
760
|
|
|
"add": "edit", |
761
|
|
|
"secondary": "disabled", |
762
|
|
|
}, |
763
|
|
|
catalog_name=SETUP_CATALOG, |
764
|
|
|
query="get_sample_points_query", |
765
|
|
|
) |
766
|
|
|
), |
767
|
|
|
|
768
|
|
|
# Remove in favor of senaite.storage? |
769
|
|
|
UIDReferenceField( |
770
|
|
|
"StorageLocation", |
771
|
|
|
allowed_types=("StorageLocation",), |
772
|
|
|
mode="rw", |
773
|
|
|
read_permission=View, |
774
|
|
|
write_permission=FieldEditStorageLocation, |
775
|
|
|
widget=ReferenceWidget( |
776
|
|
|
label=_( |
777
|
|
|
"label_sample_storagelocation", |
778
|
|
|
default="Storage Location"), |
779
|
|
|
description=_( |
780
|
|
|
"description_sample_storagelocation", |
781
|
|
|
default="Location where the sample is kept"), |
782
|
|
|
render_own_label=True, |
783
|
|
|
visible={ |
784
|
|
|
"add": "edit", |
785
|
|
|
"secondary": "disabled", |
786
|
|
|
}, |
787
|
|
|
catalog_name=SETUP_CATALOG, |
788
|
|
|
query={ |
789
|
|
|
"is_active": True, |
790
|
|
|
"sort_on": "sortable_title", |
791
|
|
|
"sort_order": "ascending" |
792
|
|
|
}, |
793
|
|
|
) |
794
|
|
|
), |
795
|
|
|
|
796
|
|
|
StringField( |
797
|
|
|
'ClientOrderNumber', |
798
|
|
|
mode="rw", |
799
|
|
|
read_permission=View, |
800
|
|
|
write_permission=FieldEditClientOrderNumber, |
801
|
|
|
widget=StringWidget( |
802
|
|
|
label=_("Client Order Number"), |
803
|
|
|
description=_("The client side order number for this request"), |
804
|
|
|
size=20, |
805
|
|
|
render_own_label=True, |
806
|
|
|
visible={ |
807
|
|
|
'add': 'edit', |
808
|
|
|
'secondary': 'disabled', |
809
|
|
|
}, |
810
|
|
|
), |
811
|
|
|
), |
812
|
|
|
|
813
|
|
|
StringField( |
814
|
|
|
'ClientReference', |
815
|
|
|
mode="rw", |
816
|
|
|
read_permission=View, |
817
|
|
|
write_permission=FieldEditClientReference, |
818
|
|
|
widget=StringWidget( |
819
|
|
|
label=_("Client Reference"), |
820
|
|
|
description=_("The client side reference for this request"), |
821
|
|
|
size=20, |
822
|
|
|
render_own_label=True, |
823
|
|
|
visible={ |
824
|
|
|
'add': 'edit', |
825
|
|
|
'secondary': 'disabled', |
826
|
|
|
}, |
827
|
|
|
), |
828
|
|
|
), |
829
|
|
|
|
830
|
|
|
StringField( |
831
|
|
|
'ClientSampleID', |
832
|
|
|
mode="rw", |
833
|
|
|
read_permission=View, |
834
|
|
|
write_permission=FieldEditClientSampleID, |
835
|
|
|
widget=StringWidget( |
836
|
|
|
label=_("Client Sample ID"), |
837
|
|
|
description=_("The client side identifier of the sample"), |
838
|
|
|
size=20, |
839
|
|
|
render_own_label=True, |
840
|
|
|
visible={ |
841
|
|
|
'add': 'edit', |
842
|
|
|
'secondary': 'disabled', |
843
|
|
|
}, |
844
|
|
|
), |
845
|
|
|
), |
846
|
|
|
|
847
|
|
|
UIDReferenceField( |
848
|
|
|
"SamplingDeviation", |
849
|
|
|
allowed_types=("SamplingDeviation",), |
850
|
|
|
mode="rw", |
851
|
|
|
read_permission=View, |
852
|
|
|
write_permission=FieldEditSamplingDeviation, |
853
|
|
|
widget=ReferenceWidget( |
854
|
|
|
label=_( |
855
|
|
|
"label_sample_samplingdeviation", |
856
|
|
|
default="Sampling Deviation"), |
857
|
|
|
description=_( |
858
|
|
|
"description_sample_samplingdeviation", |
859
|
|
|
default="Deviation between the sample and how it " |
860
|
|
|
"was sampled"), |
861
|
|
|
render_own_label=True, |
862
|
|
|
visible={ |
863
|
|
|
"add": "edit", |
864
|
|
|
"secondary": "disabled", |
865
|
|
|
}, |
866
|
|
|
catalog_name=SETUP_CATALOG, |
867
|
|
|
query={ |
868
|
|
|
"is_active": True, |
869
|
|
|
"sort_on": "sortable_title", |
870
|
|
|
"sort_order": "ascending" |
871
|
|
|
}, |
872
|
|
|
) |
873
|
|
|
), |
874
|
|
|
|
875
|
|
|
UIDReferenceField( |
876
|
|
|
"SampleCondition", |
877
|
|
|
allowed_types=("SampleCondition",), |
878
|
|
|
mode="rw", |
879
|
|
|
read_permission=View, |
880
|
|
|
write_permission=FieldEditSampleCondition, |
881
|
|
|
widget=ReferenceWidget( |
882
|
|
|
label=_( |
883
|
|
|
"label_sample_samplecondition", |
884
|
|
|
default="Sample Condition"), |
885
|
|
|
description=_( |
886
|
|
|
"description_sample_samplecondition", |
887
|
|
|
default="The condition of the sample"), |
888
|
|
|
render_own_label=True, |
889
|
|
|
visible={ |
890
|
|
|
"add": "edit", |
891
|
|
|
"secondary": "disabled", |
892
|
|
|
}, |
893
|
|
|
catalog_name=SETUP_CATALOG, |
894
|
|
|
query={ |
895
|
|
|
"is_active": True, |
896
|
|
|
"sort_on": "sortable_title", |
897
|
|
|
"sort_order": "ascending" |
898
|
|
|
}, |
899
|
|
|
) |
900
|
|
|
), |
901
|
|
|
|
902
|
|
|
StringField( |
903
|
|
|
'Priority', |
904
|
|
|
default='3', |
905
|
|
|
vocabulary=PRIORITIES, |
906
|
|
|
mode='rw', |
907
|
|
|
read_permission=View, |
908
|
|
|
write_permission=FieldEditPriority, |
909
|
|
|
widget=PrioritySelectionWidget( |
910
|
|
|
label=_('Priority'), |
911
|
|
|
format='select', |
912
|
|
|
visible={ |
913
|
|
|
'add': 'edit', |
914
|
|
|
}, |
915
|
|
|
), |
916
|
|
|
), |
917
|
|
|
|
918
|
|
|
StringField( |
919
|
|
|
'EnvironmentalConditions', |
920
|
|
|
mode="rw", |
921
|
|
|
read_permission=View, |
922
|
|
|
write_permission=FieldEditEnvironmentalConditions, |
923
|
|
|
widget=StringWidget( |
924
|
|
|
label=_("Environmental conditions"), |
925
|
|
|
description=_("The environmental condition during sampling"), |
926
|
|
|
visible={ |
927
|
|
|
'add': 'edit', |
928
|
|
|
'header_table': 'prominent', |
929
|
|
|
}, |
930
|
|
|
render_own_label=True, |
931
|
|
|
size=20, |
932
|
|
|
), |
933
|
|
|
), |
934
|
|
|
|
935
|
|
|
BooleanField( |
936
|
|
|
'Composite', |
937
|
|
|
default=False, |
938
|
|
|
mode="rw", |
939
|
|
|
read_permission=View, |
940
|
|
|
write_permission=FieldEditComposite, |
941
|
|
|
widget=BooleanWidget( |
942
|
|
|
label=_("Composite"), |
943
|
|
|
render_own_label=True, |
944
|
|
|
visible={ |
945
|
|
|
'add': 'edit', |
946
|
|
|
'secondary': 'disabled', |
947
|
|
|
}, |
948
|
|
|
), |
949
|
|
|
), |
950
|
|
|
|
951
|
|
|
BooleanField( |
952
|
|
|
'InvoiceExclude', |
953
|
|
|
default=False, |
954
|
|
|
mode="rw", |
955
|
|
|
read_permission=View, |
956
|
|
|
write_permission=FieldEditInvoiceExclude, |
957
|
|
|
widget=BooleanWidget( |
958
|
|
|
label=_("Invoice Exclude"), |
959
|
|
|
description=_("Should the analyses be excluded from the invoice?"), |
960
|
|
|
render_own_label=True, |
961
|
|
|
visible={ |
962
|
|
|
'add': 'edit', |
963
|
|
|
'header_table': 'visible', |
964
|
|
|
}, |
965
|
|
|
), |
966
|
|
|
), |
967
|
|
|
|
968
|
|
|
# TODO Review permission for this field Analyses |
969
|
|
|
ARAnalysesField( |
970
|
|
|
'Analyses', |
971
|
|
|
required=1, |
972
|
|
|
mode="rw", |
973
|
|
|
read_permission=View, |
974
|
|
|
write_permission=ModifyPortalContent, |
975
|
|
|
widget=ComputedWidget( |
976
|
|
|
visible={ |
977
|
|
|
'edit': 'invisible', |
978
|
|
|
'view': 'invisible', |
979
|
|
|
'sample_registered': { |
980
|
|
|
'view': 'visible', 'edit': 'visible', 'add': 'invisible'}, |
981
|
|
|
} |
982
|
|
|
), |
983
|
|
|
), |
984
|
|
|
|
985
|
|
|
UIDReferenceField( |
986
|
|
|
'Attachment', |
987
|
|
|
multiValued=1, |
988
|
|
|
allowed_types=('Attachment',), |
989
|
|
|
relationship='AnalysisRequestAttachment', |
990
|
|
|
mode="rw", |
991
|
|
|
read_permission=View, |
992
|
|
|
# The addition and removal of attachments is governed by the specific |
993
|
|
|
# permissions "Add Sample Attachment" and "Delete Sample Attachment", |
994
|
|
|
# so we assume here that the write permission is the less restrictive |
995
|
|
|
# "ModifyPortalContent" |
996
|
|
|
write_permission=ModifyPortalContent, |
997
|
|
|
widget=ComputedWidget( |
998
|
|
|
visible={ |
999
|
|
|
'edit': 'invisible', |
1000
|
|
|
'view': 'invisible', |
1001
|
|
|
}, |
1002
|
|
|
) |
1003
|
|
|
), |
1004
|
|
|
|
1005
|
|
|
# This is a virtual field and handled only by AR Add View to allow multi |
1006
|
|
|
# attachment upload in AR Add. It should never contain an own value! |
1007
|
|
|
FileField( |
1008
|
|
|
'_ARAttachment', |
1009
|
|
|
widget=FileWidget( |
1010
|
|
|
label=_("Attachment"), |
1011
|
|
|
description=_("Add one or more attachments to describe the " |
1012
|
|
|
"sample in this sample, or to specify " |
1013
|
|
|
"your request."), |
1014
|
|
|
render_own_label=True, |
1015
|
|
|
visible={ |
1016
|
|
|
'view': 'invisible', |
1017
|
|
|
'add': 'edit', |
1018
|
|
|
'header_table': 'invisible', |
1019
|
|
|
}, |
1020
|
|
|
) |
1021
|
|
|
), |
1022
|
|
|
|
1023
|
|
|
# readonly field |
1024
|
|
|
UIDReferenceField( |
1025
|
|
|
"Invoice", |
1026
|
|
|
allowed_types=("Invoice",), |
1027
|
|
|
mode="rw", |
1028
|
|
|
read_permission=View, |
1029
|
|
|
write_permission=ModifyPortalContent, |
1030
|
|
|
widget=ReferenceWidget( |
1031
|
|
|
label=_( |
1032
|
|
|
"label_sample_invoice", |
1033
|
|
|
default="Invoice"), |
1034
|
|
|
description=_( |
1035
|
|
|
"description_sample_invoice", |
1036
|
|
|
default="Generated invoice for this sample"), |
1037
|
|
|
render_own_label=True, |
1038
|
|
|
readonly=True, |
1039
|
|
|
visible={ |
1040
|
|
|
"add": "invisible", |
1041
|
|
|
"view": "visible", |
1042
|
|
|
}, |
1043
|
|
|
catalog_name=SENAITE_CATALOG, |
1044
|
|
