bika.lims.browser.fields.aranalysesfield.ARAnalysesField.generate_analysis_id() - Code Metrics - Inspection of "Added Datamanager Adapters for Analysis and Sample..." - senaite/senaite.core - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — 2.x ( 8010f1...8ad4a8 )

by Jordi

created 2021-02-15 13:58 UTC

ARAnalysesField.generate_analysis_id() A

↳ Parent: bika.lims.browser.fields.aranalysesfield

Complexity

Conditions

Size

Total Lines	10
Code Lines	8

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	8
dl	0
loc	10
rs	10
c	0
b	0
f	0
cc	2
nop	3

# -*- coding: utf-8 -*-
#
# This file is part of SENAITE.CORE.
#
# SENAITE.CORE is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program; if not, write to the Free Software Foundation, Inc., 51
# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# Copyright 2018-2021 by it's authors.
# Some rights reserved, see README and LICENSE.

import itertools

from AccessControl import ClassSecurityInfo
from AccessControl import Unauthorized
from bika.lims import api
from bika.lims import logger
from bika.lims.api.security import check_permission
from bika.lims.catalog import CATALOG_ANALYSIS_LISTING
from bika.lims.catalog import SETUP_CATALOG
from bika.lims.interfaces import IAnalysis
from bika.lims.interfaces import IAnalysisService
from bika.lims.interfaces import IARAnalysesField
from bika.lims.interfaces import ISubmitted
from bika.lims.permissions import AddAnalysis
from bika.lims.utils.analysis import create_analysis
from Products.Archetypes.public import Field
from Products.Archetypes.public import ObjectField
from Products.Archetypes.Registry import registerField
from zope.interface import implements

DETACHED_STATES = ["cancelled", "retracted", "rejected"]


"""Field to manage Analyses on ARs

Please see the assigned doctest at tests/doctests/ARAnalysesField.rst

Run this test from the buildout directory:

    bin/test test_textual_doctests -t ARAnalysesField
"""


class ARAnalysesField(ObjectField):
    """A field that stores Analyses instances
    """
    implements(IARAnalysesField)

    security = ClassSecurityInfo()
    _properties = Field._properties.copy()
    _properties.update({
        "type": "analyses",
        "default": None,
    })

    security.declarePrivate('get')

    def get(self, instance, **kwargs):
        """Returns a list of Analyses assigned to this AR

        Return a list of catalog brains unless `full_objects=True` is passed.
        Other keyword arguments are passed to bika_analysis_catalog

        :param instance: Analysis Request object
        :param kwargs: Keyword arguments to inject in the search query
        :returns: A list of Analysis Objects/Catalog Brains
        """
        # Do we need to return objects or brains
        full_objects = kwargs.get("full_objects", False)

        # Bail out parameters from kwargs that don't match with indexes
        catalog = api.get_tool(CATALOG_ANALYSIS_LISTING)
        indexes = catalog.indexes()
        query = dict([(k, v) for k, v in kwargs.items() if k in indexes])

        # Do the search against the catalog
        query["portal_type"] = "Analysis"
        query["getAncestorsUIDs"] = api.get_uid(instance)
        brains = catalog(query)
        if full_objects:
            return map(api.get_object, brains)
        return brains

    security.declarePrivate('set')

    def set(self, instance, items, prices=None, specs=None, hidden=None, **kw):
        """Set/Assign Analyses to this AR

        :param items: List of Analysis objects/brains, AnalysisService
                      objects/brains and/or Analysis Service uids
        :type items: list
        :param prices: Mapping of AnalysisService UID -> price
        :type prices: dict
        :param specs: List of AnalysisService UID -> Result Range mappings
        :type specs: list
        :param hidden: List of AnalysisService UID -> Hidden mappings
        :type hidden: list
        :returns: list of new assigned Analyses
        """
        if items is None:
            items = []

        # Bail out if the items is not a list type
        if not isinstance(items, (list, tuple)):
            raise TypeError(
                "Items parameter must be a tuple or list, got '{}'".format(
                    type(items)))

        # Bail out if the AR is inactive
        if not api.is_active(instance):
            raise Unauthorized("Inactive ARs can not be modified")

