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# -*- coding: utf-8 -*- |
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# |
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# This file is part of SENAITE.CORE |
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# |
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# Copyright 2018 by it's authors. |
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# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst. |
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import os |
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import tempfile |
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from email.mime.multipart import MIMEMultipart |
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from email.mime.text import MIMEText |
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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 bika.lims import api |
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from bika.lims import bikaMessageFactory as _ |
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from bika.lims import logger |
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from bika.lims.idserver import renameAfterCreation |
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from bika.lims.interfaces import IAnalysisService, IRoutineAnalysis, \ |
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IAnalysisRequest |
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from bika.lims.utils import attachPdf |
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from bika.lims.utils import changeWorkflowState |
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from bika.lims.utils import createPdf |
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from bika.lims.utils import encode_header |
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from bika.lims.utils import tmpID, copy_field_values |
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from bika.lims.utils import to_utf8 |
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from bika.lims.workflow import doActionFor, ActionHandlerPool, \ |
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push_reindex_to_actions_pool |
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from email.Utils import formataddr |
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def create_analysisrequest(client, request, values, analyses=None, |
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partitions=None, specifications=None, prices=None): |
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"""This is meant for general use and should do everything necessary to |
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create and initialise an AR and any other required auxilliary objects |
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(Sample, SamplePartition, Analysis...) |
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:param client: |
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The container (Client) in which the ARs will be created. |
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:param request: |
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The current Request object. |
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:param values: |
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a dict, where keys are AR|Sample schema field names. |
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:param analyses: |
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Analysis services list. If specified, augments the values in |
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values['Analyses']. May consist of service objects, UIDs, or Keywords. |
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:param partitions: |
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A list of dictionaries, if specific partitions are required. If not |
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specified, AR's sample is created with a single partition. |
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:param specifications: |
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These values augment those found in values['Specifications'] |
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:param prices: |
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Allow different prices to be set for analyses. If not set, prices |
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are read from the associated analysis service. |
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""" |
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# Don't pollute the dict param passed in |
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values = dict(values.items()) |
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# Create new sample or locate the existing for secondary AR |
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secondary = False |
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# TODO Sample Cleanup - Manage secondary ARs properly |
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# Create the Analysis Request |
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ar = _createObjectByType('AnalysisRequest', client, tmpID()) |
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ar.processForm(REQUEST=request, values=values) |
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# Resolve the services uids and set the analyses for this Analysis Request |
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service_uids = get_services_uids(context=client, values=values, |
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analyses_serv=analyses) |
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ar.setAnalyses(service_uids, prices=prices, specs=specifications) |
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# TODO Sample Cleanup - Manage secondary ARs properly |
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if secondary: |
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# Secondary AR does not longer comes from a Sample, rather from an AR. |
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# If the Primary AR has been received, then force the transition of the |
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# secondary to received and set the description/comment in the |
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# transition accordingly so it will be displayed later in the log tab |
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logger.warn("Sync transition for secondary AR is still missing") |
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# Needs to be rejected from the very beginning? |
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reject_field = values.get("RejectionReasons", None) |
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if reject_field and reject_field.get("checkbox", False): |
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doActionFor(ar, "reject") |
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return ar |
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# Try first with no sampling transition, cause it is the most common config |
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success, message = doActionFor(ar, "no_sampling_workflow") |
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if not success: |
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doActionFor(ar, "to_be_sampled") |
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return ar |
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def get_services_uids(context=None, analyses_serv=None, values=None): |
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""" |
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This function returns a list of UIDs from analyses services from its |
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parameters. |
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:param analyses_serv: A list (or one object) of service-related info items. |
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see _resolve_items_to_service_uids() docstring. |
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:type analyses_serv: list |
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:param values: a dict, where keys are AR|Sample schema field names. |
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:type values: dict |
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:returns: a list of analyses services UIDs |
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""" |
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if not analyses_serv: |
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analyses_serv = [] |
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if not values: |
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values = {} |