|
query={ |
1045
|
|
|
"is_active": True, |
1046
|
|
|
"sort_on": "sortable_title", |
1047
|
|
|
"sort_order": "ascending" |
1048
|
|
|
}, |
1049
|
|
|
) |
1050
|
|
|
), |
1051
|
|
|
|
1052
|
|
|
DateTimeField( |
1053
|
|
|
'DateReceived', |
1054
|
|
|
mode="rw", |
1055
|
|
|
min="DateSampled", |
1056
|
|
|
max="current", |
1057
|
|
|
read_permission=View, |
1058
|
|
|
write_permission=FieldEditDateReceived, |
1059
|
|
|
widget=DateTimeWidget( |
1060
|
|
|
label=_("Date Sample Received"), |
1061
|
|
|
show_time=True, |
1062
|
|
|
description=_("The date when the sample was received"), |
1063
|
|
|
render_own_label=True, |
1064
|
|
|
), |
1065
|
|
|
), |
1066
|
|
|
|
1067
|
|
|
ComputedField( |
1068
|
|
|
'DatePublished', |
1069
|
|
|
mode="r", |
1070
|
|
|
read_permission=View, |
1071
|
|
|
expression="here.getDatePublished().strftime('%Y-%m-%d %H:%M %p') if here.getDatePublished() else ''", |
1072
|
|
|
widget=DateTimeWidget( |
1073
|
|
|
label=_("Date Published"), |
1074
|
|
|
visible={ |
1075
|
|
|
'edit': 'invisible', |
1076
|
|
|
'add': 'invisible', |
1077
|
|
|
'secondary': 'invisible', |
1078
|
|
|
}, |
1079
|
|
|
), |
1080
|
|
|
), |
1081
|
|
|
|
1082
|
|
|
RemarksField( |
1083
|
|
|
'Remarks', |
1084
|
|
|
read_permission=View, |
1085
|
|
|
write_permission=FieldEditRemarks, |
1086
|
|
|
widget=RemarksWidget( |
1087
|
|
|
label=_("Remarks"), |
1088
|
|
|
description=_("Remarks and comments for this request"), |
1089
|
|
|
render_own_label=True, |
1090
|
|
|
visible={ |
1091
|
|
|
'add': 'edit', |
1092
|
|
|
'header_table': 'invisible', |
1093
|
|
|
}, |
1094
|
|
|
), |
1095
|
|
|
), |
1096
|
|
|
|
1097
|
|
|
FixedPointField( |
1098
|
|
|
'MemberDiscount', |
1099
|
|
|
default_method='getDefaultMemberDiscount', |
1100
|
|
|
mode="rw", |
1101
|
|
|
read_permission=View, |
1102
|
|
|
write_permission=FieldEditMemberDiscount, |
1103
|
|
|
widget=DecimalWidget( |
1104
|
|
|
label=_("Member discount %"), |
1105
|
|
|
description=_("Enter percentage value eg. 33.0"), |
1106
|
|
|
render_own_label=True, |
1107
|
|
|
visible={ |
1108
|
|
|
'add': 'invisible', |
1109
|
|
|
}, |
1110
|
|
|
), |
1111
|
|
|
), |
1112
|
|
|
|
1113
|
|
|
ComputedField( |
1114
|
|
|
'SampleTypeTitle', |
1115
|
|
|
expression="here.getSampleType().Title() if here.getSampleType() " |
1116
|
|
|
"else ''", |
1117
|
|
|
widget=ComputedWidget( |
1118
|
|
|
visible=False, |
1119
|
|
|
), |
1120
|
|
|
), |
1121
|
|
|
|
1122
|
|
|
ComputedField( |
1123
|
|
|
'SamplePointTitle', |
1124
|
|
|
expression="here.getSamplePoint().Title() if here.getSamplePoint() " |
1125
|
|
|
"else ''", |
1126
|
|
|
widget=ComputedWidget( |
1127
|
|
|
visible=False, |
1128
|
|
|
), |
1129
|
|
|
), |
1130
|
|
|
|
1131
|
|
|
ComputedField( |
1132
|
|
|
'ContactUID', |
1133
|
|
|
expression="here.getContact() and here.getContact().UID() or ''", |
1134
|
|
|
widget=ComputedWidget( |
1135
|
|
|
visible=False, |
1136
|
|
|
), |
1137
|
|
|
), |
1138
|
|
|
|
1139
|
|
|
ComputedField( |
1140
|
|
|
'Invoiced', |
1141
|
|
|
expression='here.getInvoice() and True or False', |
1142
|
|
|
default=False, |
1143
|
|
|
widget=ComputedWidget( |
1144
|
|
|
visible=False, |
1145
|
|
|
), |
1146
|
|
|
), |
1147
|
|
|
|
1148
|
|
|
ComputedField( |
1149
|
|
|
'ReceivedBy', |
1150
|
|
|
expression='here.getReceivedBy()', |
1151
|
|
|
default='', |
1152
|
|
|
widget=ComputedWidget(visible=False,), |
1153
|
|
|
), |
1154
|
|
|
|
1155
|
|
|
ComputedField( |
1156
|
|
|
'BatchID', |
1157
|
|
|
expression="here.getBatch().getId() if here.getBatch() else ''", |
1158
|
|
|
widget=ComputedWidget(visible=False), |
1159
|
|
|
), |
1160
|
|
|
|
1161
|
|
|
ComputedField( |
1162
|
|
|
'BatchURL', |
1163
|
|
|
expression="here.getBatch().absolute_url_path() " \ |
1164
|
|
|
"if here.getBatch() else ''", |
1165
|
|
|
widget=ComputedWidget(visible=False), |
1166
|
|
|
), |
1167
|
|
|
|
1168
|
|
|
ComputedField( |
1169
|
|
|
'ContactUsername', |
1170
|
|
|
expression="here.getContact().getUsername() " \ |
1171
|
|
|
"if here.getContact() else ''", |
1172
|
|
|
widget=ComputedWidget(visible=False), |
1173
|
|
|
), |
1174
|
|
|
|
1175
|
|
|
ComputedField( |
1176
|
|
|
'ContactFullName', |
1177
|
|
|
expression="here.getContact().getFullname() " \ |
1178
|
|
|
"if here.getContact() else ''", |
1179
|
|
|
widget=ComputedWidget(visible=False), |
1180
|
|
|
), |
1181
|
|
|
|
1182
|
|
|
ComputedField( |
1183
|
|
|
'ContactEmail', |
1184
|
|
|
expression="here.getContact().getEmailAddress() " \ |
1185
|
|
|
"if here.getContact() else ''", |
1186
|
|
|
widget=ComputedWidget(visible=False), |
1187
|
|
|
), |
1188
|
|
|
|
1189
|
|
|
ComputedField( |
1190
|
|
|
'SampleTypeUID', |
1191
|
|
|
expression="here.getSampleType().UID() " \ |
1192
|
|
|
"if here.getSampleType() else ''", |
1193
|
|
|
widget=ComputedWidget(visible=False), |
1194
|
|
|
), |
1195
|
|
|
|
1196
|
|
|
ComputedField( |
1197
|
|
|
'SamplePointUID', |
1198
|
|
|
expression="here.getSamplePoint().UID() " \ |
1199
|
|
|
"if here.getSamplePoint() else ''", |
1200
|
|
|
widget=ComputedWidget(visible=False), |
1201
|
|
|
), |
1202
|
|
|
ComputedField( |
1203
|
|
|
'StorageLocationUID', |
1204
|
|
|
expression="here.getStorageLocation().UID() " \ |
1205
|
|
|
"if here.getStorageLocation() else ''", |
1206
|
|
|
widget=ComputedWidget(visible=False), |
1207
|
|
|
), |
1208
|
|
|
|
1209
|
|
|
ComputedField( |
1210
|
|
|
'TemplateUID', |
1211
|
|
|
expression="here.getTemplate().UID() if here.getTemplate() else ''", |
1212
|
|
|
widget=ComputedWidget(visible=False), |
1213
|
|
|
), |
1214
|
|
|
|
1215
|
|
|
ComputedField( |
1216
|
|
|
'TemplateURL', |
1217
|
|
|
expression="here.getTemplate().absolute_url_path() " \ |
1218
|
|
|
"if here.getTemplate() else ''", |
1219
|
|
|
widget=ComputedWidget(visible=False), |
1220
|
|
|
), |
1221
|
|
|
|
1222
|
|
|
ComputedField( |
1223
|
|
|
'TemplateTitle', |
1224
|
|
|
expression="here.getTemplate().Title() if here.getTemplate() else ''", |
1225
|
|
|
widget=ComputedWidget(visible=False), |
1226
|
|
|
), |
1227
|
|
|
|
1228
|
|
|
# readonly field |
1229
|
|
|
UIDReferenceField( |
1230
|
|
|
"ParentAnalysisRequest", |
1231
|
|
|
allowed_types=("AnalysisRequest",), |
1232
|
|
|
relationship="AnalysisRequestParentAnalysisRequest", |
1233
|
|
|
mode="rw", |
1234
|
|
|
read_permission=View, |
1235
|
|
|
write_permission=ModifyPortalContent, |
1236
|
|
|
widget=ReferenceWidget( |
1237
|
|
|
label=_( |
1238
|
|
|
"label_sample_parent_sample", |
1239
|
|
|
default="Parent sample"), |
1240
|
|
|
description=_( |
1241
|
|
|
"description_sample_parent_sample", |
1242
|
|
|
default="Reference to parent sample"), |
1243
|
|
|
render_own_label=True, |
1244
|
|
|
readonly=True, |
1245
|
|
|
visible=False, |
1246
|
|
|
catalog_name=SAMPLE_CATALOG, |
1247
|
|
|
query={ |
1248
|
|
|
"is_active": True, |
1249
|
|
|
"sort_on": "sortable_title", |
1250
|
|
|
"sort_order": "ascending" |
1251
|
|
|
}, |
1252
|
|
|
) |
1253
|
|
|
), |
1254
|
|
|
|
1255
|
|
|
# The Primary Sample the current sample was detached from |
1256
|
|
|
UIDReferenceField( |
1257
|
|
|
"DetachedFrom", |
1258
|
|
|
allowed_types=("AnalysisRequest",), |
1259
|
|
|
mode="rw", |
1260
|
|
|
read_permission=View, |
1261
|
|
|
write_permission=ModifyPortalContent, |
1262
|
|
|
widget=ReferenceWidget( |
1263
|
|
|
label=_( |
1264
|
|
|
"label_sample_detached_from", |
1265
|
|
|
default="Detached from sample"), |
1266
|
|
|
description=_( |
1267
|
|
|
"description_sample_detached_from", |
1268
|
|
|
default="Reference to detached sample"), |
1269
|
|
|
render_own_label=True, |
1270
|
|
|
readonly=True, |
1271
|
|
|
visible=False, |
1272
|
|
|
catalog_name=SAMPLE_CATALOG, |
1273
|
|
|
query={ |
1274
|
|
|
"is_active": True, |
1275
|
|
|
"sort_on": "sortable_title", |
1276
|
|
|
"sort_order": "ascending" |
1277
|
|
|
}, |
1278
|
|
|
) |
1279
|
|
|
), |
1280
|
|
|
|
1281
|
|
|
# The Analysis Request the current Analysis Request comes from because of |
1282
|
|
|
# an invalidation of the former |
1283
|
|
|
UIDReferenceField( |
1284
|
|
|
"Invalidated", |
1285
|
|
|
allowed_types=("AnalysisRequest",), |
1286
|
|
|
relationship="AnalysisRequestRetracted", |
1287
|
|
|
mode="rw", |
1288
|
|
|
read_permission=View, |
1289
|
|
|
write_permission=ModifyPortalContent, |
1290
|
|
|
widget=ReferenceWidget( |
1291
|
|
|
label=_( |
1292
|
|
|
"label_sample_retracted", |
1293
|
|
|
default="Retest from sample"), |
1294
|
|
|
description=_( |
1295
|
|
|
"description_sample_retracted", |
1296
|
|
|
default="Reference to retracted sample"), |
1297
|
|
|
render_own_label=True, |
1298
|
|
|
readonly=True, |
1299
|
|
|
visible=False, |
1300
|
|
|
catalog_name=SAMPLE_CATALOG, |
1301
|
|
|
query={ |
1302
|
|
|
"is_active": True, |
1303
|
|
|
"sort_on": "sortable_title", |
1304
|
|
|
"sort_order": "ascending" |
1305
|
|
|
}, |
1306
|
|
|
) |
1307
|
|
|
), |
1308
|
|
|
|
1309
|
|
|
# For comments or results interpretation |
1310
|
|
|
# Old one, to be removed because of the incorporation of |
1311
|
|
|
# ResultsInterpretationDepts (due to LIMS-1628) |
1312