        # Bail out if the user has not the right permission
        if not check_permission(AddAnalysis, instance):
            raise Unauthorized("You do not have the '{}' permission"
                               .format(AddAnalysis))

        # Convert the items to a valid list of AnalysisServices
        services = filter(None, map(self._to_service, items))

        # Calculate dependencies
        dependencies = map(lambda s: s.getServiceDependencies(), services)
        dependencies = list(itertools.chain.from_iterable(dependencies))

        # Merge dependencies and services
        services = set(services + dependencies)

        # Modify existing AR specs with new form values of selected analyses
        specs = self.resolve_specs(instance, specs)

        # Add analyses
        params = dict(prices=prices, hidden=hidden, specs=specs)
        map(lambda serv: self.add_analysis(instance, serv, **params), services)

        # Get all analyses (those from descendants included)
        analyses = instance.objectValues("Analysis")
        analyses.extend(self.get_analyses_from_descendants(instance))

        # Bail out those not in services list or submitted
        uids = map(api.get_uid, services)
        to_remove = filter(lambda an: an.getServiceUID() not in uids, analyses)
        to_remove = filter(lambda an: not ISubmitted.providedBy(an), to_remove)

        # Remove analyses
        map(self.remove_analysis, to_remove)

    def resolve_specs(self, instance, results_ranges):
        """Returns a dictionary where the key is the service_uid and the value
        is its results range. The dictionary is made by extending the
        results_ranges passed-in with the Sample's ResultsRanges (a copy of the
        specifications initially set)
        """
        rrs = results_ranges or []

        # Sample's Results ranges
        sample_rrs = instance.getResultsRange()

        # Ensure all subfields from specification are kept and missing values
        # for subfields are filled in accordance with the specs
        rrs = map(lambda rr: self.resolve_range(rr, sample_rrs), rrs)

        # Append those from sample that are missing in the ranges passed-in
        service_uids = map(lambda rr: rr["uid"], rrs)
        rrs.extend(filter(lambda rr: rr["uid"] not in service_uids, sample_rrs))

        # Create a dict for easy access to results ranges
        return dict(map(lambda rr: (rr["uid"], rr), rrs))

    def resolve_range(self, result_range, sample_result_ranges):
        """Resolves the range by adding the uid if not present and filling the
        missing subfield values with those that come from the Sample
        specification if they are not present in the result_range passed-in
        """
        # Resolve result_range to make sure it contain uid subfield
        rrs = self.resolve_uid(result_range)
        uid = rrs.get("uid")

        for sample_rr in sample_result_ranges:
            if uid and sample_rr.get("uid") == uid:
                # Keep same fields from sample
                rr = sample_rr.copy()
                rr.update(rrs)
                return rr

        # Return the original with no changes
        return rrs

    def resolve_uid(self, result_range):

        """Resolves the uid key for the result_range passed in if it does not
        exist when contains a keyword
        """
        value = result_range.copy()
        uid = value.get("uid")
        if api.is_uid(uid) and uid != "0":
            return value

        # uid key does not exist or is not valid, try to infere from keyword
        keyword = value.get("keyword")
        if keyword:
            query = dict(portal_type="AnalysisService", getKeyword=keyword)
            brains = api.search(query, SETUP_CATALOG)
            if len(brains) == 1:
                uid = api.get_uid(brains[0])
        value["uid"] = uid
        return value

    def add_analysis(self, instance, service, **kwargs):
        service_uid = api.get_uid(service)

        # Ensure we have suitable parameters
        specs = kwargs.get("specs") or {}

        # Get the hidden status for the service
        hidden = kwargs.get("hidden") or []
        hidden = filter(lambda d: d.get("uid") == service_uid, hidden)
        hidden = hidden and hidden[0].get("hidden") or service.getHidden()

        # Get the price for the service
        prices = kwargs.get("prices") or {}
        price = prices.get(service_uid) or service.getPrice()

        # Gets the analysis or creates the analysis for this service
        # Note this returns a list, because is possible to have multiple
        # partitions with same analysis
        analyses = self.resolve_analyses(instance, service)

