1
|
|
|
# -*- coding: utf-8 -*- |
2
|
|
|
|
3
|
|
|
from collections import OrderedDict |
4
|
|
|
from collections import defaultdict |
5
|
|
|
|
6
|
|
|
from bika.lims import bikaMessageFactory as _ |
7
|
|
|
from bika.lims import logger |
8
|
|
|
from bika.lims.decorators import returns_super_model |
9
|
|
|
from bika.lims.workflow import doActionFor |
10
|
|
|
from bika.lims import api |
11
|
|
|
from bika.lims.interfaces import IProxyField |
12
|
|
|
from bika.lims.utils.analysisrequest import create_analysisrequest as crar |
13
|
|
|
from Products.Five.browser import BrowserView |
14
|
|
|
from Products.Five.browser.pagetemplatefile import ViewPageTemplateFile |
15
|
|
|
|
16
|
|
|
DEFAULT_NUMBER_OF_PARTITIONS = 0 |
17
|
|
|
|
18
|
|
|
PARTITION_SKIP_FIELDS = [ |
19
|
|
|
"Analyses", |
20
|
|
|
"Attachment", |
21
|
|
|
"Client", |
22
|
|
|
"Container", |
23
|
|
|
"Preservation", |
24
|
|
|
"Profile", |
25
|
|
|
"Profiles", |
26
|
|
|
"RejectionReasons", |
27
|
|
|
"Remarks", |
28
|
|
|
"ResultsInterpretation", |
29
|
|
|
"ResultsInterpretationDepts", |
30
|
|
|
"Sample", |
31
|
|
|
"SampleType", |
32
|
|
|
"Template", |
33
|
|
|
"creation_date", |
34
|
|
|
"id", |
35
|
|
|
"modification_date", |
36
|
|
|
"ParentAnalysisRequest", |
37
|
|
|
] |
38
|
|
|
|
39
|
|
|
|
40
|
|
|
class PartitionMagicView(BrowserView): |
41
|
|
|
"""Manage Partitions of primary ARs |
42
|
|
|
""" |
43
|
|
|
template = ViewPageTemplateFile("templates/partition_magic.pt") |
44
|
|
|
|
45
|
|
|
def __init__(self, context, request): |
46
|
|
|
super(PartitionMagicView, self).__init__(context, request) |
47
|
|
|
self.context = context |
48
|
|
|
self.request = request |
49
|
|
|
self.back_url = self.context.absolute_url() |
50
|
|
|
self.analyses_to_remove = dict() |
51
|
|
|
|
52
|
|
|
|
53
|
|
|
def __call__(self): |
54
|
|
|
form = self.request.form |
55
|
|
|
|
56
|
|
|
# Form submit toggle |
57
|
|
|
form_submitted = form.get("submitted", False) |
58
|
|
|
|
59
|
|
|
# Buttons |
60
|
|
|
form_preview = form.get("button_preview", False) |
61
|
|
|
form_create = form.get("button_create", False) |
62
|
|
|
form_cancel = form.get("button_cancel", False) |
63
|
|
|
|
64
|
|
|
objs = self.get_objects() |
65
|
|
|
|
66
|
|
|
# No ARs selected |
67
|
|
|
if not objs: |
68
|
|
|
return self.redirect(message=_("No items selected"), |
69
|
|
|
level="warning") |
70
|
|
|
|
71
|
|
|
# Handle preview |
72
|
|
|
if form_submitted and form_preview: |
73
|
|
|
logger.info("*** PREVIEW ***") |
74
|
|
|
|
75
|
|
|
# Handle create |
76
|
|
|
if form_submitted and form_create: |
77
|
|
|
logger.info("*** CREATE PARTITIONS ***") |
78
|
|
|
|
79
|
|
|
partitions = [] |
80
|
|
|
|
81
|
|
|
# create the partitions |
82
|
|
|
for partition in form.get("partitions", []): |
83
|
|
|
primary_uid = partition.get("primary_uid") |
84
|
|
|
sampletype_uid = partition.get("sampletype_uid") |
85
|
|
|
container_uid = partition.get("container_uid") |
86
|
|
|
preservation_uid = partition.get("preservation_uid") |
87
|
|
|
analyses_uids = partition.get("analyses") |
88
|
|
|
if not analyses_uids or not primary_uid: |
89
|
|
|
# Cannot create a partition w/o analyses! |
90
|
|
|
continue |
91
|
|
|
|
92
|
|
|
partition = self.create_partition( |
