forked from SunghanKim/openkim-pipeline
/
mongodb.py
303 lines (265 loc) · 9.77 KB
/
mongodb.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
import pymongo
import os
import re
import datetime
import database
import config as cf
from logger import logging
logger = logging.getLogger('pipeline').getChild('mongodb')
client = pymongo.MongoClient(host='db0')
db = client[MONGODB]
PATH_RESULT = cf.RSYNC_LOCAL_ROOT
PATH_APPROVED = cf.RSYNC_LOCAL_ROOT
def config_edn(flname):
with open(flname) as f:
doc = cf.loadedn(f)
doc.setdefault("created_on", str(datetime.datetime.fromtimestamp(os.path.getctime(flname))))
return doc
def parse_kim_code(kim_code):
RE_KIMID = r"(?:([_a-zA-Z][_a-zA-Z0-9]*?)__)?([A-Z]{2})_([0-9]{12})(?:_([0-9]{3}))?"
return re.match(RE_KIMID,kim_code).groups()
def drop_tables():
check = raw_input("Are you sure? [y/n] ")
if check == "y":
db['obj'].drop()
db['data'].drop()
db['log'].drop()
db['job'].drop()
db['agent'].drop()
BADKEYS = { "kimspec", "profiling", "inserted_on", "latest" }
def rmbadkeys(dd):
return { k:v for k,v in dd.iteritems() if k not in BADKEYS }
def flatten(o):
if isinstance(o, dict):
out = {}
for key, value in o.iteritems():
c = flatten(value)
if isinstance(c, dict):
out.update({key + "." + subkey: subval for subkey, subval in c.iteritems()})
else:
out.update({key: c})
return out
elif hasattr(o, "__iter__"):
ll = [ flatten(item) for item in o ]
return ll
else:
return o
def kimcode_to_dict(kimcode):
name,leader,num,version = parse_kim_code(kimcode)
if not name:
name = database.look_for_name(leader, num, version)
kimcode = database.format_kim_code(name, leader, num, version)
leader = leader.lower()
foo = { "name": name, "type": leader.lower(),
"kimnum": num, "version": int(version),
"shortcode": "_".join((leader.upper(),num)),
"kimcode": kimcode,
"path" : os.path.join(leader.lower(),kimcode),
"approved" : True,
'_id' : kimcode,
"inserted_on": str(datetime.datetime.utcnow()),
"latest": True,
}
if foo['type'] in ('te','mo','md','tv','mv'):
foo['makeable'] = True
if foo['type'] in ('te','tv','mv'):
foo['runner'] = True
if foo['type'] in ('te','mo'):
foo['subject'] = True
if foo['type'] in ('md','td'):
foo['driver'] = True
else:
foo['driver'] = False
specpath = os.path.join(PATH_APPROVED,leader,kimcode,cf.CONFIG_FILE)
spec = config_edn(specpath)
if foo['type'] == 'te':
try:
testresult = spec.get('test-driver')
if testresult:
foo['driver'] = rmbadkeys(kimcode_to_dict(testresult))
except:
pass
if foo['type'] == 'mo':
try:
modeldriver = spec.get('model-driver')
if modeldriver:
foo['driver'] = rmbadkeys(kimcode_to_dict(modeldriver))
except:
pass
foo.update(spec)
return foo
def uuid_to_dict(leader,uuid):
foo = {'uuid': uuid ,
'path': os.path.join(leader.lower(),uuid),
'type': leader,
'_id' : uuid ,
"inserted_on": str(datetime.datetime.utcnow()),
"latest": True,
}
specpath = os.path.join(PATH_RESULT,leader,uuid,cf.CONFIG_FILE)
spec = config_edn(specpath)
pipespec = {}
try:
pipespecpath = os.path.join(PATH_RESULT,leader,uuid,cf.PIPELINESPEC_FILE)
pipespec = config_edn(pipespecpath)
except:
pass
#Extend runner and subject
runner = None
subject = None
if leader == 'tr' or leader=='er':
# IF wer are a TR get the test and model documents (cleaned up)
runner = rmbadkeys(kimcode_to_dict(spec['test']))
subject = rmbadkeys(kimcode_to_dict(spec['model']))
elif leader == 'vr':
# IF we are a vr, get either the verification_Test or
# verification_model and test or model
runner_code = spec.get('verification-test',None)
if not runner_code:
runner_code = spec.get('verification-model',None)
if runner_code:
runner = rmbadkeys(kimcode_to_dict(runner_code))
subject_code = spec.get('test',None)
if not subject_code:
subject_code = spec.get('model',None)
if subject_code:
subject = rmbadkeys(kimcode_to_dict(subject_code))
if runner:
foo['runner'] = runner
if subject:
foo['subject'] = subject
foo.update(spec)
foo.update(pipespec)
return foo
def doc_to_dict(doc,leader,uuid):
foo = doc
#copy info about result obj
result_obj_doc = uuid_to_dict(leader,uuid)
meta = rmbadkeys(result_obj_doc)
if leader == 'tr':
# IF wer are a TR get the test and model documents (cleaned up)
runner = rmbadkeys(kimcode_to_dict(result_obj_doc['test']))
