|
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 2018-2019 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 Products.Archetypes.Registry import registerField |
|
26
|
|
|
from Products.Archetypes.public import Field |
|
27
|
|
|
from Products.Archetypes.public import ObjectField |
|
28
|
|
|
from zope.interface import implements |
|
29
|
|
|
|
|
30
|
|
|
from bika.lims import api |
|
31
|
|
|
from bika.lims import logger |
|
32
|
|
|
from bika.lims.api.security import check_permission |
|
33
|
|
|
from bika.lims.catalog import CATALOG_ANALYSIS_LISTING |
|
34
|
|
|
from bika.lims.interfaces import IARAnalysesField |
|
35
|
|
|
from bika.lims.interfaces import IAnalysis |
|
36
|
|
|
from bika.lims.interfaces import IAnalysisService |
|
37
|
|
|
from bika.lims.interfaces import ISubmitted |
|
38
|
|
|
from bika.lims.permissions import AddAnalysis |
|
39
|
|
|
from bika.lims.utils.analysis import create_analysis |
|
40
|
|
|
|
|
41
|
|
|
"""Field to manage Analyses on ARs |
|
42
|
|
|
|
|
43
|
|
|
Please see the assigned doctest at tests/doctests/ARAnalysesField.rst |
|
44
|
|
|
|
|
45
|
|
|
Run this test from the buildout directory: |
|
46
|
|
|
|
|
47
|
|
|
bin/test test_textual_doctests -t ARAnalysesField |
|
48
|
|
|
""" |
|
49
|
|
|
|
|
50
|
|
|
|
|
51
|
|
|
class ARAnalysesField(ObjectField): |
|
52
|
|
|
"""A field that stores Analyses instances |
|
53
|
|
|
""" |
|
54
|
|
|
implements(IARAnalysesField) |
|
55
|
|
|
|
|
56
|
|
|
security = ClassSecurityInfo() |
|
57
|
|
|
_properties = Field._properties.copy() |
|
58
|
|
|
_properties.update({ |
|
59
|
|
|
"type": "analyses", |
|
60
|
|
|
"default": None, |
|
61
|
|
|
}) |
|
62
|
|
|
|
|
63
|
|
|
security.declarePrivate('get') |
|
64
|
|
|
|
|
65
|
|
|
def get(self, instance, **kwargs): |
|
66
|
|
|
"""Returns a list of Analyses assigned to this AR |
|
67
|
|
|
|
|
68
|
|
|
Return a list of catalog brains unless `full_objects=True` is passed. |
|
69
|
|
|
Other keyword arguments are passed to bika_analysis_catalog |
|
70
|
|
|
|
|
71
|
|
|
:param instance: Analysis Request object |
|
72
|
|
|
:param kwargs: Keyword arguments to inject in the search query |
|
73
|
|
|
:returns: A list of Analysis Objects/Catalog Brains |
|
74
|
|
|
""" |
|
75
|
|
|
# Do we need to return objects or brains |
|
76
|
|
|
full_objects = kwargs.get("full_objects", False) |
|
77
|
|
|
|
|
78
|
|
|
# Bail out parameters from kwargs that don't match with indexes |
|
79
|
|
|
catalog = api.get_tool(CATALOG_ANALYSIS_LISTING) |
|
80
|
|
|
indexes = catalog.indexes() |
|
81
|
|
|
query = dict([(k, v) for k, v in kwargs.items() if k in indexes]) |
|
82
|
|
|
|
|
83
|
|
|
# Do the search against the catalog |
|
84
|
|
|
query["portal_type"] = "Analysis" |
|
85
|
|
|
query["getAncestorsUIDs"] = api.get_uid(instance) |
|
86
|
|
|
brains = catalog(query) |
|
87
|
|
|
if full_objects: |
|
88
|
|
|
return map(api.get_object, brains) |
|
89
|
|
|
return brains |
|
90
|
|
|
|
|
91
|
|
|
security.declarePrivate('set') |
|
92
|
|
|
|
|
93
|
|
|
