forked from mxcube/HardwareObjects
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ISPyBClient2Mockup.py
574 lines (471 loc) · 16.9 KB
/
ISPyBClient2Mockup.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
"""
A client for ISPyB Webservices.
"""
import logging
import os
import datetime
from HardwareRepository import HardwareRepository
from HardwareRepository.BaseHardwareObjects import HardwareObject
# to simulate wrong loginID, use "wrong" for loginID
# to simulate wrong psd, use "wrong" for password
# to simulate ispybDown, but ldap login succeeds, use "ispybDown" for password
# to simulate no session scheduled, use "nosession" for password
class ISPyBClient2Mockup(HardwareObject):
"""
Web-service client for ISPyB.
"""
def __init__(self, name):
HardwareObject.__init__(self, name)
self.__translations = {}
self.__disabled = False
self.__test_proposal = None
self.loginType = None
def init(self):
"""
Init method declared by HardwareObject.
"""
self.authServerType = self.getProperty('authServerType') or "ldap"
if self.authServerType == "ldap":
# Initialize ldap
self.ldapConnection=self.getObjectByRole('ldapServer')
if self.ldapConnection is None:
logging.getLogger("HWR").debug('LDAP Server is not available')
self.loginType = self.getProperty("loginType") or "proposal"
self.session_hwobj = self.getObjectByRole('session')
self.beamline_name = self.session_hwobj.beamline_name
self.__test_proposal = {'status': {'code': 'ok'},
'Person': {'personId': 1,
'laboratoryId': 1,
'login': None,
'familyName':'operator on IDTESTeh1'},
'Proposal': {'code': 'idtest',
'title': 'operator on IDTESTeh1',
'personId': 1,
'number': '000',
'proposalId': 1,
'type': 'MX'},
'Session': [{'scheduled': 0,
'startDate': '2013-06-11 00:00:00',
'endDate': '2013-06-12 07:59:59',
'beamlineName': 'ID:TEST',
'timeStamp': datetime.datetime(2013, 6, 11, 9, 40, 36),
'comments': 'Session created by the BCM',
'sessionId': 34591,
'proposalId': 1, 'nbShifts': 3}],
'Laboratory': {'laboratoryId': 1,
'name': 'TEST eh1'}}
def get_login_type(self):
self.loginType = self.getProperty("loginType") or "proposal"
def login (self,loginID, psd, ldap_connection=None):
# to simulate wrong loginID
if loginID == "wrong":
return {'status':{ "code": "error", "msg": "loginID 'wrong' does not exist!" }, 'Proposal': None, 'Session': None}
# to simulate wrong psd
if psd == "wrong":
return {'status':{ "code": "error", "msg": "Wrong password!" }, 'Proposal': None, 'Session': None}
# to simulate ispybDown, but login succeed
if psd == "ispybDown":
return {'status':{ "code": "ispybDown", "msg": "ispyb is down" }, 'Proposal': None, 'Session': None}
new_session = False
if psd == "nosession":
new_session=True
prop=self.get_proposal(loginID,"")
return {'status':{ "code": "ok", "msg": "Successful login" }, 'Proposal': prop['Proposal'],
'session': {"session": prop['Session'],"new_session_flag":new_session, "is_inhouse": False},
'local_contact': "BL Scientist",
'person': prop['Person'],
'laboratory': prop['Laboratory']}
def get_proposal(self, proposal_code, proposal_number):
"""
Returns the tuple (Proposal, Person, Laboratory, Session, Status).
Containing the data from the coresponding tables in the database
the status of the database operations are returned in Status.
:param proposal_code: The proposal code
:type proposal_code: str
:param proposal_number: The proposal number
:type propsoal_number: int
:returns: The dict (Proposal, Person, Laboratory, Sessions, Status).
:rtype: dict
"""
return self.__test_proposal
def get_proposals_by_user(self, user_name):
return [self.__test_proposal]
def get_session_local_contact(self, session_id):
return {'personId': 1,
'laboratoryId': 1,
'login': None,
'familyName':'operator on ID14eh1'}
def translate(self, code, what):
"""
Given a proposal code, returns the correct code to use in the GUI,
or what to send to LDAP, user office database, or the ISPyB database.