        # Filter out analyses in detached states
        # This allows to re-add an analysis that was retracted or cancelled
        analyses = filter(
            lambda an: api.get_workflow_status_of(an) not in DETACHED_STATES,
            analyses)

        if not analyses:
            # Create the analysis
            new_id = self.generate_analysis_id(instance, service)
            logger.info("Creating new analysis '{}'".format(new_id))
            analysis = create_analysis(instance, service, id=new_id)
            analyses.append(analysis)

        for analysis in analyses:
            # Set the hidden status
            analysis.setHidden(hidden)

            # Set the price of the Analysis
            analysis.setPrice(price)

            # Set the internal use status
            parent_sample = analysis.getRequest()
            analysis.setInternalUse(parent_sample.getInternalUse())

            # Set the result range to the analysis
            analysis_rr = specs.get(service_uid) or analysis.getResultsRange()
            analysis.setResultsRange(analysis_rr)
            analysis.reindexObject()

    def generate_analysis_id(self, instance, service):
        """Generate a new analysis ID
        """
        count = 1
        keyword = service.getKeyword()
        new_id = keyword
        while new_id in instance.objectIds():
            new_id = "{}-{}".format(keyword, count)
            count += 1
        return new_id

    def remove_analysis(self, analysis):
        """Removes a given analysis from the instance
        """
        # Remember assigned attachments
        # https://github.com/senaite/senaite.core/issues/1025
        attachments = analysis.getAttachment()
        analysis.setAttachment([])

        # If assigned to a worksheet, unassign it before deletion
        worksheet = analysis.getWorksheet()
        if worksheet:
            worksheet.removeAnalysis(analysis)

        # handle retest source deleted
        retest = analysis.getRetest()
        if retest:
            # unset reference link
            retest.setRetestOf(None)

        # Remove the analysis
        # Note the analysis might belong to a partition
        analysis.aq_parent.manage_delObjects(ids=[api.get_id(analysis)])

        # Remove orphaned attachments
        for attachment in attachments:
            if not attachment.getLinkedAnalyses():
                # only delete attachments which are no further linked
                logger.info(
                    "Deleting attachment: {}".format(attachment.getId()))
                attachment_id = api.get_id(attachment)
                api.get_parent(attachment).manage_delObjects(attachment_id)

    def resolve_analyses(self, instance, service):
        """Resolves analyses for the service and instance
        It returns a list, cause for a given sample, multiple analyses for same
        service can exist due to the possibility of having multiple partitions
        """
        analyses = []

        # Does the analysis exists in this instance already?
        instance_analyses = self.get_from_instance(instance, service)

        if instance_analyses:
            analyses.extend(instance_analyses)

        # Does the analysis exists in an ancestor?
        from_ancestor = self.get_from_ancestor(instance, service)
        for ancestor_analysis in from_ancestor:
            # Move the analysis into this instance. The ancestor's
            # analysis will be masked otherwise
            analysis_id = api.get_id(ancestor_analysis)
            logger.info("Analysis {} is from an ancestor".format(analysis_id))
            cp = ancestor_analysis.aq_parent.manage_cutObjects(analysis_id)
            instance.manage_pasteObjects(cp)
            analyses.append(instance._getOb(analysis_id))

        # Does the analysis exists in descendants?
        from_descendant = self.get_from_descendant(instance, service)
        analyses.extend(from_descendant)

        return analyses

    def get_analyses_from_descendants(self, instance):
        """Returns all the analyses from descendants
        """
        analyses = []
        for descendant in instance.getDescendants(all_descendants=True):
            analyses.extend(descendant.objectValues("Analysis"))
        return analyses

    def get_from_instance(self, instance, service):
        """Returns analyses for the given service from the instance
        """
        service_uid = api.get_uid(service)
        analyses = instance.objectValues("Analysis")
        # Filter those analyses with same keyword. Note that a Sample can
        # contain more than one analysis with same keyword because of retests
        return filter(lambda an: an.getServiceUID() == service_uid, analyses)

    def get_from_ancestor(self, instance, service):
        """Returns analyses for the given service from ancestors
        """
        ancestor = instance.getParentAnalysisRequest()
        if not ancestor:
            return []

        analyses = self.get_from_instance(ancestor, service)
        return analyses or self.get_from_ancestor(ancestor, service)

    def get_from_descendant(self, instance, service):
        """Returns analyses for the given service from descendants
        """
        analyses = []
        for descendant in instance.getDescendants():
            # Does the analysis exists in the current descendant?
            descendant_analyses = self.get_from_instance(descendant, service)
            if descendant_analyses:
                analyses.extend(descendant_analyses)