def set(self, instance, items, prices=None, specs=None, hidden=None, **kw): |
|
94
|
|
|
"""Set/Assign Analyses to this AR |
|
95
|
|
|
|
|
96
|
|
|
:param items: List of Analysis objects/brains, AnalysisService |
|
97
|
|
|
objects/brains and/or Analysis Service uids |
|
98
|
|
|
:type items: list |
|
99
|
|
|
:param prices: Mapping of AnalysisService UID -> price |
|
100
|
|
|
:type prices: dict |
|
101
|
|
|
:param specs: List of AnalysisService UID -> Result Range mappings |
|
102
|
|
|
:type specs: list |
|
103
|
|
|
:param hidden: List of AnalysisService UID -> Hidden mappings |
|
104
|
|
|
:type hidden: list |
|
105
|
|
|
:returns: list of new assigned Analyses |
|
106
|
|
|
""" |
|
107
|
|
|
if items is None: |
|
108
|
|
|
items = [] |
|
109
|
|
|
|
|
110
|
|
|
# Bail out if the items is not a list type |
|
111
|
|
|
if not isinstance(items, (list, tuple)): |
|
112
|
|
|
raise TypeError( |
|
113
|
|
|
"Items parameter must be a tuple or list, got '{}'".format( |
|
114
|
|
|
type(items))) |
|
115
|
|
|
|
|
116
|
|
|
# Bail out if the AR is inactive |
|
117
|
|
|
if not api.is_active(instance): |
|
118
|
|
|
raise Unauthorized("Inactive ARs can not be modified" |
|
119
|
|
|
.format(AddAnalysis)) |
|
120
|
|
|
|
|
121
|
|
|
# Bail out if the user has not the right permission |
|
122
|
|
|
if not check_permission(AddAnalysis, instance): |
|
123
|
|
|
raise Unauthorized("You do not have the '{}' permission" |
|
124
|
|
|
.format(AddAnalysis)) |
|
125
|
|
|
|
|
126
|
|
|
# Convert the items to a valid list of AnalysisServices |
|
127
|
|
|
services = filter(None, map(self._to_service, items)) |
|
128
|
|
|
|
|
129
|
|
|
# Calculate dependencies |
|
130
|
|
|
# FIXME Infinite recursion error possible here, if the formula includes |
|
131
|
|
|
# the Keyword of the Service that includes the Calculation |
|
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
|
|
|
self._update_specs(instance, specs) |
|
140
|
|
|
|
|
141
|
|
|
# Create a mapping of Service UID -> Hidden status |
|
142
|
|
|
if hidden is None: |
|
143
|
|
|
hidden = [] |
|
144
|
|
|
hidden = dict(map(lambda d: (d.get("uid"), d.get("hidden")), hidden)) |
|
145
|
|
|
|
|
146
|
|
|
# Ensure we have a prices dictionary |
|
147
|
|
|
if prices is None: |
|
148
|
|
|
prices = dict() |
|
149
|
|
|
|
|
150
|
|
|
# Add analyses |
|
151
|
|
|
new_analyses = map(lambda service: |
|
152
|
|
|
self.add_analysis(instance, service, prices, hidden), |
|
153
|
|
|
services) |
|
154
|
|
|
new_analyses = filter(None, new_analyses) |
|
155
|
|
|
|
|
156
|
|
|
# Remove analyses |
|
157
|
|
|
# Since Manage Analyses view displays the analyses from partitions, we |
|
158
|
|
|
# also need to take them into consideration here. Analyses from |
|
159
|
|
|
# ancestors can be omitted. |
|
160
|
|
|
analyses = instance.objectValues("Analysis") |
|
161
|
|
|
analyses.extend(self.get_analyses_from_descendants(instance)) |
|
162
|
|
|
|
|
163
|
|
|
# Service UIDs |
|
164
|
|
|
service_uids = map(api.get_uid, services) |
|
165
|
|
|
|
|
166
|
|
|
# Assigned Attachments |
|