"""
try:
translated = self.__translations[code][what]
except KeyError:
translated = code
return translated
def isInhouseUser(self, proposal_code, proposal_number):
"""
Returns True if the proposal is considered to be a
in-house user.
:param proposal_code:
:type proposal_code: str
:param proposal_number:
:type proposal_number: str
:rtype: bool
"""
for proposal in self['inhouse']:
if proposal_code == proposal.code:
if str(proposal_number) == str(proposal.number):
return True
return False
def store_data_collection(self, mx_collection, beamline_setup = None):
"""
Stores the data collection mx_collection, and the beamline setup
if provided.
:param mx_collection: The data collection parameters.
:type mx_collection: dict
:param beamline_setup: The beamline setup.
:type beamline_setup: dict
:returns: None
"""
return None, None
def store_beamline_setup(self, session_id, beamline_setup):
"""
Stores the beamline setup dict <beamline_setup>.
:param session_id: The session id that the beamline_setup
should be associated with.
:type session_id: int
:param beamline_setup: The dictonary with beamline settings.
:type beamline_setup: dict
:returns beamline_setup_id: The database id of the beamline setup.
:rtype: str
"""
pass
def update_data_collection(self, mx_collection, wait=False):
"""
Updates the datacollction mx_collection, this requires that the
collectionId attribute is set and exists in the database.
:param mx_collection: The dictionary with collections parameters.
:type mx_collection: dict
:returns: None
"""
pass
def update_bl_sample(self, bl_sample):
"""
Creates or stos a BLSample entry.
:param sample_dict: A dictonary with the properties for the entry.
:type sample_dict: dict
"""
pass
def store_image(self, image_dict):
"""
Stores the image (image parameters) <image_dict>
:param image_dict: A dictonary with image pramaters.
:type image_dict: dict
:returns: None
"""
pass
def __find_sample(self, sample_ref_list, code = None, location = None):
"""
Returns the sample with the matching "search criteria" <code> and/or
<location> with-in the list sample_ref_list.
The sample_ref object is defined in the head of the file.
:param sample_ref_list: The list of sample_refs to search.
:type sample_ref: list
:param code: The vial datamatrix code (or bar code)
:param type: str
:param location: A tuple (<basket>, <vial>) to search for.
:type location: tuple
"""
pass
def get_samples(self, proposal_id, session_id):
return [{"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "1",
"crystalSpaceGroup": "P212121",
"diffractionPlan": {
"diffractionPlanId": 457980,
"experimentKind": "Default",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "Default",
"proteinAcronym": "A-TIM",
"sampleId": 515485,
"sampleLocation": "1",
"sampleName": "fghfg",
"smiles": None
},
{
"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "2",
"crystalSpaceGroup": "P2",
"diffractionPlan": {
"diffractionPlanId": 457833,
"experimentKind": "OSC",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "OSC",
"proteinAcronym": "B2 hexa",
"sampleId": 515419,
"sampleLocation": "1",
"sampleName": "sample"
},
{
"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "2",
"crystalSpaceGroup": "P2",
"diffractionPlan": {
"diffractionPlanId": 457834,
"experimentKind": "OSC",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "OSC",
"proteinAcronym": "B2 hexa",
"sampleId": 515420,
"sampleLocation": "2",
"sampleName": "sample"
},
{
"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "2",
"crystalSpaceGroup": "P2",
"diffractionPlan": {
"diffractionPlanId": 457835,
"experimentKind": "OSC",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "OSC",
"proteinAcronym": "B2 hexa",
"sampleId": 515421,
"sampleLocation": "3",
"sampleName": "sample"
},
{
"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "2",
"crystalSpaceGroup": "P2",
"diffractionPlan": {
"diffractionPlanId": 457836,
"experimentKind": "OSC",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "OSC",
"proteinAcronym": "B2 hexa",
"sampleId": 515422,
"sampleLocation": "5",
"sampleName": "sample"
},
{
"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "2",
"crystalSpaceGroup": "P2",
"diffractionPlan": {
"diffractionPlanId": 457837,
"experimentKind": "OSC",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "OSC",
"proteinAcronym": "B2 hexa",
"sampleId": 515423,
"sampleLocation": "6",
"sampleName": "sample"
},
{
"cellA": 0.0,
"cellAlpha": 0.0,
"cellB": 0.0,
"cellBeta": 0.0,
"cellC": 0.0,
"cellGamma": 0.0,
"containerSampleChangerLocation": "2",
"crystalSpaceGroup": "P2",
"diffractionPlan": {
"diffractionPlanId": 457838,
"experimentKind": "OSC",
"numberOfPositions": 0,
"observedResolution": 0.0,
"preferredBeamDiameter": 0.0,
"radiationSensitivity": 0.0,
"requiredCompleteness": 0.0,
"requiredMultiplicity": 0.0,
"requiredResolution": 0.0
},
"experimentType": "OSC",
"proteinAcronym": "B2 hexa",
"sampleId": 515424,
"sampleLocation": "7",
"sampleName": "sample"
}]
def get_session_samples(self, proposal_id, session_id, sample_refs):
"""
Retrives the list of samples associated with the session <session_id>.