            # Search in descendants from current descendant
            from_descendant = self.get_from_descendant(descendant, service)
            analyses.extend(from_descendant)

        return analyses

    def _to_service(self, thing):
        """Convert to Analysis Service

        :param thing: UID/Catalog Brain/Object/Something
        :returns: Analysis Service object or None
        """

        # Convert UIDs to objects
        if api.is_uid(thing):
            thing = api.get_object_by_uid(thing, None)

        # Bail out if the thing is not a valid object
        if not api.is_object(thing):
            logger.warn("'{}' is not a valid object!".format(repr(thing)))
            return None

        # Ensure we have an object here and not a brain
        obj = api.get_object(thing)

        if IAnalysisService.providedBy(obj):
            return obj

        if IAnalysis.providedBy(obj):
            return obj.getAnalysisService()

        # An object, but neither an Analysis nor AnalysisService?
        # This should never happen.
        portal_type = api.get_portal_type(obj)
        logger.error("ARAnalysesField doesn't accept objects from {} type. "
                     "The object will be dismissed.".format(portal_type))
        return None


registerField(ARAnalysesField,
              title="Analyses",
              description="Manages Analyses of ARs")


1		# -- coding: utf-8 --
2		#
3		# This file is part of SENAITE.CORE.
4		#
5		# SENAITE.CORE is free software: you can redistribute it and/or modify it under
6		# the terms of the GNU General Public License as published by the Free Software
7		# Foundation, version 2.
8		#
9		# This program is distributed in the hope that it will be useful, but WITHOUT
10		# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11		# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
12		# details.
13		#
14		# You should have received a copy of the GNU General Public License along with
15		# this program; if not, write to the Free Software Foundation, Inc., 51
16		# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
17		#
18		# Copyright 2018-2021 by it's authors.
19		# Some rights reserved, see README and LICENSE.
20
21		import itertools
22
23		from AccessControl import ClassSecurityInfo
24		from AccessControl import Unauthorized
25		from bika.lims import api
26		from bika.lims import logger
27		from bika.lims.api.security import check_permission
28		from bika.lims.catalog import CATALOG_ANALYSIS_LISTING
29		from bika.lims.catalog import SETUP_CATALOG
30		from bika.lims.interfaces import IAnalysis
31		from bika.lims.interfaces import IAnalysisService
32		from bika.lims.interfaces import IARAnalysesField
33		from bika.lims.interfaces import ISubmitted
34		from bika.lims.permissions import AddAnalysis
35		from bika.lims.utils.analysis import create_analysis
36		from Products.Archetypes.public import Field
37		from Products.Archetypes.public import ObjectField
38		from Products.Archetypes.Registry import registerField
39		from zope.interface import implements
40
41		DETACHED_STATES = ["cancelled", "retracted", "rejected"]
42
43
44		"""Field to manage Analyses on ARs
45
46		Please see the assigned doctest at tests/doctests/ARAnalysesField.rst
47
48		Run this test from the buildout directory:
49
50		bin/test test_textual_doctests -t ARAnalysesField
51		"""
52
53
54		class ARAnalysesField(ObjectField):
55		"""A field that stores Analyses instances
56		"""
57		implements(IARAnalysesField)
58
59		security = ClassSecurityInfo()
60		_properties = Field._properties.copy()
61		_properties.update({
62		"type": "analyses",
63		"default": None,
64		})
65
66		security.declarePrivate('get')
67
68		def get(self, instance, **kwargs):
69		"""Returns a list of Analyses assigned to this AR
70
71		Return a list of catalog brains unless `full_objects=True` is passed.
72		Other keyword arguments are passed to bika_analysis_catalog
73
74		:param instance: Analysis Request object
75		:param kwargs: Keyword arguments to inject in the search query
76		:returns: A list of Analysis Objects/Catalog Brains
77		"""
78		# Do we need to return objects or brains
79		full_objects = kwargs.get("full_objects", False)