167
|
|
|
assigned_attachments = [] |
|
168
|
|
|
|
|
169
|
|
|
for analysis in analyses: |
|
170
|
|
|
service_uid = analysis.getServiceUID() |
|
171
|
|
|
|
|
172
|
|
|
# Skip if the Service is selected |
|
173
|
|
|
if service_uid in service_uids: |
|
174
|
|
|
continue |
|
175
|
|
|
|
|
176
|
|
|
# Skip non-open Analyses |
|
177
|
|
|
if ISubmitted.providedBy(analysis): |
|
178
|
|
|
continue |
|
179
|
|
|
|
|
180
|
|
|
# Remember assigned attachments |
|
181
|
|
|
# https://github.com/senaite/senaite.core/issues/1025 |
|
182
|
|
|
assigned_attachments.extend(analysis.getAttachment()) |
|
183
|
|
|
analysis.setAttachment([]) |
|
184
|
|
|
|
|
185
|
|
|
# If it is assigned to a worksheet, unassign it before deletion. |
|
186
|
|
|
worksheet = analysis.getWorksheet() |
|
187
|
|
|
if worksheet: |
|
188
|
|
|
worksheet.removeAnalysis(analysis) |
|
189
|
|
|
|
|
190
|
|
|
# Remove the analysis |
|
191
|
|
|
# Note the analysis might belong to a partition |
|
192
|
|
|
analysis.aq_parent.manage_delObjects(ids=[api.get_id(analysis)]) |
|
193
|
|
|
|
|
194
|
|
|
# Remove orphaned attachments |
|
195
|
|
|
for attachment in assigned_attachments: |
|
196
|
|
|
# only delete attachments which are no further linked |
|
197
|
|
|
if not attachment.getLinkedAnalyses(): |
|
198
|
|
|
logger.info( |
|
199
|
|
|
"Deleting attachment: {}".format(attachment.getId())) |
|
200
|
|
|
attachment_id = api.get_id(attachment) |
|
201
|
|
|
api.get_parent(attachment).manage_delObjects(attachment_id) |
|
202
|
|
|
|
|
203
|
|
|
return new_analyses |
|
204
|
|
|
|
|
205
|
|
|
def add_analysis(self, instance, service, prices, hidden): |
|
206
|
|
|
service_uid = api.get_uid(service) |
|
207
|
|
|
new_analysis = False |
|
208
|
|
|
|
|
209
|
|
|
# Gets the analysis or creates the analysis for this service |
|
210
|
|
|
# Note this analysis might not belong to this current instance, but |
|
211
|
|
|
# from a descendant (partition) |
|
212
|
|
|
analysis = self.resolve_analysis(instance, service) |
|
213
|
|
|
if not analysis: |
|
214
|
|
|
# Create the analysis |
|
215
|
|
|
new_analysis = True |
|
216
|
|
|
keyword = service.getKeyword() |
|
217
|
|
|
logger.info("Creating new analysis '{}'".format(keyword)) |
|
218
|
|
|
analysis = create_analysis(instance, service) |
|
219
|
|
|
|
|
220
|
|
|
# Set the hidden status |
|
221
|
|
|
analysis.setHidden(hidden.get(service_uid, False)) |
|
222
|
|
|
|
|
223
|
|
|
# Set the price of the Analysis |
|
224
|
|
|
analysis.setPrice(prices.get(service_uid, service.getPrice())) |
|
225
|
|
|
|
|
226
|
|
|
# Only return the analysis if is a new one |
|
227
|
|
|
if new_analysis: |
|
228
|
|
|
return analysis |
|
229
|
|
|
|
|
230
|
|
|
return None |
|
231
|
|
|
|
|
232
|
|
|
def resolve_analysis(self, instance, service): |
|
233
|
|
|
"""Resolves an analysis for the service and instance |
|
234
|
|
|
""" |
|
235
|
|
|
# Does the analysis exists in this instance already? |
|
236
|
|
|
analysis = self.get_from_instance(instance, service) |
|
237
|
|
|
if analysis: |