subject = rmbadkeys(kimcode_to_dict(result_obj_doc['model']))
elif leader == 'vr':
# IF we are a vr, get either the verification_Test or
# verification_model and test or model
runner_code = result_obj_doc.get('verification-test',None)
if not runner_code:
runner_code = result_obj_doc.get('verification-model',None)
if runner_code:
runner = rmbadkeys(kimcode_to_dict(runner_code))
subject_code = result_obj_doc.get('test',None)
if not subject_code:
subject_code = result_obj_doc.get('model',None)
if subject_code:
subject = rmbadkeys(kimcode_to_dict(subject_code))
try:
meta['runner'] = runner
except:
pass
try:
meta['subject'] = subject
except:
pass
foo['meta'] = meta
foo['created_on'] = result_obj_doc['created_on']
foo['inserted_on'] = result_obj_doc['inserted_on']
foo['latest'] = True
return foo
def deprecate_similar_objects(dbname, info, keys):
tinfo = flatten(info)
query = { key:tinfo[key] for key in keys }
query.update({'created_on': {"$lt": tinfo['created_on']}})
update = { "$set": {"latest": False } }
status = db[dbname].update(spec=query, document=update, multi=True)
if status['n'] > 0:
logger.info("Updated %i existing documents to deprecated" % status['n'])
def insert_one_object(kimcode):
logger.info("Inserting object %s", kimcode)
info = kimcode_to_dict(kimcode)
try:
db.obj.insert(info)
deprecate_similar_objects('obj', info, ['shortcode'])
except:
logger.error("Already have %s", kimcode)
def insert_one_result(leader, kimcode):
logger.info("Inserting result %s ", kimcode)
stuff = None
info = uuid_to_dict(leader, kimcode)
try:
resultobj = db.obj.insert(info)
deprecate_similar_objects('obj', info, ['runner.kimcode', 'subject.kimcode'])
except:
logger.error("Aready have %s", kimcode)
return
try:
with open(os.path.join(PATH_RESULT,leader,kimcode,'results.edn')) as f:
edn_docs = cf.loadedn(f)
edn_docs = edn_docs if isinstance(edn_docs, list) else [edn_docs]
for doc in edn_docs:
stuff = doc_to_dict(doc,leader,kimcode)
db.data.insert(stuff)
deprecate_similar_objects('data', stuff, ['meta.runner.kimcode', 'meta.subject.kimcode'])
except:
logger.info("Could not read document for %s/%s", leader, kimcode)
stuff = doc_to_dict({}, leader, kimcode)
db.data.insert(stuff)
deprecate_similar_objects('data', stuff, ['meta.runner.kimcode', 'meta.subject.kimcode'])
def insert_one_reference_data(leader, kimcode):
logger.info("Inserting reference data %s ", kimcode)
info = kimcode_to_dict(kimcode)
try:
resultobj = db.obj.insert(info)
except:
logger.error("Aready have %s", kimcode)
return
try:
with open(os.path.join(PATH_APPROVED,leader,kimcode,kimcode+'.edn')) as f:
edn_docs = cf.loadedn(f)
edn_docs = edn_docs if isinstance(edn_docs, list) else [edn_docs]
for doc in edn_docs:
stuff = doc_to_dict(doc,leader,kimcode)
db.data.insert(stuff)
except:
logger.info("Could not read document for %s/%s", leader, kimcode)
stuff = doc_to_dict({}, leader, kimcode)
db.data.insert(stuff)
def insert_objs():
logger.info("Filling with objects")
leaders = ('te','tv','mv','mo','md','td')
for leader in leaders:
for i,folder in enumerate(os.listdir(os.path.join(PATH_APPROVED,leader))):
if folder.startswith("Make"):
continue
insert_one_object(folder)
def insert_results():
logger.info("Filling with test results")
leaders = ('tr','vr','er')
for leader in leaders:
for i, folder in enumerate(os.listdir(os.path.join(PATH_RESULT,leader))):
insert_one_result(leader, folder)
def insert_reference_data():
logger.info("Filling with reference data")
leaders = ('rd',)
for leader in leaders:
for i, folder in enumerate(os.listdir(os.path.join(PATH_APPROVED,leader))):
insert_one_reference_data(leader, folder)
def insert_all():
insert_objs()
insert_results()
def create_indices():
""" Create the useful indices """
db.obj.ensure_index("uuid")
db.obj.ensure_index("kimcode")
db.obj.ensure_index("type")
db.obj.ensure_index("shortcode")
db.obj.ensure_index("version")
db.obj.ensure_index("driver.kimcode")
db.obj.ensure_index("ensured_on")
db.data.ensure_index("meta.type")
db.data.ensure_index("meta.ensured_on")
db.data.ensure_index("meta.runner.kimcode")
db.data.ensure_index("meta.subject.kimcode")
db.data.ensure_index("property")
db.data.ensure_index("kim-template-tags")
db.data.ensure_index("uuid")