93
|
|
|
primary_uid=primary_uid, |
94
|
|
|
sampletype_uid=sampletype_uid, |
95
|
|
|
container_uid=container_uid, |
96
|
|
|
preservation_uid=preservation_uid, |
97
|
|
|
analyses_uids=analyses_uids) |
98
|
|
|
partitions.append(partition) |
99
|
|
|
logger.info("Successfully created partition: {}".format( |
100
|
|
|
api.get_path(partition))) |
101
|
|
|
|
102
|
|
|
# Force the reception of the partition |
103
|
|
|
doActionFor(partition, "receive") |
104
|
|
|
|
105
|
|
|
if not partitions: |
106
|
|
|
# If no partitions were created, show a warning message |
107
|
|
|
return self.redirect(message=_("No partitions were created")) |
108
|
|
|
|
109
|
|
|
# Remove analyses from primary Analysis Requests |
110
|
|
|
self.remove_primary_analyses() |
111
|
|
|
|
112
|
|
|
message = _("Created {} partitions: {}".format( |
113
|
|
|
len(partitions), ", ".join(map(api.get_title, partitions)))) |
114
|
|
|
return self.redirect(message=message) |
115
|
|
|
|
116
|
|
|
# Handle cancel |
117
|
|
|
if form_submitted and form_cancel: |
118
|
|
|
logger.info("*** CANCEL ***") |
119
|
|
|
return self.redirect(message=_("Partitioning canceled")) |
120
|
|
|
|
121
|
|
|
return self.template() |
122
|
|
|
|
123
|
|
|
def create_partition(self, primary_uid, sampletype_uid, container_uid, |
124
|
|
|
preservation_uid, analyses_uids): |
125
|
|
|
"""Create a new partition (AR) |
126
|
|
|
""" |
127
|
|
|
logger.info("*** CREATE PARTITION ***") |
128
|
|
|
|
129
|
|
|
ar = self.get_object_by_uid(primary_uid) |
130
|
|
|
record = { |
131
|
|
|
"InternalUse": True, |
132
|
|
|
"ParentAnalysisRequest": primary_uid, |
133
|
|
|
"SampleType": sampletype_uid, |
134
|
|
|
"Container": container_uid, |
135
|
|
|
"Preservation": preservation_uid, |
136
|
|
|
} |
137
|
|
|
|
138
|
|
|
for fieldname, field in api.get_fields(ar).items(): |
139
|
|
|
# if self.is_proxy_field(field): |
140
|
|
|
# logger.info("Skipping proxy field {}".format(fieldname)) |
141
|
|
|
# continue |
142
|
|
|
if self.is_computed_field(field): |
143
|
|
|
logger.info("Skipping computed field {}".format(fieldname)) |
144
|
|
|
continue |
145
|
|
|
if fieldname in PARTITION_SKIP_FIELDS: |
146
|
|
|
logger.info("Skipping field {}".format(fieldname)) |
147
|
|
|
continue |
148
|
|
|
fieldvalue = field.get(ar) |
149
|
|
|
record[fieldname] = fieldvalue |
150
|
|
|
logger.info("Update record '{}': {}".format( |
151
|
|
|
fieldname, repr(fieldvalue))) |
152
|
|
|
|
153
|
|
|
client = ar.getClient() |
154
|
|
|
analyses = map(self.get_object_by_uid, analyses_uids) |
155
|
|
|
services = map(lambda an: an.getAnalysisService(), analyses) |
156
|
|
|
|
157
|
|
|
partition = crar( |
158
|
|
|
client, |
159
|
|
|
self.request, |
160
|
|
|
record, |
161
|
|
|
analyses=services, |
162
|
|
|
specifications=self.get_specifications_for(ar) |
163
|
|
|
) |
164
|
|
|
|
165
|
|
|
# Remove selected analyses from the parent Analysis Request |
166
|
|
|
self.push_primary_analyses_for_removal(ar, analyses) |
167
|
|
|
|
168
|
|
|
# Reindex Parent Analysis Request |
169
|
|
|
# TODO Workflow - AnalysisRequest - Partitions creation |
170
|
|
|
ar.reindexObject(idxs=["isRootAncestor"]) |
171
|
|
|
|
172
|
|
|
return partition |
173
|
|
|
|
174