|
238
|
|
|
keyword = service.getKeyword() |
|
239
|
|
|
logger.info("Analysis for '{}' already exists".format(keyword)) |
|
240
|
|
|
return analysis |
|
241
|
|
|
|
|
242
|
|
|
# Does the analysis exists in an ancestor? |
|
243
|
|
|
from_ancestor = self.get_from_ancestor(instance, service) |
|
244
|
|
|
if from_ancestor: |
|
245
|
|
|
# Move the analysis into this instance. The ancestor's |
|
246
|
|
|
# analysis will be masked otherwise |
|
247
|
|
|
analysis_id = api.get_id(from_ancestor) |
|
248
|
|
|
logger.info("Analysis {} is from an ancestor".format(analysis_id)) |
|
249
|
|
|
cp = from_ancestor.aq_parent.manage_cutObjects(analysis_id) |
|
250
|
|
|
instance.manage_pasteObjects(cp) |
|
251
|
|
|
return instance._getOb(analysis_id) |
|
252
|
|
|
|
|
253
|
|
|
# Does the analysis exists in a descendant? |
|
254
|
|
|
from_descendant = self.get_from_descendant(instance, service) |
|
255
|
|
|
if from_descendant: |
|
256
|
|
|
# The analysis already exists in a partition, keep it. The |
|
257
|
|
|
# analysis from current instance will be masked otherwise |
|
258
|
|
|
analysis_id = api.get_id(from_descendant) |
|
259
|
|
|
logger.info("Analysis {} is from a descendant".format(analysis_id)) |
|
260
|
|
|
return from_descendant |
|
261
|
|
|
|
|
262
|
|
|
return None |
|
263
|
|
|
|
|
264
|
|
|
def get_analyses_from_descendants(self, instance): |
|
265
|
|
|
"""Returns all the analyses from descendants |
|
266
|
|
|
""" |
|
267
|
|
|
analyses = [] |
|
268
|
|
|
for descendant in instance.getDescendants(all_descendants=True): |
|
269
|
|
|
analyses.extend(descendant.objectValues("Analysis")) |
|
270
|
|
|
return analyses |
|
271
|
|
|
|
|
272
|
|
|
def get_from_instance(self, instance, service): |
|
273
|
|
|
"""Returns an analysis for the given service from the instance |
|
274
|
|
|
""" |
|
275
|
|
|
service_uid = api.get_uid(service) |
|
276
|
|
|
for analysis in instance.objectValues("Analysis"): |
|
277
|
|
|
if analysis.getServiceUID() == service_uid: |
|
278
|
|
|
return analysis |
|
279
|
|
|
return None |
|
280
|
|
|
|
|
281
|
|
|
def get_from_ancestor(self, instance, service): |
|
282
|
|
|
"""Returns an analysis for the given service from ancestors |
|
283
|
|
|
""" |
|
284
|
|
|
ancestor = instance.getParentAnalysisRequest() |
|
285
|
|
|
if not ancestor: |
|
286
|
|
|
return None |
|
287
|
|
|
|
|
288
|
|
|
analysis = self.get_from_instance(ancestor, service) |
|
289
|
|
|
return analysis or self.get_from_ancestor(ancestor, service) |
|
290
|
|
|
|
|
291
|
|
|
def get_from_descendant(self, instance, service): |
|
292
|
|
|
"""Returns an analysis for the given service from descendants |
|
293
|
|
|
""" |
|
294
|
|
|
for descendant in instance.getDescendants(): |
|
295
|
|
|
# Does the analysis exists in the current descendant? |
|
296
|
|
|
analysis = self.get_from_instance(descendant, service) |
|
297
|
|
|
if analysis: |
|
298
|
|
|
return analysis |
|
299
|
|
|
|
|
300
|
|
|
# Search in descendants from current descendant |
|
301
|
|
|