80
81		# Bail out parameters from kwargs that don't match with indexes
82		catalog = api.get_tool(CATALOG_ANALYSIS_LISTING)
83		indexes = catalog.indexes()
84		query = dict([(k, v) for k, v in kwargs.items() if k in indexes])
85
86		# Do the search against the catalog
87		query["portal_type"] = "Analysis"
88		query["getAncestorsUIDs"] = api.get_uid(instance)
89		brains = catalog(query)
90		if full_objects:
91		return map(api.get_object, brains)
92		return brains
93
94		security.declarePrivate('set')
95
96		def set(self, instance, items, prices=None, specs=None, hidden=None, **kw):
97		"""Set/Assign Analyses to this AR
98
99		:param items: List of Analysis objects/brains, AnalysisService
100		objects/brains and/or Analysis Service uids
101		:type items: list
102		:param prices: Mapping of AnalysisService UID -> price
103		:type prices: dict
104		:param specs: List of AnalysisService UID -> Result Range mappings
105		:type specs: list
106		:param hidden: List of AnalysisService UID -> Hidden mappings
107		:type hidden: list
108		:returns: list of new assigned Analyses
109		"""
110		if items is None:
111		items = []
112
113		# Bail out if the items is not a list type
114		if not isinstance(items, (list, tuple)):
115		raise TypeError(
116		"Items parameter must be a tuple or list, got '{}'".format(
117		type(items)))
118
119		# Bail out if the AR is inactive
120		if not api.is_active(instance):
121		raise Unauthorized("Inactive ARs can not be modified")
122
123		# Bail out if the user has not the right permission
124		if not check_permission(AddAnalysis, instance):
125		raise Unauthorized("You do not have the '{}' permission"
126		.format(AddAnalysis))
127
128		# Convert the items to a valid list of AnalysisServices
129		services = filter(None, map(self._to_service, items))
130
131		# Calculate dependencies
132		dependencies = map(lambda s: s.getServiceDependencies(), services)
133		dependencies = list(itertools.chain.from_iterable(dependencies))
134
135		# Merge dependencies and services
136		services = set(services + dependencies)
137
138		# Modify existing AR specs with new form values of selected analyses
139		specs = self.resolve_specs(instance, specs)
140
141		# Add analyses
142		params = dict(prices=prices, hidden=hidden, specs=specs)
143		map(lambda serv: self.add_analysis(instance, serv, **params), services)
144
145		# Get all analyses (those from descendants included)
146		analyses = instance.objectValues("Analysis")
147		analyses.extend(self.get_analyses_from_descendants(instance))
148
149		# Bail out those not in services list or submitted
150		uids = map(api.get_uid, services)
151		to_remove = filter(lambda an: an.getServiceUID() not in uids, analyses)
152		to_remove = filter(lambda an: not ISubmitted.providedBy(an), to_remove)
153
154		# Remove analyses
155		map(self.remove_analysis, to_remove)
156
157		def resolve_specs(self, instance, results_ranges):
158		"""Returns a dictionary where the key is the service_uid and the value
159		is its results range. The dictionary is made by extending the
160		results_ranges passed-in with the Sample's ResultsRanges (a copy of the
161		specifications initially set)
162		"""
163		rrs = results_ranges or []
164
165		# Sample's Results ranges
166		sample_rrs = instance.getResultsRange()
167
168		# Ensure all subfields from specification are kept and missing values
169		# for subfields are filled in accordance with the specs
170		rrs = map(lambda rr: self.resolve_range(rr, sample_rrs), rrs)
171
172		# Append those from sample that are missing in the ranges passed-in
173		service_uids = map(lambda rr: rr["uid"], rrs)
174		rrs.extend(filter(lambda rr: rr["uid"] not in service_uids, sample_rrs))
175
176		# Create a dict for easy access to results ranges
177		return dict(map(lambda rr: (rr["uid"], rr), rrs))
178
179		def resolve_range(self, result_range, sample_result_ranges):
180		"""Resolves the range by adding the uid if not present and filling the
181		missing subfield values with those that come from the Sample
182		specification if they are not present in the result_range passed-in
183		"""
184		# Resolve result_range to make sure it contain uid subfield
185		rrs = self.resolve_uid(result_range)