|
|
|
TextField( |
1313
|
|
|
'ResultsInterpretation', |
1314
|
|
|
mode="rw", |
1315
|
|
|
default_content_type='text/html', |
1316
|
|
|
# Input content type for the textfield |
1317
|
|
|
default_output_type='text/x-html-safe', |
1318
|
|
|
# getResultsInterpretation returns a str with html tags |
1319
|
|
|
# to conserve the txt format in the report. |
1320
|
|
|
read_permission=View, |
1321
|
|
|
write_permission=FieldEditResultsInterpretation, |
1322
|
|
|
widget=RichWidget( |
1323
|
|
|
description=_("Comments or results interpretation"), |
1324
|
|
|
label=_("Results Interpretation"), |
1325
|
|
|
size=10, |
1326
|
|
|
allow_file_upload=False, |
1327
|
|
|
default_mime_type='text/x-rst', |
1328
|
|
|
output_mime_type='text/x-html', |
1329
|
|
|
rows=3, |
1330
|
|
|
visible=False), |
1331
|
|
|
), |
1332
|
|
|
|
1333
|
|
|
RecordsField( |
1334
|
|
|
'ResultsInterpretationDepts', |
1335
|
|
|
read_permission=View, |
1336
|
|
|
write_permission=FieldEditResultsInterpretation, |
1337
|
|
|
subfields=('uid', 'richtext'), |
1338
|
|
|
subfield_labels={ |
1339
|
|
|
'uid': _('Department'), |
1340
|
|
|
'richtext': _('Results Interpretation')}, |
1341
|
|
|
widget=RichWidget(visible=False), |
1342
|
|
|
), |
1343
|
|
|
# Custom settings for the assigned analysis services |
1344
|
|
|
# https://jira.bikalabs.com/browse/LIMS-1324 |
1345
|
|
|
# Fields: |
1346
|
|
|
# - uid: Analysis Service UID |
1347
|
|
|
# - hidden: True/False. Hide/Display in results reports |
1348
|
|
|
RecordsField('AnalysisServicesSettings', |
1349
|
|
|
required=0, |
1350
|
|
|
subfields=('uid', 'hidden',), |
1351
|
|
|
widget=ComputedWidget(visible=False), |
1352
|
|
|
), |
1353
|
|
|
StringField( |
1354
|
|
|
'Printed', |
1355
|
|
|
mode="rw", |
1356
|
|
|
read_permission=View, |
1357
|
|
|
widget=StringWidget( |
1358
|
|
|
label=_("Printed"), |
1359
|
|
|
description=_("Indicates if the last SampleReport is printed,"), |
1360
|
|
|
visible=False, |
1361
|
|
|
), |
1362
|
|
|
), |
1363
|
|
|
BooleanField( |
1364
|
|
|
"InternalUse", |
1365
|
|
|
mode="rw", |
1366
|
|
|
required=0, |
1367
|
|
|
default=False, |
1368
|
|
|
read_permission=View, |
1369
|
|
|
write_permission=FieldEditInternalUse, |
1370
|
|
|
widget=BooleanWidget( |
1371
|
|
|
label=_("Internal use"), |
1372
|
|
|
description=_("Mark the sample for internal use only. This means " |
1373
|
|
|
"it is only accessible to lab personnel and not to " |
1374
|
|
|
"clients."), |
1375
|
|
|
format="radio", |
1376
|
|
|
render_own_label=True, |
1377
|
|
|
visible={'add': 'edit'} |
1378
|
|
|
), |
1379
|
|
|
), |
1380
|
|
|
|
1381
|
|
|
# Initial conditions for analyses set on Sample registration |
1382
|
|
|
RecordsField( |
1383
|
|
|
"ServiceConditions", |
1384
|
|
|
widget=ComputedWidget(visible=False) |
1385
|
|
|
), |
1386
|
|
|
|
1387
|
|
|
# Number of samples to create on add form |
1388
|
|
|
IntegerField( |
1389
|
|
|
"NumSamples", |
1390
|
|
|
default=1, |
1391
|
|
|
widget=IntegerWidget( |
1392
|
|
|
label=_( |
1393
|
|
|
u"label_analysisrequest_numsamples", |
1394
|
|
|
default=u"Number of samples" |
1395
|
|
|
), |
1396
|
|
|
description=_( |
1397
|
|
|
u"description_analysisrequest_numsamples", |
1398
|
|
|
default=u"Number of samples to create with the information " |
1399
|
|
|
u"provided"), |
1400
|
|
|
# This field is only visible in add sample form |
1401
|
|
|
visible={ |
1402
|
|
|
"add": "edit", |
1403
|
|
|
"view": "invisible", |
1404
|
|
|
"header_table": "invisible", |
1405
|
|
|
"secondary": "invisible", |
1406
|
|
|
}, |
1407
|
|
|
render_own_label=True, |
1408
|
|
|
), |
1409
|
|
|
), |
1410
|
|
|
)) |
1411
|
|
|
|
1412
|
|
|
|
1413
|
|
|
# Some schema rearrangement |
1414
|
|
|
schema['title'].required = False |
1415
|
|
|
schema['id'].widget.visible = False |
1416
|
|
|
schema['title'].widget.visible = False |
1417
|
|
|
schema.moveField('Client', before='Contact') |
1418
|
|
|
schema.moveField('ResultsInterpretation', pos='bottom') |
1419
|
|
|
schema.moveField('ResultsInterpretationDepts', pos='bottom') |
1420
|
|
|
schema.moveField("PrimaryAnalysisRequest", before="Client") |
1421
|
|
|
|
1422
|
|
|
|
1423
|
|
|
class AnalysisRequest(BaseFolder, ClientAwareMixin): |
1424
|
|
|
implements(IAnalysisRequest, ICancellable) |
1425
|
|
|
security = ClassSecurityInfo() |
1426
|
|
|
displayContentsTab = False |
1427
|
|
|
schema = schema |
|
|
|
|
1428
|
|
|
|
1429
|
|
|
def _getCatalogTool(self): |
1430
|
|
|
from bika.lims.catalog import getCatalog |
1431
|
|
|
return getCatalog(self) |
1432
|
|
|
|
1433
|
|
|
def Title(self): |
1434
|
|
|
""" Return the Request ID as title """ |
1435
|
|
|
return self.getId() |
1436
|
|
|
|
1437
|
|
|
def sortable_title(self): |
1438
|
|
|
""" |
1439
|
|
|
Some lists expects this index |
1440
|
|
|
""" |
1441
|
|
|
return self.getId() |
1442
|
|
|
|
1443
|
|
|
def Description(self): |
1444
|
|
|
"""Returns searchable data as Description""" |
1445
|
|
|
descr = " ".join((self.getId(), self.aq_parent.Title())) |
1446
|
|
|
return safe_unicode(descr).encode('utf-8') |
1447
|
|
|
|
1448
|
|
|
def setSpecification(self, value): |
1449
|
|
|
"""Sets the Specifications and ResultRange values |
1450
|
|
|
""" |
1451
|
|
|
current_spec = self.getRawSpecification() |
1452
|
|
|
if value and current_spec == api.get_uid(value): |
1453
|
|
|
# Specification has not changed, preserve the current value to |
1454
|
|
|
# prevent result ranges (both from Sample and from analyses) from |
1455
|
|
|
# being overriden |
1456
|
|
|
return |
1457
|
|
|
|
1458
|
|
|
self.getField("Specification").set(self, value) |
1459
|
|
|
|
1460
|
|
|
# Set the value for field ResultsRange, cause Specification is only |
1461
|
|
|
# used as a template: all the results range logic relies on |
1462
|
|
|
# ResultsRange field, so changes in setup's Specification object won't |
1463
|
|
|
# have effect to already created samples |
1464
|
|
|
spec = self.getSpecification() |
1465
|
|
|
if spec: |
1466
|
|
|
# Update only results ranges if specs is not None, so results |
1467
|
|
|
# ranges manually set previously (e.g. via ManageAnalyses view) are |
1468
|
|
|
# preserved unless a new Specification overrides them |
1469
|
|
|
self.setResultsRange(spec.getResultsRange(), recursive=False) |
1470
|
|
|
|
1471
|
|
|
# Cascade the changes to partitions, but only to those that are in a |
1472
|
|
|
# status in which the specification can be updated. This prevents the |
1473
|
|
|
# re-assignment of Specifications to already verified or published |
1474
|
|
|
# samples |
1475
|
|
|
permission = self.getField("Specification").write_permission |
1476
|
|
|
for descendant in self.getDescendants(): |
1477
|
|
|
if check_permission(permission, descendant): |
1478
|
|
|
descendant.setSpecification(spec) |
1479
|
|
|
|
1480
|
|
|
def setResultsRange(self, value, recursive=True): |
1481
|
|
|
"""Sets the results range for this Sample and analyses it contains. |
1482
|
|
|
If recursive is True, then applies the results ranges to descendants |
1483
|
|
|
(partitions) as well as their analyses too |
1484
|
|
|
""" |
1485
|
|
|
# Set Results Range to the Sample |
1486
|
|
|
field = self.getField("ResultsRange") |
1487
|
|
|
field.set(self, value) |
1488
|
|
|
|
1489
|
|
|
# Set Results Range to analyses |
1490
|
|
|
for analysis in self.objectValues("Analysis"): |
1491
|
|
|
if not ISubmitted.providedBy(analysis): |
1492
|
|
|
service_uid = analysis.getRawAnalysisService() |
1493
|
|
|
result_range = field.get(self, search_by=service_uid) |
1494
|
|
|
analysis.setResultsRange(result_range) |
1495
|
|
|
analysis.reindexObject() |
1496
|
|
|
|
1497
|
|
|
if recursive: |
1498
|
|
|
# Cascade the changes to partitions |
1499
|
|
|
permission = self.getField("Specification").write_permission |
1500
|
|
|
for descendant in self.getDescendants(): |
1501
|
|
|
if check_permission(permission, descendant): |
1502
|
|
|
descendant.setResultsRange(value) |
1503
|
|
|
|
1504
|
|
|
def setProfiles(self, value): |
1505
|
|
|
"""Set Analysis Profiles to the Sample |
1506
|
|
|
""" |
1507
|
|
|
if not isinstance(value, (list, tuple)): |
1508
|
|
|
value = [value] |
1509
|
|
|
# filter out empties |
1510
|
|
|
value = filter(None, value) |
1511
|
|
|
# ensure we have UIDs |
1512
|
|
|
uids = map(api.get_uid, value) |
1513
|
|
|
# get the current set profiles |
1514
|
|
|
current_profiles = self.getRawProfiles() |
1515
|
|
|
# return immediately if nothing changed |
1516
|
|
|
if current_profiles == uids: |
1517
|
|
|
return |
1518
|
|
|
|
1519
|
|
|
# Don't add analyses from profiles during sample creation. |
1520
|
|
|
# In this case the required analyses are already extracted from all |
1521
|
|
|
# profiles. |
1522
|
|
|
# |
1523
|
|
|
# Also only add analyses if a profile (value) is selected: |
1524
|
|
|
# https://github.com/senaite/senaite.core/pull/2672 |
1525
|
|
|
if value and not api.is_temporary(self): |
1526
|
|
|
# get the profiles |
1527
|
|
|
profiles = map(api.get_object_by_uid, uids) |
1528
|
|
|
|
1529
|
|
|