|
|
|
def push_primary_analyses_for_removal(self, analysis_request, analyses): |
175
|
|
|
"""Stores the analyses to be removed after partitions creation |
176
|
|
|
""" |
177
|
|
|
to_remove = self.analyses_to_remove.get(analysis_request, []) |
178
|
|
|
to_remove.extend(analyses) |
179
|
|
|
self.analyses_to_remove[analysis_request] = to_remove |
180
|
|
|
|
181
|
|
|
def remove_primary_analyses(self): |
182
|
|
|
"""Remove analyses relocated to partitions |
183
|
|
|
""" |
184
|
|
|
for ar, analyses in self.analyses_to_remove.items(): |
185
|
|
|
analyses_ids = list(set(map(api.get_id, analyses))) |
186
|
|
|
ar.manage_delObjects(analyses_ids) |
187
|
|
|
self.analyses_to_remove = dict() |
188
|
|
|
|
189
|
|
|
def get_specifications_for(self, ar): |
190
|
|
|
"""Returns a mapping of service uid -> specification |
191
|
|
|
""" |
192
|
|
|
spec = ar.getSpecification() |
193
|
|
|
if not spec: |
194
|
|
|
return [] |
195
|
|
|
return spec.getResultsRange() |
196
|
|
|
|
197
|
|
|
def is_proxy_field(self, field): |
198
|
|
|
"""Checks if the field is a proxy field |
199
|
|
|
""" |
200
|
|
|
return IProxyField.providedBy(field) |
201
|
|
|
|
202
|
|
|
def is_computed_field(self, field): |
203
|
|
|
"""Checks if the field is a coumputed field |
204
|
|
|
""" |
205
|
|
|
return field.type == "computed" |
206
|
|
|
|
207
|
|
|
def get_ar_data(self): |
208
|
|
|
"""Returns a list of AR data |
209
|
|
|
""" |
210
|
|
|
for obj in self.get_objects(): |
211
|
|
|
info = self.get_base_info(obj) |
212
|
|
|
info.update({ |
213
|
|
|
"analyses": self.get_analysis_data_for(obj), |
214
|
|
|
"sampletype": self.get_base_info(obj.getSampleType()), |
215
|
|
|
"number_of_partitions": self.get_number_of_partitions_for(obj), |
216
|
|
|
"template": self.get_template_data_for(obj), |
217
|
|
|
}) |
218
|
|
|
yield info |
219
|
|
|
|
220
|
|
|
def get_sampletype_data(self): |
221
|
|
|
"""Returns a list of SampleType data |
222
|
|
|
""" |
223
|
|
|
for obj in self.get_sampletypes(): |
224
|
|
|
info = self.get_base_info(obj) |
225
|
|
|
yield info |
226
|
|
|
|
227
|
|
|
def get_container_data(self): |
228
|
|
|
"""Returns a list of Container data |
229
|
|
|
""" |
230
|
|
|
for obj in self.get_containers(): |
231
|
|
|
info = self.get_base_info(obj) |
232
|
|
|
yield info |
233
|
|
|
|
234
|
|
|
def get_preservation_data(self): |
235
|
|
|
"""Returns a list of Preservation data |
236
|
|
|
""" |
237
|
|
|
for obj in self.get_preservations(): |
238
|
|
|
info = self.get_base_info(obj) |
239
|
|
|
yield info |
240
|
|
|
|
241
|
|
|
def get_objects(self): |
242
|
|
|
"""Returns a list of objects coming from the "uids" request parameter |
243
|
|
|
""" |
244
|
|
|
# Create a mapping of source ARs for copy |
245
|
|
|
uids = self.request.form.get("uids", "") |
246
|
|
|
if not uids: |
247
|
|
|
# check for the `items` parammeter |
248
|
|
|
uids = self.request.form.get("items", "") |
249
|
|
|
if isinstance(uids, basestring): |
250
|
|
|
uids = uids.split(",") |
251
|
|
|
unique_uids = OrderedDict().fromkeys(uids).keys() |
252
|
|
|
return filter(None, map(self.get_object_by_uid, unique_uids)) |
253
|
|
|
|
254
|
|
|
def get_sampletypes(self): |
255
|
|
|
"""Returns the available SampleTypes of the system |