186		uid = rrs.get("uid")
187
188		for sample_rr in sample_result_ranges:
189		if uid and sample_rr.get("uid") == uid:
190		# Keep same fields from sample
191		rr = sample_rr.copy()
192		rr.update(rrs)
193		return rr
194
195		# Return the original with no changes
196		return rrs
197
198	View Code Duplication	def resolve_uid(self, result_range):
		0 ignored issues – show Duplication introduced 2020-01-23 19:50 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
199		"""Resolves the uid key for the result_range passed in if it does not
200		exist when contains a keyword
201		"""
202		value = result_range.copy()
203		uid = value.get("uid")
204		if api.is_uid(uid) and uid != "0":
205		return value
206
207		# uid key does not exist or is not valid, try to infere from keyword
208		keyword = value.get("keyword")
209		if keyword:
210		query = dict(portal_type="AnalysisService", getKeyword=keyword)
211		brains = api.search(query, SETUP_CATALOG)
212		if len(brains) == 1:
213		uid = api.get_uid(brains[0])
214		value["uid"] = uid
215		return value
216
217		def add_analysis(self, instance, service, **kwargs):
218		service_uid = api.get_uid(service)
219
220		# Ensure we have suitable parameters
221		specs = kwargs.get("specs") or {}
222
223		# Get the hidden status for the service
224		hidden = kwargs.get("hidden") or []
225		hidden = filter(lambda d: d.get("uid") == service_uid, hidden)
226		hidden = hidden and hidden[0].get("hidden") or service.getHidden()
227
228		# Get the price for the service
229		prices = kwargs.get("prices") or {}
230		price = prices.get(service_uid) or service.getPrice()
231
232		# Gets the analysis or creates the analysis for this service
233		# Note this returns a list, because is possible to have multiple
234		# partitions with same analysis
235		analyses = self.resolve_analyses(instance, service)
236
237		# Filter out analyses in detached states
238		# This allows to re-add an analysis that was retracted or cancelled
239		analyses = filter(
240		lambda an: api.get_workflow_status_of(an) not in DETACHED_STATES,
241		analyses)
242
243		if not analyses:
244		# Create the analysis
245		new_id = self.generate_analysis_id(instance, service)
246		logger.info("Creating new analysis '{}'".format(new_id))
247		analysis = create_analysis(instance, service, id=new_id)
248		analyses.append(analysis)
249
250		for analysis in analyses:
251		# Set the hidden status
252		analysis.setHidden(hidden)
253
254		# Set the price of the Analysis
255		analysis.setPrice(price)
256
257		# Set the internal use status
258		parent_sample = analysis.getRequest()
259		analysis.setInternalUse(parent_sample.getInternalUse())
260
261		# Set the result range to the analysis
262		analysis_rr = specs.get(service_uid) or analysis.getResultsRange()
263		analysis.setResultsRange(analysis_rr)
264		analysis.reindexObject()
265
266		def generate_analysis_id(self, instance, service):
267		"""Generate a new analysis ID
268		"""
269		count = 1
270		keyword = service.getKeyword()
271		new_id = keyword
272		while new_id in instance.objectIds():
273		new_id = "{}-{}".format(keyword, count)
274		count += 1
275		return new_id
276
277		def remove_analysis(self, analysis):
278		"""Removes a given analysis from the instance
279		"""
280		# Remember assigned attachments
281		# https://github.com/senaite/senaite.core/issues/1025
282		attachments = analysis.getAttachment()
283		analysis.setAttachment([])
284
285		# If assigned to a worksheet, unassign it before deletion
286		worksheet = analysis.getWorksheet()
287		if worksheet:
288		worksheet.removeAnalysis(analysis)
289
290		# handle retest source deleted
291		retest = analysis.getRetest()
292		if retest:
293		# unset reference link
294		retest.setRetestOf(None)
295
296		# Remove the analysis
297		# Note the analysis might belong to a partition
298		analysis.aq_parent.manage_delObjects(ids=[api.get_id(analysis)])
299
300		# Remove orphaned attachments
301		for attachment in attachments:
302		if not attachment.getLinkedAnalyses():
303		# only delete attachments which are no further linked
304		logger.info(
305		"Deleting attachment: {}".format(attachment.getId()))
306		attachment_id = api.get_id(attachment)