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if not context or (not analyses_serv and not values): |
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raise RuntimeError( |
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"get_services_uids: Missing or wrong parameters.") |
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# Merge analyses from analyses_serv and values into one list |
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analyses_services = analyses_serv + (values.get("Analyses", None) or []) |
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# It is possible to create analysis requests |
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# by JSON petitions and services, profiles or types aren't allways send. |
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# Sometimes we can get analyses and profiles that doesn't match and we |
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# should act in consequence. |
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# Getting the analyses profiles |
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analyses_profiles = values.get('Profiles', []) |
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if not isinstance(analyses_profiles, (list, tuple)): |
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# Plone converts the incoming form value to a list, if there are |
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# multiple values; but if not, it will send a string (a single UID). |
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analyses_profiles = [analyses_profiles] |
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if not analyses_services and not analyses_profiles: |
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raise RuntimeError( |
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"create_analysisrequest: no analyses services or analysis" |
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" profile provided") |
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# Add analysis services UIDs from profiles to analyses_services variable. |
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if analyses_profiles: |
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uid_catalog = getToolByName(context, 'uid_catalog') |
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for brain in uid_catalog(UID=analyses_profiles): |
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profile = api.get_object(brain) |
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# Only services UIDs |
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services_uids = profile.getRawService() |
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# _resolve_items_to_service_uids() will remove duplicates |
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analyses_services += services_uids |
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return _resolve_items_to_service_uids(analyses_services) |
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def _resolve_items_to_service_uids(items): |
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""" Returns a list of service uids without duplicates based on the items |
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:param items: |
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A list (or one object) of service-related info items. The list can be |
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heterogeneous and each item can be: |
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- Analysis Service instance |
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- Analysis instance |
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- Analysis Service title |
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- Analysis Service UID |
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- Analysis Service Keyword |
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If an item that doesn't match any of the criterias above is found, the |
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function will raise a RuntimeError |
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""" |
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def resolve_to_uid(item): |
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if api.is_uid(item): |
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return item |
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elif IAnalysisService.providedBy(item): |
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return item.UID() |
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elif IRoutineAnalysis.providedBy(item): |
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return item.getServiceUID() |
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bsc = api.get_tool("bika_setup_catalog") |
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brains = bsc(portal_type='AnalysisService', getKeyword=item) |
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if brains: |
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return brains[0].UID |
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brains = bsc(portal_type='AnalysisService', title=item) |
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if brains: |
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return brains[0].UID |
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raise RuntimeError( |
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str(item) + " should be the UID, title, keyword " |
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" or title of an AnalysisService.") |
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# Maybe only a single item was passed |
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if type(items) not in (list, tuple): |
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items = [items, ] |
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service_uids = map(resolve_to_uid, list(set(items))) |
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return list(set(service_uids)) |
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def notify_rejection(analysisrequest): |
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""" |
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Notifies via email that a given Analysis Request has been rejected. The |
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notification is sent to the Client contacts assigned to the Analysis |
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Request. |
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:param analysisrequest: Analysis Request to which the notification refers |
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:returns: true if success |
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""" |
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# We do this imports here to avoid circular dependencies until we deal |
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# better with this notify_rejection thing. |
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from bika.lims.browser.analysisrequest.reject import \ |
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AnalysisRequestRejectPdfView, AnalysisRequestRejectEmailView |
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arid = analysisrequest.getId() |
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# This is the template to render for the pdf that will be either attached |
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# to the email and attached the the Analysis Request for further access |
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tpl = AnalysisRequestRejectPdfView(analysisrequest, analysisrequest.REQUEST) |
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html = tpl.template() |
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html = safe_unicode(html).encode('utf-8') |
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filename = '%s-rejected' % arid |
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pdf_fn = tempfile.mktemp(suffix=".pdf") |
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pdf = createPdf(htmlreport=html, outfile=pdf_fn) |
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if pdf: |
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# Attach the pdf to the Analysis Request |
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attid = analysisrequest.aq_parent.generateUniqueId('Attachment') |
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att = _createObjectByType( |
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"Attachment", analysisrequest.aq_parent, attid) |
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att.setAttachmentFile(open(pdf_fn)) |
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# Awkward workaround to rename the file |