analysis = self.get_from_descendant(descendant, service) |
|
302
|
|
|
if analysis: |
|
303
|
|
|
return analysis |
|
304
|
|
|
|
|
305
|
|
|
return None |
|
306
|
|
|
|
|
307
|
|
|
def _get_services(self, full_objects=False): |
|
308
|
|
|
"""Fetch and return analysis service objects |
|
309
|
|
|
""" |
|
310
|
|
|
bsc = api.get_tool("bika_setup_catalog") |
|
311
|
|
|
brains = bsc(portal_type="AnalysisService") |
|
312
|
|
|
if full_objects: |
|
313
|
|
|
return map(api.get_object, brains) |
|
314
|
|
|
return brains |
|
315
|
|
|
|
|
316
|
|
|
def _to_service(self, thing): |
|
317
|
|
|
"""Convert to Analysis Service |
|
318
|
|
|
|
|
319
|
|
|
:param thing: UID/Catalog Brain/Object/Something |
|
320
|
|
|
:returns: Analysis Service object or None |
|
321
|
|
|
""" |
|
322
|
|
|
|
|
323
|
|
|
# Convert UIDs to objects |
|
324
|
|
|
if api.is_uid(thing): |
|
325
|
|
|
thing = api.get_object_by_uid(thing, None) |
|
326
|
|
|
|
|
327
|
|
|
# Bail out if the thing is not a valid object |
|
328
|
|
|
if not api.is_object(thing): |
|
329
|
|
|
logger.warn("'{}' is not a valid object!".format(repr(thing))) |
|
330
|
|
|
return None |
|
331
|
|
|
|
|
332
|
|
|
# Ensure we have an object here and not a brain |
|
333
|
|
|
obj = api.get_object(thing) |
|
334
|
|
|
|
|
335
|
|
|
if IAnalysisService.providedBy(obj): |
|
336
|
|
|
return obj |
|
337
|
|
|
|
|
338
|
|
|
if IAnalysis.providedBy(obj): |
|
339
|
|
|
return obj.getAnalysisService() |
|
340
|
|
|
|
|
341
|
|
|
# An object, but neither an Analysis nor AnalysisService? |
|
342
|
|
|
# This should never happen. |
|
343
|
|
|
portal_type = api.get_portal_type(obj) |
|
344
|
|
|
logger.error("ARAnalysesField doesn't accept objects from {} type. " |
|
345
|
|
|
"The object will be dismissed.".format(portal_type)) |
|
346
|
|
|
return None |
|
347
|
|
|
|
|
348
|
|
|
def _update_specs(self, instance, specs): |
|
349
|
|
|
"""Update AR specifications |
|
350
|
|
|
|
|
351
|
|
|
:param instance: Analysis Request |
|
352
|
|
|
:param specs: List of Specification Records |
|
353
|
|
|
""" |
|
354
|
|
|
|
|
355
|
|
|
if specs is None: |
|
356
|
|
|
return |
|
357
|
|
|
|
|
358
|
|
|
# N.B. we copy the records here, otherwise the spec will be written to |
|
359
|
|
|
# the attached specification of this AR |
|
360
|
|
|
rr = {item["keyword"]: item.copy() |
|
361
|
|
|
for item in instance.getResultsRange()} |
|
362
|
|
|
for spec in specs: |
|
363
|
|
|
keyword = spec.get("keyword") |
|
364
|
|
|
if keyword in rr: |
|
365
|
|
|
# overwrite the instance specification only, if the specific |
|
366
|
|
|
# analysis spec has min/max values set |
|
367
|
|
|
if all([spec.get("min"), spec.get("max")]): |
|
368
|
|
|
rr[keyword].update(spec) |
|
369
|
|
|
else: |
|
370
|
|
|
rr[keyword] = spec |
|
371
|
|
|
else: |
|
372
|
|
|
rr[keyword] = spec |
|
373
|
|
|
return instance.setResultsRange(rr.values()) |
|
374
|
|
|
|
|
375
|
|
|
|
|
376
|
|
|
registerField(ARAnalysesField, |
|
377
|
|
|
title="Analyses", |
|
378
|
|
|
description="Manages Analyses of ARs") |
|
379
|
|
|
|