# create a mapping of service UID -> list of analysis review states |
1530
|
|
|
assigned_services = defaultdict(list) |
1531
|
|
|
for analysis in self.getAnalyses(): |
1532
|
|
|
service_uid = analysis.getServiceUID |
1533
|
|
|
review_status = api.get_review_status(analysis) |
1534
|
|
|
assigned_services[service_uid].append(review_status) |
1535
|
|
|
|
1536
|
|
|
# create a list of all open services that need to be added |
1537
|
|
|
# NOTE: missing services will be otherwise removed! |
1538
|
|
|
services_to_add = [k for k, v in assigned_services.items() if any( |
1539
|
|
|
filter(lambda rs: rs not in DETACHED_STATES, v))] |
1540
|
|
|
|
1541
|
|
|
for profile in profiles: |
1542
|
|
|
for service_uid in profile.getRawServiceUIDs(): |
1543
|
|
|
# skip previously assigned services, as they are already |
1544
|
|
|
# added above |
1545
|
|
|
if service_uid in assigned_services.keys(): |
1546
|
|
|
continue |
1547
|
|
|
# add any new service |
1548
|
|
|
services_to_add.append(service_uid) |
1549
|
|
|
|
1550
|
|
|
# set all analyses |
1551
|
|
|
self.setAnalyses(list(services_to_add)) |
1552
|
|
|
|
1553
|
|
|
# set the profiles value |
1554
|
|
|
self.getField("Profiles").set(self, value) |
1555
|
|
|
|
1556
|
|
|
# apply hidden services *after* the profiles have been set |
1557
|
|
|
apply_hidden_services(self) |
1558
|
|
|
|
1559
|
|
|
def getClient(self): |
1560
|
|
|
"""Returns the client this object is bound to. We override getClient |
1561
|
|
|
from ClientAwareMixin because the "Client" schema field is only used to |
1562
|
|
|
allow the user to set the client while creating the Sample through |
1563
|
|
|
Sample Add form, but cannot be changed afterwards. The Sample is |
1564
|
|
|
created directly inside the selected client folder on submit |
1565
|
|
|
""" |
1566
|
|
|
parent = self.aq_parent |
1567
|
|
|
if IClient.providedBy(parent): |
1568
|
|
|
return parent |
1569
|
|
|
elif IBatch.providedBy(parent): |
1570
|
|
|
return parent.getClient() |
1571
|
|
|
# Fallback to UID reference field value |
1572
|
|
|
field = self.getField("Client") |
1573
|
|
|
return field.get(self) |
1574
|
|
|
|
1575
|
|
|
@deprecated("Will be removed in SENAITE 3.0") |
1576
|
|
|
def getProfilesURL(self): |
1577
|
|
|
"""Returns a list of all profile URLs |
1578
|
|
|
|
1579
|
|
|
Backwards compatibility for removed computed field: |
1580
|
|
|
https://github.com/senaite/senaite.core/pull/2213 |
1581
|
|
|
""" |
1582
|
|
|
return [profile.absolute_url_path() for profile in self.getProfiles()] |
1583
|
|
|
|
1584
|
|
|
@deprecated("Please use getRawProfiles instead. Will be removed in SENAITE 3.0") |
1585
|
|
|
def getProfilesUID(self): |
1586
|
|
|
"""Returns a list of all profile UIDs |
1587
|
|
|
|
1588
|
|
|
Backwards compatibility for removed computed field: |
1589
|
|
|
https://github.com/senaite/senaite.core/pull/2213 |
1590
|
|
|
""" |
1591
|
|
|
return self.getRawProfiles() |
1592
|
|
|
|
1593
|
|
|
def getProfilesTitle(self): |
1594
|
|
|
"""Returns a list of all profile titles |
1595
|
|
|
|
1596
|
|
|
Backwards compatibility for removed computed field: |
1597
|
|
|
https://github.com/senaite/senaite.core/pull/2213 |
1598
|
|
|
""" |
1599
|
|
|
return [profile.Title() for profile in self.getProfiles()] |
1600
|
|
|
|
1601
|
|
|
def getProfilesTitleStr(self, separator=", "): |
1602
|
|
|
"""Returns a comma-separated string withg the titles of the profiles |
1603
|
|
|
assigned to this Sample. Used to populate a metadata field |
1604
|
|
|
""" |
1605
|
|
|
return separator.join(self.getProfilesTitle()) |
1606
|
|
|
|
1607
|
|
|
def getAnalysisService(self): |
1608
|
|
|
proxies = self.getAnalyses(full_objects=False) |
1609
|
|
|
value = set() |
1610
|
|
|
for proxy in proxies: |
1611
|
|
|
value.add(proxy.Title) |
1612
|
|
|
return list(value) |
1613
|
|
|
|
1614
|
|
|
def getAnalysts(self): |
1615
|
|
|
proxies = self.getAnalyses(full_objects=True) |
1616
|
|
|
value = [] |
1617
|
|
|
for proxy in proxies: |
1618
|
|
|
val = proxy.getAnalyst() |
1619
|
|
|
if val not in value: |
1620
|
|
|
value.append(val) |
1621
|
|
|
return value |
1622
|
|
|
|
1623
|
|
|
def getDistrict(self): |
1624
|
|
|
client = self.aq_parent |
1625
|
|
|
return client.getDistrict() |
1626
|
|
|
|
1627
|
|
|
def getProvince(self): |
1628
|
|
|
client = self.aq_parent |
1629
|
|
|
return client.getProvince() |
1630
|
|
|
|
1631
|
|
|
@security.public |
1632
|
|
|
def getBatch(self): |
1633
|
|
|
# The parent type may be "Batch" during ar_add. |
1634
|
|
|
# This function fills the hidden field in ar_add.pt |
1635
|
|
|
if self.aq_parent.portal_type == 'Batch': |
1636
|
|
|
return self.aq_parent |
1637
|
|
|
else: |
1638
|
|
|
return self.Schema()['Batch'].get(self) |
1639
|
|
|
|
1640
|
|
|
@security.public |
1641
|
|
|
def getBatchUID(self): |
1642
|
|
|
batch = self.getBatch() |
1643
|
|
|
if batch: |
1644
|
|
|
return batch.UID() |
1645
|
|
|
|
1646
|
|
|
@security.public |
1647
|
|
|
def setBatch(self, value=None): |
1648
|
|
|
original_value = self.Schema().getField('Batch').get(self) |
1649
|
|
|
if original_value != value: |
1650
|
|
|
self.Schema().getField('Batch').set(self, value) |
1651
|
|
|
|
1652
|
|
|
def getDefaultMemberDiscount(self): |
1653
|
|
|
"""Compute default member discount if it applies |
1654
|
|
|
""" |
1655
|
|
|
if hasattr(self, 'getMemberDiscountApplies'): |
1656
|
|
|
if self.getMemberDiscountApplies(): |
1657
|
|
|
settings = self.bika_setup |
1658
|
|
|
return settings.getMemberDiscount() |
1659
|
|
|
else: |
1660
|
|
|
return "0.00" |
1661
|
|
|
|
1662
|
|
|
@security.public |
1663
|
|
|
def getAnalysesNum(self): |
1664
|
|
|
""" Returns an array with the number of analyses for the current AR in |
1665
|
|
|
different statuses, like follows: |
1666
|
|
|
[verified, total, not_submitted, to_be_verified] |
1667
|
|
|
""" |
1668
|
|
|
an_nums = [0, 0, 0, 0] |
1669
|
|
|
for analysis in self.getAnalyses(): |
1670
|
|
|
review_state = analysis.review_state |
1671
|
|
|
if review_state in ['retracted', 'rejected', 'cancelled']: |
1672
|
|
|
continue |
1673
|
|
|
if review_state == 'to_be_verified': |
1674
|
|
|
an_nums[3] += 1 |
1675
|
|
|
elif review_state in ['published', 'verified']: |
1676
|
|
|
an_nums[0] += 1 |
1677
|
|
|
else: |
1678
|
|
|
an_nums[2] += 1 |
1679
|
|
|
an_nums[1] += 1 |
1680
|
|
|
return an_nums |
1681
|
|
|
|
1682
|
|
|
@security.public |
1683
|
|
|
def getResponsible(self): |
1684
|
|
|
"""Return all manager info of responsible departments |
1685
|
|
|
""" |
1686
|
|
|
managers = {} |
1687
|
|
|
for department in self.getDepartments(): |
1688
|
|
|
manager = department.getManager() |
1689
|
|
|
if manager is None: |
1690
|
|
|
continue |
1691
|
|
|
manager_id = manager.getId() |
1692
|
|
|
if manager_id not in managers: |
1693
|
|
|
managers[manager_id] = {} |
1694
|
|
|
managers[manager_id]['salutation'] = safe_unicode( |
1695
|
|
|
manager.getSalutation()) |
1696
|
|
|
managers[manager_id]['name'] = safe_unicode( |
1697
|
|
|
manager.getFullname()) |
1698
|
|
|
managers[manager_id]['email'] = safe_unicode( |
1699
|
|
|
manager.getEmailAddress()) |
1700
|
|
|
managers[manager_id]['phone'] = safe_unicode( |
1701
|
|
|
manager.getBusinessPhone()) |
1702
|
|
|
managers[manager_id]['job_title'] = safe_unicode( |
1703
|
|
|
manager.getJobTitle()) |
1704
|
|
|
if manager.getSignature(): |
1705
|
|
|
managers[manager_id]['signature'] = \ |
1706
|
|
|
'{}/Signature'.format(manager.absolute_url()) |
1707
|
|
|
else: |
1708
|
|
|
managers[manager_id]['signature'] = False |
1709
|
|
|
managers[manager_id]['departments'] = '' |
1710
|
|
|
mngr_dept = managers[manager_id]['departments'] |
1711
|
|
|
if mngr_dept: |
1712
|
|
|
mngr_dept += ', ' |
1713
|
|
|
mngr_dept += safe_unicode(department.Title()) |
1714
|
|
|
managers[manager_id]['departments'] = mngr_dept |
1715
|
|
|
mngr_keys = managers.keys() |
1716
|
|
|
mngr_info = {'ids': mngr_keys, 'dict': managers} |
1717
|
|
|
|
1718
|
|
|
return mngr_info |
1719
|
|
|
|
1720
|
|
|
@security.public |
1721
|
|
|
def getManagers(self): |
1722
|
|
|
"""Return all managers of responsible departments |
1723
|
|
|
""" |
1724
|
|
|
manager_ids = [] |
1725
|
|
|
manager_list = [] |
1726
|
|
|
for department in self.getDepartments(): |
1727
|
|
|
manager = department.getManager() |
1728
|
|
|
if manager is None: |
1729
|
|
|
continue |
1730
|
|
|
manager_id = manager.getId() |
1731
|
|
|
if manager_id not in manager_ids: |
1732
|
|
|
manager_ids.append(manager_id) |
1733
|
|
|
manager_list.append(manager) |
1734
|
|
|
return manager_list |
1735
|
|
|
|
1736
|
|
|
def getDueDate(self): |
1737
|
|
|
"""Returns the earliest due date of the analyses this Analysis Request |
1738
|
|
|
contains.""" |
1739
|
|
|
due_dates = map(lambda an: an.getDueDate, self.getAnalyses()) |
1740
|
|
|
return due_dates and min(due_dates) or None |
1741
|
|
|
|
1742
|
|
|
security.declareProtected(View, 'getLate') |
1743
|
|
|
|
1744
|
|
|
def getLate(self): |
1745
|
|
|
"""Return True if there is at least one late analysis in this Request |