256
|
|
|
""" |
257
|
|
|
query = { |
258
|
|
|
"portal_type": "SampleType", |
259
|
|
|
"sort_on": "sortable_title", |
260
|
|
|
"sort_order": "ascending", |
261
|
|
|
"inactive_state": "active", |
262
|
|
|
} |
263
|
|
|
results = api.search(query, "bika_setup_catalog") |
264
|
|
|
return map(api.get_object, results) |
265
|
|
|
|
266
|
|
|
def get_containers(self): |
267
|
|
|
"""Returns the available Containers of the system |
268
|
|
|
""" |
269
|
|
|
query = dict(portal_type="Container", |
270
|
|
|
sort_on="sortable_title", |
271
|
|
|
sort_order="ascending", |
272
|
|
|
inactive_state="active") |
273
|
|
|
results = api.search(query, "bika_setup_catalog") |
274
|
|
|
return map(api.get_object, results) |
275
|
|
|
|
276
|
|
|
def get_preservations(self): |
277
|
|
|
"""Returns the available Preservations of the system |
278
|
|
|
""" |
279
|
|
|
query = dict(portal_type="Preservation", |
280
|
|
|
sort_on="sortable_title", |
281
|
|
|
sort_order="ascending", |
282
|
|
|
inactive_state="active") |
283
|
|
|
results = api.search(query, "bika_setup_catalog") |
284
|
|
|
return map(api.get_object, results) |
285
|
|
|
|
286
|
|
|
@returns_super_model |
287
|
|
|
def to_super_model(self, obj_or_objs): |
288
|
|
|
"""Returns a SuperModel for a given object or a list of Supermodels if |
289
|
|
|
a list of objects was passed in |
290
|
|
|
""" |
291
|
|
|
return obj_or_objs |
292
|
|
|
|
293
|
|
|
def get_analysis_data_for(self, ar): |
294
|
|
|
"""Return the Analysis data for this AR |
295
|
|
|
""" |
296
|
|
|
# Exclude analyses from children (partitions) |
297
|
|
|
analyses = ar.objectValues("Analysis") |
298
|
|
|
out = [] |
299
|
|
|
for an in analyses: |
300
|
|
|
info = self.get_base_info(an) |
301
|
|
|
info.update({ |
302
|
|
|
"service_uid": an.getServiceUID(), |
303
|
|
|
}) |
304
|
|
|
out.append(info) |
305
|
|
|
return out |
306
|
|
|
|
307
|
|
|
def get_template_data_for(self, ar): |
308
|
|
|
"""Return the Template data for this AR |
309
|
|
|
""" |
310
|
|
|
info = None |
311
|
|
|
template = ar.getTemplate() |
312
|
|
|
ar_sampletype_uid = api.get_uid(ar.getSampleType()) |
313
|
|
|
ar_container_uid = "" |
314
|
|
|
if ar.getContainer(): |
315
|
|
|
ar_container_uid = api.get_uid(ar.getContainer()) |
316
|
|
|
ar_preservation_uid = "" |
317
|
|
|
if ar.getPreservation(): |
318
|
|
|
ar_preservation_uid = api.get_uid(ar.getPreservation()) |
319
|
|
|
|
320
|
|
|
if template: |
321
|
|
|
info = self.get_base_info(template) |
322
|
|
|
|
323
|
|
|
analyses = template.getAnalyses() |
324
|
|
|
partition_analyses = map( |
325
|
|
|
lambda x: (x.get("partition"), x.get("service_uid")), analyses) |
326
|
|
|
|
327
|
|
|
analyses_by_partition = defaultdict(list) |
328
|
|
|
for partition, service_uid in partition_analyses: |
329
|
|
|
analyses_by_partition[partition].append(service_uid) |
330
|
|
|
|
331
|
|
|
sampletypes_by_partition = defaultdict(list) |
332
|
|
|
containers_by_partition = defaultdict(list) |
333
|
|
|
preservations_by_partition = defaultdict(list) |
334
|
|
|
for part in template.getPartitions(): |
335
|
|
|
part_id = part.get("part_id") |
336
|
|
|
sampletype_uid = part.get('sampletype_uid', ar_sampletype_uid) |
337
|
|
|