The samples from ISPyB is cross checked with the ones that are
currently in the sample changer.
The datamatrix code read by the sample changer is used in case
of conflict.
:param proposal_id: ISPyB proposal id.
:type proposal_id: int
:param session_id: ISPyB session id to retreive samples for.
:type session_id: int
:param sample_refs: The list of samples currently in the
sample changer. As a list of sample_ref
objects
:type sample_refs: list (of sample_ref objects).
:returns: A list with sample_ref objects.
:rtype: list
"""
pass
def get_bl_sample(self, bl_sample_id):
"""
Fetch the BLSample entry with the id bl_sample_id
:param bl_sample_id:
:type bl_sample_id: int
:returns: A BLSampleWSValue, defined in the wsdl.
:rtype: BLSampleWSValue
"""
pass
def create_session(self, session_dict):
pass
def update_session(self, session_dict):
pass
def store_energy_scan(self, energyscan_dict):
pass
def associate_bl_sample_and_energy_scan(self, entry_dict):
pass
def get_data_collection(self, data_collection_id):
"""
Retrives the data collection with id <data_collection_id>
:param data_collection_id: Id of data collection.
:type data_collection_id: int
:rtype: dict
"""
pass
def get_data_collection_id(self, dc_dict):
pass
def get_session(self, session_id):
pass
def store_xfe_spectrum(self, xfespectrum_dict):
"""
Stores a xfe spectrum.
:returns: A dictionary with the xfe spectrum id.
:rtype: dict
"""
pass
def disable(self):
self.__disabled = True
def enable(self):
self.__disabled = False
def find_detector(self, type, manufacturer,
model, mode):
"""
Returns the Detector3VO object with the characteristics
matching the ones given.
"""
pass
def store_data_collection_group(self, mx_collection):
"""
Stores or updates a DataCollectionGroup object.
The entry is updated of the group_id in the
mx_collection dictionary is set to an exisitng
DataCollectionGroup id.
:param mx_collection: The dictionary of values to create the object from.
:type mx_collection: dict
:returns: DataCollectionGroup id
:rtype: int
"""
pass
def _store_data_collection_group(self, group_data):
pass
def store_centred_position(self, end_cpos, gridx=None, gridy=None):
pass
def store_autoproc_program(self, autoproc_program_dict):
pass
def store_workflow(self, *args, **kwargs):
return 1, 1, 1
def _store_workflow(self, info_dict):
pass
def store_image_quality_indicators(self, image_dict):
pass
# Bindings to methods called from older bricks.
getProposal = get_proposal
getSessionLocalContact = get_session_local_contact
createSession = create_session
getSessionSamples = get_session_samples
getSession = get_session
storeDataCollection = store_data_collection
storeBeamLineSetup = store_beamline_setup
getDataCollection = get_data_collection
updateBLSample = update_bl_sample
getBLSample = get_bl_sample
associateBLSampleAndEnergyScan = associate_bl_sample_and_energy_scan
updateDataCollection = update_data_collection
storeImage = store_image
storeEnergyScan = store_energy_scan
storeXfeSpectrum = store_xfe_spectrum