1746
|
|
|
""" |
1747
|
|
|
for analysis in self.getAnalyses(): |
1748
|
|
|
if analysis.review_state == "retracted": |
1749
|
|
|
continue |
1750
|
|
|
analysis_obj = api.get_object(analysis) |
1751
|
|
|
if analysis_obj.isLateAnalysis(): |
1752
|
|
|
return True |
1753
|
|
|
return False |
1754
|
|
|
|
1755
|
|
|
def getRawReports(self): |
1756
|
|
|
"""Returns UIDs of reports with a reference to this sample |
1757
|
|
|
|
1758
|
|
|
see: ARReport.ContainedAnalysisRequests field |
1759
|
|
|
|
1760
|
|
|
:returns: List of report UIDs |
1761
|
|
|
""" |
1762
|
|
|
return get_backreferences(self, "ARReportAnalysisRequest") |
1763
|
|
|
|
1764
|
|
|
def getReports(self): |
1765
|
|
|
"""Returns a list of report objects |
1766
|
|
|
|
1767
|
|
|
:returns: List of report objects |
1768
|
|
|
""" |
1769
|
|
|
return list(map(api.get_object, self.getRawReports())) |
1770
|
|
|
|
1771
|
|
|
def getPrinted(self): |
1772
|
|
|
""" returns "0", "1" or "2" to indicate Printed state. |
1773
|
|
|
0 -> Never printed. |
1774
|
|
|
1 -> Printed after last publish |
1775
|
|
|
2 -> Printed but republished afterwards. |
1776
|
|
|
""" |
1777
|
|
|
if not self.getDatePublished(): |
1778
|
|
|
return "0" |
1779
|
|
|
|
1780
|
|
|
report_uids = self.getRawReports() |
1781
|
|
|
if not report_uids: |
1782
|
|
|
return "0" |
1783
|
|
|
|
1784
|
|
|
last_report = api.get_object(report_uids[-1]) |
1785
|
|
|
if last_report.getDatePrinted(): |
1786
|
|
|
return "1" |
1787
|
|
|
|
1788
|
|
|
for report_uid in report_uids[:-1]: |
1789
|
|
|
report = api.get_object(report_uid) |
1790
|
|
|
if report.getDatePrinted(): |
1791
|
|
|
return "2" |
1792
|
|
|
|
1793
|
|
|
return "0" |
1794
|
|
|
|
1795
|
|
|
@security.protected(View) |
1796
|
|
|
def getBillableItems(self): |
1797
|
|
|
"""Returns the items to be billed |
1798
|
|
|
""" |
1799
|
|
|
# Assigned profiles |
1800
|
|
|
profiles = self.getProfiles() |
1801
|
|
|
# Billable profiles which have a fixed price set |
1802
|
|
|
billable_profiles = filter( |
1803
|
|
|
lambda pr: pr.getUseAnalysisProfilePrice(), profiles) |
1804
|
|
|
# All services contained in the billable profiles |
1805
|
|
|
billable_profile_services = functools.reduce(lambda a, b: a+b, map( |
1806
|
|
|
lambda profile: profile.getServices(), billable_profiles), []) |
1807
|
|
|
# Keywords of the contained services |
1808
|
|
|
billable_service_keys = map( |
1809
|
|
|
lambda s: s.getKeyword(), set(billable_profile_services)) |
1810
|
|
|
# Billable items contain billable profiles and single selected analyses |
1811
|
|
|
billable_items = billable_profiles |
1812
|
|
|
# Get the analyses to be billed |
1813
|
|
|
exclude_rs = ["retracted", "rejected"] |
1814
|
|
|
for analysis in self.getAnalyses(is_active=True): |
1815
|
|
|
if analysis.review_state in exclude_rs: |
1816
|
|
|
continue |
1817
|
|
|
if analysis.getKeyword in billable_service_keys: |
1818
|
|
|
continue |
1819
|
|
|
billable_items.append(api.get_object(analysis)) |
1820
|
|
|
return billable_items |
1821
|
|
|
|
1822
|
|
|
@security.protected(View) |
1823
|
|
|
def getSubtotal(self): |
1824
|
|
|
"""Compute Subtotal (without member discount and without vat) |
1825
|
|
|
""" |
1826
|
|
|
return sum([Decimal(obj.getPrice()) for obj in self.getBillableItems()]) |
1827
|
|
|
|
1828
|
|
|
@security.protected(View) |
1829
|
|
|
def getSubtotalVATAmount(self): |
1830
|
|
|
"""Compute VAT amount without member discount |
1831
|
|
|
""" |
1832
|
|
|
return sum([Decimal(o.getVATAmount()) for o in self.getBillableItems()]) |
1833
|
|
|
|
1834
|
|
|
@security.protected(View) |
1835
|
|
|
def getSubtotalTotalPrice(self): |
1836
|
|
|
"""Compute the price with VAT but no member discount |
1837
|
|
|
""" |
1838
|
|
|
return self.getSubtotal() + self.getSubtotalVATAmount() |
1839
|
|
|
|
1840
|
|
|
@security.protected(View) |
1841
|
|
|
def getDiscountAmount(self): |
1842
|
|
|
"""It computes and returns the analysis service's discount amount |
1843
|
|
|
without VAT |
1844
|
|
|
""" |
1845
|
|
|
has_client_discount = self.aq_parent.getMemberDiscountApplies() |
1846
|
|
|
if has_client_discount: |
1847
|
|
|
discount = Decimal(self.getDefaultMemberDiscount()) |
1848
|
|
|
return Decimal(self.getSubtotal() * discount / 100) |
1849
|
|
|
else: |
1850
|
|
|
return 0 |
1851
|
|
|
|
1852
|
|
|
@security.protected(View) |
1853
|
|
|
def getVATAmount(self): |
1854
|
|
|
"""It computes the VAT amount from (subtotal-discount.)*VAT/100, but |
1855
|
|
|
each analysis has its own VAT! |
1856
|
|
|
|
1857
|
|
|
:returns: the analysis request VAT amount with the discount |
1858
|
|
|
""" |
1859
|
|
|
has_client_discount = self.aq_parent.getMemberDiscountApplies() |
1860
|
|
|
VATAmount = self.getSubtotalVATAmount() |
1861
|
|
|
if has_client_discount: |
1862
|
|
|
discount = Decimal(self.getDefaultMemberDiscount()) |
1863
|
|
|
return Decimal((1 - discount / 100) * VATAmount) |
1864
|
|
|
else: |
1865
|
|
|
return VATAmount |
1866
|
|
|
|
1867
|
|
|
@security.protected(View) |
1868
|
|
|
def getTotalPrice(self): |
1869
|
|
|
"""It gets the discounted price from analyses and profiles to obtain the |
1870
|
|
|
total value with the VAT and the discount applied |
1871
|
|
|
|
1872
|
|
|
:returns: analysis request's total price including VATs and discounts |
1873
|
|
|
""" |
1874
|
|
|
price = (self.getSubtotal() - self.getDiscountAmount() + |
1875
|
|
|
self.getVATAmount()) |
1876
|
|
|
return price |
1877
|
|
|
|
1878
|
|
|
getTotal = getTotalPrice |
1879
|
|
|
|
1880
|
|
|
@security.protected(ManageInvoices) |
1881
|
|
|
def createInvoice(self, pdf): |
1882
|
|
|
"""Issue invoice |
1883
|
|
|
""" |
1884
|
|
|
client = self.getClient() |
1885
|
|
|
invoice = self.getInvoice() |
1886
|
|
|
if not invoice: |
1887
|
|
|
invoice = _createObjectByType("Invoice", client, tmpID()) |
1888
|
|
|
invoice.edit( |
1889
|
|
|
AnalysisRequest=self, |
1890
|
|
|
Client=client, |
1891
|
|
|
InvoiceDate=DateTime(), |
1892
|
|
|
InvoicePDF=pdf |
1893
|
|
|
) |
1894
|
|
|
invoice.processForm() |
1895
|
|
|
self.setInvoice(invoice) |
1896
|
|
|
return invoice |
1897
|
|
|
|
1898
|
|
|
@security.public |
1899
|
|
|
def printInvoice(self, REQUEST=None, RESPONSE=None): |
1900
|
|
|
"""Print invoice |
1901
|
|
|
""" |
1902
|
|
|
invoice = self.getInvoice() |
1903
|
|
|
invoice_url = invoice.absolute_url() |
1904
|
|
|
RESPONSE.redirect('{}/invoice_print'.format(invoice_url)) |
1905
|
|
|
|
1906
|
|
|
@deprecated("Use getVerifiers instead. Will be removed in SENAITE 3.0") |
1907
|
|
|
@security.public |
1908
|
|
|
def getVerifier(self): |
1909
|
|
|
"""Returns the user that verified the whole Analysis Request. Since the |
1910
|
|
|
verification is done automatically as soon as all the analyses it |
1911
|
|
|
contains are verified, this function returns the user that verified the |
1912
|
|
|
last analysis pending. |
1913
|
|
|
""" |
1914
|
|
|
wtool = getToolByName(self, 'portal_workflow') |
1915
|
|
|
mtool = getToolByName(self, 'portal_membership') |
1916
|
|
|
|
1917
|
|
|
verifier = None |
1918
|
|
|
try: |
1919
|
|
|
review_history = wtool.getInfoFor(self, 'review_history') |
1920
|
|
|
except Exception: |
1921
|
|
|
return 'access denied' |
1922
|
|
|
|
1923
|
|
|
if not review_history: |
1924
|
|
|
return 'no history' |
1925
|
|
|
for items in review_history: |
1926
|
|
|
action = items.get('action') |
1927
|
|
|
if action != 'verify': |
1928
|
|
|
continue |
1929
|
|
|
actor = items.get('actor') |
1930
|
|
|
member = mtool.getMemberById(actor) |
1931
|
|
|
verifier = member.getProperty('fullname') |
1932
|
|
|
if verifier is None or verifier == '': |
1933
|
|
|
verifier = actor |
1934
|
|
|
return verifier |
1935
|
|
|
|
1936
|
|
|
@security.public |
1937
|
|
|
def getVerifiersIDs(self): |
1938
|
|
|
"""Returns the ids from users that have verified at least one analysis |
1939
|
|
|
from this Analysis Request |
1940
|
|
|
""" |
1941
|
|
|
verifiers_ids = list() |
1942
|
|
|
for brain in self.getAnalyses(): |
1943
|
|
|
verifiers_ids += brain.getVerificators |
1944
|
|
|
return list(set(verifiers_ids)) |
1945
|
|
|
|
1946
|
|
|
@security.public |
1947
|
|
|
def getVerifiers(self): |
1948
|
|
|
"""Returns the list of lab contacts that have verified at least one |
1949
|
|
|
analysis from this Analysis Request |
1950
|
|
|
""" |
1951
|
|
|
contacts = list() |
1952
|
|
|
for verifier in self.getVerifiersIDs(): |
1953
|
|
|
user = api.get_user(verifier) |
1954
|
|
|
contact = api.get_user_contact(user, ["LabContact"]) |
1955
|
|
|
if contact: |
1956
|
|
|
contacts.append(contact) |
1957
|
|
|
return contacts |
1958
|
|
|
|
1959
|
|
|
security.declarePublic('current_date') |
1960
|
|
|
|
1961
|
|
|
def current_date(self): |
1962
|
|
|
"""return current date |
1963
|
|
|
""" |
1964
|
|
|
# noinspection PyCallingNonCallable |
1965
|
|
|
return DateTime() |
1966
|
|
|
|
1967
|
|
|
def getWorksheets(self, full_objects=False): |
1968
|
|
|
"""Returns the worksheets that contains analyses from this Sample |
1969
|
|
|
""" |