sampletypes_by_partition[part_id] = sampletype_uid |
338
|
|
|
container_uid = part.get("container_uid", ar_container_uid) |
339
|
|
|
containers_by_partition[part_id] = container_uid |
340
|
|
|
preserv_uid = part.get("preservation_uid", ar_preservation_uid) |
341
|
|
|
preservations_by_partition[part_id] = preserv_uid |
342
|
|
|
|
343
|
|
|
partitions = map(lambda p: p.get("part_id"), |
344
|
|
|
template.getPartitions()) |
345
|
|
|
info.update({ |
346
|
|
|
"analyses": analyses_by_partition, |
347
|
|
|
"partitions": partitions, |
348
|
|
|
"sample_types": sampletypes_by_partition, |
349
|
|
|
"containers": containers_by_partition, |
350
|
|
|
"preservations": preservations_by_partition, |
351
|
|
|
}) |
352
|
|
|
else: |
353
|
|
|
info = { |
354
|
|
|
"analyses": {}, |
355
|
|
|
"partitions": [], |
356
|
|
|
"sample_types": {}, |
357
|
|
|
"containers": {}, |
358
|
|
|
"preservations": {}, |
359
|
|
|
} |
360
|
|
|
return info |
361
|
|
|
|
362
|
|
|
def get_number_of_partitions_for(self, ar): |
363
|
|
|
"""Return the number of selected partitions |
364
|
|
|
""" |
365
|
|
|
# fetch the number of partitions from the request |
366
|
|
|
uid = api.get_uid(ar) |
367
|
|
|
num = self.request.get("primary", {}).get(uid) |
368
|
|
|
|
369
|
|
|
if num is None: |
370
|
|
|
# get the number of partitions from the template |
371
|
|
|
template = ar.getTemplate() |
372
|
|
|
if template: |
373
|
|
|
num = len(template.getPartitions()) |
374
|
|
|
else: |
375
|
|
|
num = DEFAULT_NUMBER_OF_PARTITIONS |
376
|
|
|
try: |
377
|
|
|
num = int(num) |
378
|
|
|
except (TypeError, ValueError): |
379
|
|
|
num = DEFAULT_NUMBER_OF_PARTITIONS |
380
|
|
|
return num |
381
|
|
|
|
382
|
|
|
def get_base_info(self, obj): |
383
|
|
|
"""Extract the base info from the given object |
384
|
|
|
""" |
385
|
|
|
obj = api.get_object(obj) |
386
|
|
|
review_state = api.get_workflow_status_of(obj) |
387
|
|
|
state_title = review_state.capitalize().replace("_", " ") |
388
|
|
|
return { |
389
|
|
|
"obj": obj, |
390
|
|
|
"id": api.get_id(obj), |
391
|
|
|
"uid": api.get_uid(obj), |
392
|
|
|
"title": api.get_title(obj), |
393
|
|
|
"path": api.get_path(obj), |
394
|
|
|
"url": api.get_url(obj), |
395
|
|
|
"review_state": review_state, |
396
|
|
|
"state_title": state_title, |
397
|
|
|
} |
398
|
|
|
|
399
|
|
|
def redirect(self, redirect_url=None, message=None, level="info"): |
400
|
|
|
"""Redirect with a message |
401
|
|
|
""" |
402
|
|
|
if redirect_url is None: |
403
|
|
|
redirect_url = self.back_url |
404
|
|
|
if message is not None: |
405
|
|
|
self.add_status_message(message, level) |
406
|
|
|
return self.request.response.redirect(redirect_url) |
407
|
|
|
|
408
|
|
|
def get_object_by_uid(self, uid): |
409
|
|
|
"""Get the object by UID |
410
|
|
|
""" |
411
|
|
|
logger.debug("get_object_by_uid::UID={}".format(uid)) |
412
|
|
|
obj = api.get_object_by_uid(uid, None) |
413
|
|
|
if obj is None: |
414
|
|
|
logger.warn("!! No object found for UID #{} !!") |
415
|
|
|
return obj |
416
|
|
|
|
417
|
|
|
def add_status_message(self, message, level="info"): |
418
|
|
|
"""Set a portal status message |
419
|
|
|
""" |
420
|
|
|
return self.context.plone_utils.addPortalMessage(message, level) |
421
|
|
|
|