307		api.get_parent(attachment).manage_delObjects(attachment_id)
308
309		def resolve_analyses(self, instance, service):
310		"""Resolves analyses for the service and instance
311		It returns a list, cause for a given sample, multiple analyses for same
312		service can exist due to the possibility of having multiple partitions
313		"""
314		analyses = []
315
316		# Does the analysis exists in this instance already?
317		instance_analyses = self.get_from_instance(instance, service)
318
319		if instance_analyses:
320		analyses.extend(instance_analyses)
321
322		# Does the analysis exists in an ancestor?
323		from_ancestor = self.get_from_ancestor(instance, service)
324		for ancestor_analysis in from_ancestor:
325		# Move the analysis into this instance. The ancestor's
326		# analysis will be masked otherwise
327		analysis_id = api.get_id(ancestor_analysis)
328		logger.info("Analysis {} is from an ancestor".format(analysis_id))
329		cp = ancestor_analysis.aq_parent.manage_cutObjects(analysis_id)
330		instance.manage_pasteObjects(cp)
331		analyses.append(instance._getOb(analysis_id))
332
333		# Does the analysis exists in descendants?
334		from_descendant = self.get_from_descendant(instance, service)
335		analyses.extend(from_descendant)
336
337		return analyses
338
339		def get_analyses_from_descendants(self, instance):
340		"""Returns all the analyses from descendants
341		"""
342		analyses = []
343		for descendant in instance.getDescendants(all_descendants=True):
344		analyses.extend(descendant.objectValues("Analysis"))
345		return analyses
346
347		def get_from_instance(self, instance, service):
348		"""Returns analyses for the given service from the instance
349		"""
350		service_uid = api.get_uid(service)
351		analyses = instance.objectValues("Analysis")
352		# Filter those analyses with same keyword. Note that a Sample can
353		# contain more than one analysis with same keyword because of retests
354		return filter(lambda an: an.getServiceUID() == service_uid, analyses)
355
356		def get_from_ancestor(self, instance, service):
357		"""Returns analyses for the given service from ancestors
358		"""
359		ancestor = instance.getParentAnalysisRequest()
360		if not ancestor:
361		return []
362
363		analyses = self.get_from_instance(ancestor, service)
364		return analyses or self.get_from_ancestor(ancestor, service)
365
366		def get_from_descendant(self, instance, service):
367		"""Returns analyses for the given service from descendants
368		"""
369		analyses = []
370		for descendant in instance.getDescendants():
371		# Does the analysis exists in the current descendant?
372		descendant_analyses = self.get_from_instance(descendant, service)
373		if descendant_analyses:
374		analyses.extend(descendant_analyses)
375
376		# Search in descendants from current descendant
377		from_descendant = self.get_from_descendant(descendant, service)
378		analyses.extend(from_descendant)
379
380		return analyses
381
382		def _to_service(self, thing):
383		"""Convert to Analysis Service
384
385		:param thing: UID/Catalog Brain/Object/Something
386		:returns: Analysis Service object or None
387		"""
388
389		# Convert UIDs to objects
390		if api.is_uid(thing):
391		thing = api.get_object_by_uid(thing, None)
392
393		# Bail out if the thing is not a valid object
394		if not api.is_object(thing):
395		logger.warn("'{}' is not a valid object!".format(repr(thing)))
396		return None
397
398		# Ensure we have an object here and not a brain
399		obj = api.get_object(thing)
400
401		if IAnalysisService.providedBy(obj):
402		return obj
403
404		if IAnalysis.providedBy(obj):
405		return obj.getAnalysisService()
406
407		# An object, but neither an Analysis nor AnalysisService?
408		# This should never happen.
409		portal_type = api.get_portal_type(obj)
410		logger.error("ARAnalysesField doesn't accept objects from {} type. "
411		"The object will be dismissed.".format(portal_type))
412		return None
413
414
415		registerField(ARAnalysesField,
416		title="Analyses",
417		description="Manages Analyses of ARs")
418

senaite / senaite.core

Push — 2.x ( 8010f1...8ad4a8 )

ARAnalysesField.generate_analysis_id() A

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