1970
|
|
|
# Get the Analyses UIDs of this Sample |
1971
|
|
|
analyses_uids = map(api.get_uid, self.getAnalyses()) |
1972
|
|
|
if not analyses_uids: |
1973
|
|
|
return [] |
1974
|
|
|
|
1975
|
|
|
# Get the worksheets that contain any of these analyses |
1976
|
|
|
query = dict(getAnalysesUIDs=analyses_uids) |
1977
|
|
|
worksheets = api.search(query, WORKSHEET_CATALOG) |
1978
|
|
|
if full_objects: |
1979
|
|
|
worksheets = map(api.get_object, worksheets) |
1980
|
|
|
return worksheets |
1981
|
|
|
|
1982
|
|
|
def getQCAnalyses(self, review_state=None): |
1983
|
|
|
"""Returns the Quality Control analyses assigned to worksheets that |
1984
|
|
|
contains analyses from this Sample |
1985
|
|
|
""" |
1986
|
|
|
# Get the worksheet uids |
1987
|
|
|
worksheet_uids = map(api.get_uid, self.getWorksheets()) |
1988
|
|
|
if not worksheet_uids: |
1989
|
|
|
return [] |
1990
|
|
|
|
1991
|
|
|
# Get reference qc analyses from these worksheets |
1992
|
|
|
query = dict(portal_type="ReferenceAnalysis", |
1993
|
|
|
getWorksheetUID=worksheet_uids) |
1994
|
|
|
qc_analyses = api.search(query, ANALYSIS_CATALOG) |
1995
|
|
|
|
1996
|
|
|
# Extend with duplicate qc analyses from these worksheets and Sample |
1997
|
|
|
query = dict(portal_type="DuplicateAnalysis", |
1998
|
|
|
getWorksheetUID=worksheet_uids, |
1999
|
|
|
getAncestorsUIDs=[api.get_uid(self)]) |
2000
|
|
|
qc_analyses += api.search(query, ANALYSIS_CATALOG) |
2001
|
|
|
|
2002
|
|
|
# Bail out analyses with a different review_state |
2003
|
|
|
if review_state: |
2004
|
|
|
qc_analyses = filter( |
2005
|
|
|
lambda an: api.get_review_status(an) in review_state, |
2006
|
|
|
qc_analyses |
2007
|
|
|
) |
2008
|
|
|
|
2009
|
|
|
# Return the objects |
2010
|
|
|
return map(api.get_object, qc_analyses) |
2011
|
|
|
|
2012
|
|
|
def isInvalid(self): |
2013
|
|
|
"""return if the Analysis Request has been invalidated |
2014
|
|
|
""" |
2015
|
|
|
workflow = getToolByName(self, 'portal_workflow') |
2016
|
|
|
return workflow.getInfoFor(self, 'review_state') == 'invalid' |
2017
|
|
|
|
2018
|
|
|
def getStorageLocationTitle(self): |
2019
|
|
|
""" A method for AR listing catalog metadata |
2020
|
|
|
:return: Title of Storage Location |
2021
|
|
|
""" |
2022
|
|
|
sl = self.getStorageLocation() |
2023
|
|
|
if sl: |
2024
|
|
|
return sl.Title() |
2025
|
|
|
return '' |
2026
|
|
|
|
2027
|
|
|
def getDatePublished(self): |
2028
|
|
|
""" |
2029
|
|
|
Returns the transition date from the Analysis Request object |
2030
|
|
|
""" |
2031
|
|
|
return getTransitionDate(self, 'publish', return_as_datetime=True) |
2032
|
|
|
|
2033
|
|
|
@security.public |
2034
|
|
|
def getSamplingDeviationTitle(self): |
2035
|
|
|
""" |
2036
|
|
|
It works as a metacolumn. |
2037
|
|
|
""" |
2038
|
|
|
sd = self.getSamplingDeviation() |
2039
|
|
|
if sd: |
2040
|
|
|
return sd.Title() |
2041
|
|
|
return '' |
2042
|
|
|
|
2043
|
|
|
@security.public |
2044
|
|
|
def getSampleConditionTitle(self): |
2045
|
|
|
"""Helper method to access the title of the sample condition |
2046
|
|
|
""" |
2047
|
|
|
obj = self.getSampleCondition() |
2048
|
|
|
if not obj: |
2049
|
|
|
return "" |
2050
|
|
|
return api.get_title(obj) |
2051
|
|
|
|
2052
|
|
|
@security.public |
2053
|
|
|
def getHazardous(self): |
2054
|
|
|
""" |
2055
|
|
|
It works as a metacolumn. |
2056
|
|
|
""" |
2057
|
|
|
sample_type = self.getSampleType() |
2058
|
|
|
if sample_type: |
2059
|
|
|
return sample_type.getHazardous() |
2060
|
|
|
return False |
2061
|
|
|
|
2062
|
|
|
@security.public |
2063
|
|
|
def getSamplingWorkflowEnabled(self): |
2064
|
|
|
"""Returns True if the sample of this Analysis Request has to be |
2065
|
|
|
collected by the laboratory personnel |
2066
|
|
|
""" |
2067
|
|
|
template = self.getTemplate() |
2068
|
|
|
if template: |
2069
|
|
|
return template.getSamplingRequired() |
2070
|
|
|
return self.bika_setup.getSamplingWorkflowEnabled() |
2071
|
|
|
|
2072
|
|
|
def getSamplers(self): |
2073
|
|
|
return getUsers(self, ['Sampler', ]) |
2074
|
|
|
|
2075
|
|
|
def getPreservers(self): |
2076
|
|
|
return getUsers(self, ['Preserver', 'Sampler']) |
2077
|
|
|
|
2078
|
|
|
def getDepartments(self): |
2079
|
|
|
"""Returns a list of the departments assigned to the Analyses |
2080
|
|
|
from this Analysis Request |
2081
|
|
|
""" |
2082
|
|
|
departments = list() |
2083
|
|
|
for analysis in self.getAnalyses(full_objects=True): |
2084
|
|
|
department = analysis.getDepartment() |
2085
|
|
|
if department and department not in departments: |
2086
|
|
|
departments.append(department) |
2087
|
|
|
return departments |
2088
|
|
|
|
2089
|
|
|
def getResultsInterpretationByDepartment(self, department=None): |
2090
|
|
|
"""Returns the results interpretation for this Analysis Request |
2091
|
|
|
and department. If department not set, returns the results |
2092
|
|
|
interpretation tagged as 'General'. |
2093
|
|
|
|
2094
|
|
|
:returns: a dict with the following keys: |
2095
|
|
|
{'uid': <department_uid> or 'general', 'richtext': <text/plain>} |
2096
|
|
|
""" |
2097
|
|
|
uid = department.UID() if department else 'general' |
2098
|
|
|
rows = self.Schema()['ResultsInterpretationDepts'].get(self) |
2099
|
|
|
row = [row for row in rows if row.get('uid') == uid] |
2100
|
|
|
if len(row) > 0: |
2101
|
|
|
row = row[0] |
2102
|
|
|
elif uid == 'general' \ |
2103
|
|
|
and hasattr(self, 'getResultsInterpretation') \ |
2104
|
|
|
and self.getResultsInterpretation(): |
2105
|
|
|
row = {'uid': uid, 'richtext': self.getResultsInterpretation()} |
2106
|
|
|
else: |
2107
|
|
|
row = {'uid': uid, 'richtext': ''} |
2108
|
|
|
return row |
2109
|
|
|
|
2110
|
|
|
def getAnalysisServiceSettings(self, uid): |
2111
|
|
|
"""Returns a dictionary with the settings for the analysis service that |
2112
|
|
|
match with the uid provided. |
2113
|
|
|
|
2114
|
|
|
If there are no settings for the analysis service and |
2115
|
|
|
analysis requests: |
2116
|
|
|
|
2117
|
|
|
1. looks for settings in AR's ARTemplate. If found, returns the |
2118
|
|
|
settings for the AnalysisService set in the Template |
2119
|
|
|
2. If no settings found, looks in AR's ARProfile. If found, returns the |
2120
|
|
|
settings for the AnalysisService from the AR Profile. Otherwise, |
2121
|
|
|
returns a one entry dictionary with only the key 'uid' |
2122
|
|
|
""" |
2123
|
|
|
sets = [s for s in self.getAnalysisServicesSettings() |
2124
|
|
|
if s.get("uid", "") == uid] |
2125
|
|
|
|
2126
|
|
|
# Created by using an ARTemplate? |
2127
|
|
|
if not sets and self.getTemplate(): |
2128
|
|
|
adv = self.getTemplate().getAnalysisServiceSettings(uid) |
2129
|
|
|
sets = [adv] if "hidden" in adv else [] |
2130
|
|
|
|
2131
|
|
|
# Created by using an AR Profile? |
2132
|
|
|
profiles = self.getProfiles() |
2133
|
|
|
if not sets and profiles: |
2134
|
|
|
adv = [profile.getAnalysisServiceSettings(uid) for profile in |
2135
|
|
|
profiles] |
2136
|
|
|
sets = adv if adv[0].get("hidden") else [] |
2137
|
|
|
|
2138
|
|
|
return sets[0] if sets else {"uid": uid} |
2139
|
|
|
|
2140
|
|
|
# TODO Sample Cleanup - Remove (Use getContainer instead) |
2141
|
|
|
def getContainers(self): |
2142
|
|
|
"""This functions returns the containers from the analysis request's |
2143
|
|
|
analyses |
2144
|
|
|
|
2145
|
|
|
:returns: a list with the full partition objects |
2146
|
|
|
""" |
2147
|
|
|
return self.getContainer() and [self.getContainer] or [] |
2148
|
|
|
|
2149
|
|
|
def isAnalysisServiceHidden(self, uid): |
2150
|
|
|
"""Checks if the analysis service that match with the uid provided must |
2151
|
|
|
be hidden in results. If no hidden assignment has been set for the |
2152
|
|
|
analysis in this request, returns the visibility set to the analysis |
2153
|
|
|
itself. |
2154
|
|
|
|
2155
|
|
|
Raise a TypeError if the uid is empty or None |
2156
|
|
|
|
2157
|
|
|
Raise a ValueError if there is no hidden assignment in this request or |
2158
|
|
|
no analysis service found for this uid. |
2159
|
|
|
""" |
2160
|
|
|
if not api.is_uid(uid): |
2161
|
|
|
raise TypeError("Expected a UID, got '%s'" % type(uid)) |
2162
|
|
|
|
2163
|
|
|
# get the local (analysis/template/profile) service settings |
2164
|
|
|
settings = self.getAnalysisServiceSettings(uid) |
2165
|
|
|
|
2166
|
|
|
# TODO: Rethink this logic and remove it afterwards! |
2167
|
|
|
# NOTE: profiles provide always the "hidden" key now! |
2168
|
|
|
if not settings or "hidden" not in settings.keys(): |
2169
|
|
|
# lookup the service |
2170
|
|
|
serv = api.search({"UID": uid}, catalog="uid_catalog") |
2171
|
|
|
if serv and len(serv) == 1: |
2172
|
|
|
return serv[0].getObject().getRawHidden() |
2173
|
|
|
else: |
2174
|
|
|
raise ValueError("{} is not valid".format(uid)) |
2175
|
|
|
|
2176
|
|
|
return settings.get("hidden", False) |
2177
|
|
|
|
2178
|
|
|
def getRejecter(self): |
2179
|
|
|
"""If the Analysis Request has been rejected, returns the user who did the |
2180
|
|
|
rejection. If it was not rejected or the current user has not enough |