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attf = att.getAttachmentFile() |
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attf.filename = '%s.pdf' % filename |
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att.setAttachmentFile(attf) |
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att.unmarkCreationFlag() |
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renameAfterCreation(att) |
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atts = analysisrequest.getAttachment() + [att] if \ |
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analysisrequest.getAttachment() else [att] |
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atts = [a.UID() for a in atts] |
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analysisrequest.setAttachment(atts) |
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os.remove(pdf_fn) |
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# This is the message for the email's body |
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tpl = AnalysisRequestRejectEmailView( |
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analysisrequest, analysisrequest.REQUEST) |
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html = tpl.template() |
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html = safe_unicode(html).encode('utf-8') |
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# compose and send email. |
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mailto = [] |
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lab = analysisrequest.bika_setup.laboratory |
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mailfrom = formataddr((encode_header(lab.getName()), lab.getEmailAddress())) |
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mailsubject = _('%s has been rejected') % arid |
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contacts = [analysisrequest.getContact()] + analysisrequest.getCCContact() |
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for contact in contacts: |
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name = to_utf8(contact.getFullname()) |
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email = to_utf8(contact.getEmailAddress()) |
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if email: |
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mailto.append(formataddr((encode_header(name), email))) |
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if not mailto: |
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return False |
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mime_msg = MIMEMultipart('related') |
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mime_msg['Subject'] = mailsubject |
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mime_msg['From'] = mailfrom |
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mime_msg['To'] = ','.join(mailto) |
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mime_msg.preamble = 'This is a multi-part MIME message.' |
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msg_txt = MIMEText(html, _subtype='html') |
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mime_msg.attach(msg_txt) |
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if pdf: |
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attachPdf(mime_msg, pdf, filename) |
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try: |
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host = getToolByName(analysisrequest, 'MailHost') |
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host.send(mime_msg.as_string(), immediate=True) |
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except: |
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logger.warning( |
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"Email with subject %s was not sent (SMTP connection error)" % mailsubject) |
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return True |
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def create_retest(ar): |
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"""Creates a retest (Analysis Request) from an invalidated Analysis Request |
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:param ar: The invalidated Analysis Request |
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:type ar: IAnalysisRequest |
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:rtype: IAnalysisRequest |
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""" |
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if not ar: |
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raise ValueError("Source Analysis Request cannot be None") |
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if not IAnalysisRequest.providedBy(ar): |
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raise ValueError("Type not supported: {}".format(repr(type(ar)))) |
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if ar.getRetest(): |
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# Do not allow the creation of another retest! |
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raise ValueError("Retest already set") |
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if not ar.isInvalid(): |
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# Analysis Request must be in 'invalid' state |
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raise ValueError("Cannot do a retest from an invalid Analysis Request" |
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.format(repr(ar))) |
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# 0. Open the actions pool |
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actions_pool = ActionHandlerPool.get_instance() |
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actions_pool.queue_pool() |
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# 1. Create the Retest (Analysis Request) |
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ignore = ['Analyses', 'DatePublished', 'Invalidated', 'Sample'] |
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retest = _createObjectByType("AnalysisRequest", ar.aq_parent, tmpID()) |
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copy_field_values(ar, retest, ignore_fieldnames=ignore) |
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renameAfterCreation(retest) |
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# 2. Copy the analyses from the source |
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intermediate_states = ['retracted', 'reflexed'] |
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for an in ar.getAnalyses(full_objects=True): |
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if (api.get_workflow_status_of(an) in intermediate_states): |
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# Exclude intermediate analyses |
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continue |
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nan = _createObjectByType("Analysis", retest, an.getKeyword()) |
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# Make a copy |
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ignore_fieldnames = ['DataAnalysisPublished'] |
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copy_field_values(an, nan, ignore_fieldnames=ignore_fieldnames) |
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nan.unmarkCreationFlag() |
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push_reindex_to_actions_pool(nan) |
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# 3. Assign the source to retest |
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retest.setInvalidated(ar) |
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# 4. Transition the retest to "sample_received"! |
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changeWorkflowState(retest, 'bika_ar_workflow', 'sample_received') |
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# 5. Initialize analyses |
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for analysis in retest.getAnalyses(full_objects=True): |
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if not IRoutineAnalysis.providedBy(analysis): |
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continue |
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changeWorkflowState(analysis, "bika_analysis_workflow", "unassigned") |
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# 6. Reindex and other stuff |
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push_reindex_to_actions_pool(retest) |
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push_reindex_to_actions_pool(retest.aq_parent) |
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# 7. Resume the actions pool |
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actions_pool.resume() |
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return retest |
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