2181
|
|
|
privileges to access to this information, returns None. |
2182
|
|
|
""" |
2183
|
|
|
wtool = getToolByName(self, 'portal_workflow') |
2184
|
|
|
mtool = getToolByName(self, 'portal_membership') |
2185
|
|
|
try: |
2186
|
|
|
review_history = wtool.getInfoFor(self, 'review_history') |
2187
|
|
|
except Exception: |
2188
|
|
|
return None |
2189
|
|
|
for items in review_history: |
2190
|
|
|
action = items.get('action') |
2191
|
|
|
if action != 'reject': |
2192
|
|
|
continue |
2193
|
|
|
actor = items.get('actor') |
2194
|
|
|
return mtool.getMemberById(actor) |
2195
|
|
|
return None |
2196
|
|
|
|
2197
|
|
|
def getReceivedBy(self): |
2198
|
|
|
""" |
2199
|
|
|
Returns the User who received the analysis request. |
2200
|
|
|
:returns: the user id |
2201
|
|
|
""" |
2202
|
|
|
user = getTransitionUsers(self, 'receive', last_user=True) |
2203
|
|
|
return user[0] if user else '' |
2204
|
|
|
|
2205
|
|
|
def getDateVerified(self): |
2206
|
|
|
""" |
2207
|
|
|
Returns the date of verification as a DateTime object. |
2208
|
|
|
""" |
2209
|
|
|
return getTransitionDate(self, 'verify', return_as_datetime=True) |
2210
|
|
|
|
2211
|
|
|
@security.public |
2212
|
|
|
def getPrioritySortkey(self): |
2213
|
|
|
"""Returns the key that will be used to sort the current Analysis |
2214
|
|
|
Request based on both its priority and creation date. On ASC sorting, |
2215
|
|
|
the oldest item with highest priority will be displayed. |
2216
|
|
|
:return: string used for sorting |
2217
|
|
|
""" |
2218
|
|
|
priority = self.getPriority() |
2219
|
|
|
created_date = self.created().ISO8601() |
2220
|
|
|
return '%s.%s' % (priority, created_date) |
2221
|
|
|
|
2222
|
|
|
@security.public |
2223
|
|
|
def setPriority(self, value): |
2224
|
|
|
if not value: |
2225
|
|
|
value = self.Schema().getField('Priority').getDefault(self) |
2226
|
|
|
original_value = self.Schema().getField('Priority').get(self) |
2227
|
|
|
if original_value != value: |
2228
|
|
|
self.Schema().getField('Priority').set(self, value) |
2229
|
|
|
self._reindexAnalyses(['getPrioritySortkey'], True) |
2230
|
|
|
|
2231
|
|
|
@security.private |
2232
|
|
|
def _reindexAnalyses(self, idxs=None, update_metadata=False): |
2233
|
|
|
if not idxs and not update_metadata: |
2234
|
|
|
return |
2235
|
|
|
if not idxs: |
2236
|
|
|
idxs = [] |
2237
|
|
|
analyses = self.getAnalyses() |
2238
|
|
|
catalog = getToolByName(self, ANALYSIS_CATALOG) |
2239
|
|
|
for analysis in analyses: |
2240
|
|
|
analysis_obj = analysis.getObject() |
2241
|
|
|
catalog.reindexObject(analysis_obj, idxs=idxs, update_metadata=1) |
2242
|
|
|
|
2243
|
|
|
def getPriorityText(self): |
2244
|
|
|
""" |
2245
|
|
|
This function looks up the priority text from priorities vocab |
2246
|
|
|
:returns: the priority text or '' |
2247
|
|
|
""" |
2248
|
|
|
if self.getPriority(): |
2249
|
|
|
return PRIORITIES.getValue(self.getPriority()) |
2250
|
|
|
return '' |
2251
|
|
|
|
2252
|
|
|
def get_ARAttachment(self): |
2253
|
|
|
return None |
2254
|
|
|
|
2255
|
|
|
def set_ARAttachment(self, value): |
2256
|
|
|
return None |
2257
|
|
|
|
2258
|
|
|
def getRawRetest(self): |
2259
|
|
|
"""Returns the UID of the Analysis Request that has been generated |
2260
|
|
|
automatically because of the retraction of the current Analysis Request |
2261
|
|
|
""" |
2262
|
|
|
relationship = self.getField("Invalidated").relationship |
2263
|
|
|
uids = get_backreferences(self, relationship=relationship) |
2264
|
|
|
return uids[0] if uids else None |
2265
|
|
|
|
2266
|
|
|
def getRetest(self): |
2267
|
|
|
"""Returns the Analysis Request that has been generated automatically |
2268
|
|
|
because of the retraction of the current Analysis Request |
2269
|
|
|
""" |
2270
|
|
|
uid = self.getRawRetest() |
2271
|
|
|
return api.get_object_by_uid(uid, default=None) |
2272
|
|
|
|
2273
|
|
|
def getAncestors(self, all_ancestors=True): |
2274
|
|
|
"""Returns the ancestor(s) of this Analysis Request |
2275
|
|
|
param all_ancestors: include all ancestors, not only the parent |
2276
|
|
|
""" |
2277
|
|
|
parent = self.getParentAnalysisRequest() |
2278
|
|
|
if not parent: |
2279
|
|
|
return list() |
2280
|
|
|
if not all_ancestors: |
2281
|
|
|
return [parent] |
2282
|
|
|
return [parent] + parent.getAncestors(all_ancestors=True) |
2283
|
|
|
|
2284
|
|
|
def isRootAncestor(self): |
2285
|
|
|
"""Returns True if the AR is the root ancestor |
2286
|
|
|
|
2287
|
|
|
:returns: True if the AR has no more parents |
2288
|
|
|
""" |
2289
|
|
|
parent = self.getParentAnalysisRequest() |
2290
|
|
|
if parent: |
2291
|
|
|
return False |
2292
|
|
|
return True |
2293
|
|
|
|
2294
|
|
|
def getDescendants(self, all_descendants=False): |
2295
|
|
|
"""Returns the descendant Analysis Requests |
2296
|
|
|
|
2297
|
|
|
:param all_descendants: recursively include all descendants |
2298
|
|
|
""" |
2299
|
|
|
|
2300
|
|
|
uids = self.getDescendantsUIDs() |
2301
|
|
|
if not uids: |
2302
|
|
|
return [] |
2303
|
|
|
|
2304
|
|
|
# Extract the descendant objects |
2305
|
|
|
descendants = [] |
2306
|
|
|
cat = api.get_tool(UID_CATALOG) |
2307
|
|
|
for brain in cat(UID=uids): |
2308
|
|
|
descendant = api.get_object(brain) |
2309
|
|
|
descendants.append(descendant) |
2310
|
|
|
if all_descendants: |
2311
|
|
|
# Extend with grandchildren |
2312
|
|
|
descendants += descendant.getDescendants(all_descendants=True) |
2313
|
|
|
|
2314
|
|
|
return descendants |
2315
|
|
|
|
2316
|
|
|
def getDescendantsUIDs(self): |
2317
|
|
|
"""Returns the UIDs of the descendant Analysis Requests |
2318
|
|
|
|
2319
|
|
|
This method is used as metadata |
2320
|
|
|
""" |
2321
|
|
|
relationship = self.getField("ParentAnalysisRequest").relationship |
2322
|
|
|
return get_backreferences(self, relationship=relationship) |
2323
|
|
|
|
2324
|
|
|
def isPartition(self): |
2325
|
|
|
"""Returns true if this Analysis Request is a partition |
2326
|
|
|
""" |
2327
|
|
|
return not self.isRootAncestor() |
2328
|
|
|
|
2329
|
|
|
# TODO Remove in favour of getSamplingWorkflowEnabled |
2330
|
|
|
def getSamplingRequired(self): |
2331
|
|
|
"""Returns True if the sample of this Analysis Request has to be |
2332
|
|
|
collected by the laboratory personnel |
2333
|
|
|
""" |
2334
|
|
|
return self.getSamplingWorkflowEnabled() |
2335
|
|
|
|
2336
|
|
|
def isOpen(self): |
2337
|
|
|
"""Returns whether all analyses from this Analysis Request haven't been |
2338
|
|
|
submitted yet (are in a open status) |
2339
|
|
|
""" |
2340
|
|
|
for analysis in self.getAnalyses(): |
2341
|
|
|
if ISubmitted.providedBy(api.get_object(analysis)): |
2342
|
|
|
return False |
2343
|
|
|
return True |
2344
|
|
|
|
2345
|
|
|
def setParentAnalysisRequest(self, value): |
2346
|
|
|
"""Sets a parent analysis request, making the current a partition |
2347
|
|
|
""" |
2348
|
|
|
parent = self.getParentAnalysisRequest() |
2349
|
|
|
self.Schema().getField("ParentAnalysisRequest").set(self, value) |
2350
|
|
|
if not value: |
2351
|
|
|
noLongerProvides(self, IAnalysisRequestPartition) |
2352
|
|
|
if parent and not parent.getDescendants(all_descendants=False): |
2353
|
|
|
noLongerProvides(self, IAnalysisRequestWithPartitions) |
2354
|
|
|
else: |
2355
|
|
|
alsoProvides(self, IAnalysisRequestPartition) |
2356
|
|
|
parent = self.getParentAnalysisRequest() |
2357
|
|
|
alsoProvides(parent, IAnalysisRequestWithPartitions) |
2358
|
|
|
|
2359
|
|
|
def getRawSecondaryAnalysisRequests(self): |
2360
|
|
|
"""Returns the UIDs of the secondary Analysis Requests from this |
2361
|
|
|
Analysis Request |
2362
|
|
|
""" |
2363
|
|
|
relationship = self.getField("PrimaryAnalysisRequest").relationship |
2364
|
|
|
return get_backreferences(self, relationship) |
2365
|
|
|
|
2366
|
|
|
def getSecondaryAnalysisRequests(self): |
2367
|
|
|
"""Returns the secondary analysis requests from this analysis request |
2368
|
|
|
""" |
2369
|
|
|
uids = self.getRawSecondaryAnalysisRequests() |
2370
|
|
|
uc = api.get_tool("uid_catalog") |
2371
|
|
|
return [api.get_object(brain) for brain in uc(UID=uids)] |
2372
|
|
|
|
2373
|
|
|
def setDateReceived(self, value): |
2374
|
|
|
"""Sets the date received to this analysis request and to secondary |
2375
|
|
|
analysis requests |
2376
|
|
|
""" |
2377
|
|
|
self.Schema().getField('DateReceived').set(self, value) |
2378
|
|
|
for secondary in self.getSecondaryAnalysisRequests(): |
2379
|
|
|
secondary.setDateReceived(value) |
2380
|
|
|
secondary.reindexObject(idxs=["getDateReceived", "is_received"]) |
2381
|
|
|
|
2382
|
|
|
def setDateSampled(self, value): |
2383
|
|
|
"""Sets the date sampled to this analysis request and to secondary |
2384
|
|
|
analysis requests |
2385
|
|
|
""" |
2386
|
|
|
self.Schema().getField('DateSampled').set(self, value) |
2387
|
|
|
for secondary in self.getSecondaryAnalysisRequests(): |
2388
|
|
|
secondary.setDateSampled(value) |
2389
|
|
|
secondary.reindexObject(idxs="getDateSampled") |
2390
|
|
|
|
2391
|
|
|
def setSamplingDate(self, value): |
2392
|
|
|
"""Sets the sampling date to this analysis request and to secondary |
2393
|
|
|
analysis requests |
2394
|
|
|
""" |
2395
|
|
|
self.Schema().getField('SamplingDate').set(self, value) |
2396
|
|
|
for secondary in self.getSecondaryAnalysisRequests(): |
2397
|
|
|
secondary.setSamplingDate(value) |
2398
|
|
|
secondary.reindexObject(idxs="getSamplingDate") |
2399
|
|
|
|
2400
|
|
|
def getSelectedRejectionReasons(self): |
2401
|
|
|
"""Returns a list with the selected rejection reasons, if any |
2402
|
|
|
""" |
2403
|
|
|
reasons = self.getRejectionReasons() |
2404
|
|
|
if not reasons: |
2405
|
|
|
return [] |
2406
|
|
|
|
2407
|
|
|
# Return a copy of the list to avoid accidental writes |
2408
|
|
|
reasons = reasons[0].get("selected", [])[:] |
2409
|
|
|
return filter(None, reasons) |
2410
|
|
|
|
2411
|
|
|
def getOtherRejectionReasons(self): |
2412
|
|
|
"""Returns other rejection reasons custom text, if any |
2413
|
|
|
""" |
2414
|
|
|
reasons = self.getRejectionReasons() |
2415
|
|
|
if not reasons: |
2416
|
|
|
return "" |
2417
|
|
|
return reasons[0].get("other", "").strip() |
2418
|
|
|
|
2419
|
|
|
def createAttachment(self, filedata, filename="", **kw): |
2420
|
|
|
"""Add a new attachment to the sample |
2421
|
|
|
|
2422
|
|
|
:param filedata: Raw filedata of the attachment (not base64) |
2423
|
|
|
:param filename: Filename + extension, e.g. `image.png` |
2424
|
|
|
:param kw: Additional keywords set to the attachment |
2425
|
|
|
:returns: New created and added attachment |
2426
|
|
|
""" |
2427
|
|
|
# Add a new Attachment |
2428
|
|
|
attachment = api.create(self.getClient(), "Attachment") |
2429
|
|
|
attachment.setAttachmentFile(filedata) |
2430
|
|
|
fileobj = attachment.getAttachmentFile() |
2431
|
|
|
fileobj.filename = filename |
2432
|
|
|
attachment.edit(**kw) |
2433
|
|
|
attachment.processForm() |
2434
|
|
|
self.addAttachment(attachment) |
2435
|
|
|
return attachment |
2436
|
|
|
|
2437
|
|
|
def addAttachment(self, attachment): |
2438
|
|
|
"""Adds an attachment or a list of attachments to the Analysis Request |
2439
|
|
|
""" |
2440
|
|
|
if not isinstance(attachment, (list, tuple)): |
2441
|
|
|
attachment = [attachment] |
2442
|
|
|
|
2443
|
|
|
original = self.getAttachment() or [] |
2444
|
|
|
|
2445
|
|
|
# Function addAttachment can accept brain, objects or uids |
2446
|
|
|
original = map(api.get_uid, original) |
2447
|
|
|
attachment = map(api.get_uid, attachment) |
2448
|
|
|
|
2449
|
|
|
# Boil out attachments already assigned to this Analysis Request |
2450
|
|
|
attachment = filter(lambda at: at not in original, attachment) |
2451
|
|
|
if attachment: |
2452
|
|
|
original.extend(attachment) |
2453
|
|
|
self.setAttachment(original) |
2454
|
|
|
|
2455
|
|
|
def setResultsInterpretationDepts(self, value): |
2456
|
|
|
"""Custom setter which converts inline images to attachments |
2457
|
|
|
|
2458
|
|
|
https://github.com/senaite/senaite.core/pull/1344 |
2459
|
|
|
|
2460
|
|
|
:param value: list of dictionary records |
2461
|
|
|
""" |
2462
|
|
|
if not isinstance(value, list): |
2463
|
|
|
raise TypeError("Expected list, got {}".format(type(value))) |
2464
|
|
|
|
2465
|
|
|
# Convert inline images -> attachment files |
2466
|
|
|
records = [] |
2467
|
|
|
for record in value: |
2468
|
|
|
# N.B. we might here a ZPublisher record. Converting to dict |
2469
|
|
|
# ensures we can set values as well. |
2470
|
|
|
record = dict(record) |
2471
|
|
|
# Handle inline images in the HTML |
2472
|
|
|
html = record.get("richtext", "") |
2473
|
|
|
# Process inline images to attachments |
2474
|
|
|
record["richtext"] = self.process_inline_images(html) |
2475
|
|
|
# append the processed record for storage |
2476
|
|
|
records.append(record) |
2477
|
|
|
|
2478
|
|
|
# set the field |
2479
|
|
|
self.getField("ResultsInterpretationDepts").set(self, records) |
2480
|
|
|
|
2481
|
|
|
def process_inline_images(self, html): |
2482
|
|
|
"""Convert inline images in the HTML to attachments |
2483
|
|
|
|
2484
|
|
|
https://github.com/senaite/senaite.core/pull/1344 |
2485
|
|
|
|
2486
|
|
|
:param html: The richtext HTML |
2487
|
|
|
:returns: HTML with converted images |
2488
|
|
|
""" |
2489
|
|
|
# Check for inline images |
2490
|
|
|
inline_images = re.findall(IMG_DATA_SRC_RX, html) |
2491
|
|
|
|
2492
|
|
|
# convert to inline images -> attachments |
2493
|
|
|
for data_type, data in inline_images: |
2494
|
|
|
# decode the base64 data to filedata |
2495
|
|
|
filedata = base64.decodestring(data) |
2496
|
|
|
# extract the file extension from the data type |
2497
|
|
|
extension = data_type.lstrip("data:image/").rstrip(";base64,") |
2498
|
|
|
# generate filename + extension |
2499
|
|
|
filename = "attachment.{}".format(extension or "png") |
2500
|
|
|
# create a new attachment |
2501
|
|
|
attachment = self.createAttachment(filedata, filename) |
2502
|
|
|
# ignore the attachment in report |
2503
|
|
|
attachment.setRenderInReport(False) |
2504
|
|
|
# remove the image data base64 prefix |
2505
|
|
|
html = html.replace(data_type, "") |
2506
|
|
|
# remove the base64 image data with the attachment link |
2507
|
|
|
html = html.replace(data, "resolve_attachment?uid={}".format( |
2508
|
|
|
api.get_uid(attachment))) |
2509
|
|
|
size = attachment.getAttachmentFile().get_size() |
2510
|
|
|
logger.info("Converted {:.2f} Kb inline image for {}" |
2511
|
|
|
.format(size/1024, api.get_url(self))) |
2512
|
|
|
|
2513
|
|
|
# convert relative URLs to absolute URLs |
2514
|
|
|
# N.B. This is actually a TinyMCE issue, but hardcoded in Plone: |
2515
|
|
|
# https://www.tiny.cloud/docs/configure/url-handling/#relative_urls |
2516
|
|
|
image_sources = re.findall(IMG_SRC_RX, html) |
2517
|
|
|
|
2518
|
|
|
# add a trailing slash so that urljoin doesn't remove the last segment |
2519
|
|
|
base_url = "{}/".format(api.get_url(self)) |
2520
|
|
|
|
2521
|
|
|
for src in image_sources: |
2522
|
|
|
if re.match("(http|https|data)", src): |
2523
|
|
|
continue |
2524
|
|
|
obj = self.restrictedTraverse(src, None) |
2525
|
|
|
if obj is None: |
2526
|
|
|
continue |
2527
|
|
|
# ensure we have an absolute URL |
2528
|
|
|
html = html.replace(src, urljoin(base_url, src)) |
2529
|
|
|
|
2530
|
|
|
return html |
2531
|
|
|
|
2532
|
|
|
def getProgress(self): |
2533
|
|
|
"""Returns the progress in percent of all analyses |
2534
|
|
|
""" |
2535
|
|
|
review_state = api.get_review_status(self) |
2536
|
|
|
|
2537
|
|
|
# Consider final states as 100% |
2538
|
|
|
# https://github.com/senaite/senaite.core/pull/1544#discussion_r379821841 |
2539
|
|
|
if review_state in FINAL_STATES: |
2540
|
|
|
return 100 |
2541
|
|
|
|
2542
|
|
|
numbers = self.getAnalysesNum() |
2543
|
|
|
|
2544
|
|
|
num_analyses = numbers[1] or 0 |
2545
|
|
|
if not num_analyses: |
2546
|
|
|
return 0 |
2547
|
|
|
|
2548
|
|
|
# [verified, total, not_submitted, to_be_verified] |
2549
|
|
|
num_to_be_verified = numbers[3] or 0 |
2550
|
|
|
num_verified = numbers[0] or 0 |
2551
|
|
|
|
2552
|
|
|
# 2 steps per analysis (submit, verify) plus one step for publish |
2553
|
|
|
max_num_steps = (num_analyses * 2) + 1 |
2554
|
|
|
num_steps = num_to_be_verified + (num_verified * 2) |
2555
|
|
|
if not num_steps: |
2556
|
|
|
return 0 |
2557
|
|
|
if num_steps > max_num_steps: |
2558
|
|
|
return 100 |
2559
|
|
|
return (num_steps * 100) / max_num_steps |
2560
|
|
|
|
2561
|
|
|
def getMaxDateSampled(self): |
2562
|
|
|
"""Returns the maximum date for sample collection |
2563
|
|
|
""" |
2564
|
|
|
if not self.getSamplingWorkflowEnabled(): |
2565
|
|
|
# no future, has to be collected before registration |
2566
|
|
|
return api.get_creation_date(self) |
2567
|
|
|
return datetime.max |
2568
|
|
|
|
2569
|
|
|
def get_profiles_query(self): |
2570
|
|
|
"""Returns the query for the Profiles field, so only profiles without |
2571
|
|
|
any sample type set and those that support the sample's sample type are |
2572
|
|
|
considered |
2573
|
|
|
""" |
2574
|
|
|
sample_type_uid = self.getRawSampleType() |
2575
|
|
|
query = { |
2576
|
|
|
"portal_type": "AnalysisProfile", |
2577
|
|
|
"sampletype_uid": [sample_type_uid, ""], |
2578
|
|
|
"is_active": True, |
2579
|
|
|
"sort_on": "title", |
2580
|
|
|
"sort_order": "ascending", |
2581
|
|
|
} |
2582
|
|
|
return query |
2583
|
|
|
|
2584
|
|
|
def get_sample_points_query(self): |
2585
|
|
|
"""Returns the query for the Sample Point field, so only active sample |
2586
|
|
|
points without any sample type set and those that support the sample's |
2587
|
|
|
sample type are returned |
2588
|
|
|
""" |
2589
|
|
|
sample_type_uid = self.getRawSampleType() |
2590
|
|
|
query = { |
2591
|
|
|
"portal_type": "SamplePoint", |
2592
|
|
|
"sampletype_uid": [sample_type_uid, ""], |
2593
|
|
|
"is_active": True, |
2594
|
|
|
"sort_on": "sortable_title", |
2595
|
|
|
"sort_order": "ascending", |
2596
|
|
|
} |
2597
|
|
|
return query |
2598
|
|
|
|
2599
|
|
|
|
2600
|
|
|
registerType(AnalysisRequest, PROJECTNAME) |
2601
|
|
|
|