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#!/usr/bin/env python |
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# coding=utf-8 |
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from __future__ import division, print_function, unicode_literals |
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import pickle |
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import re |
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import os.path |
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import sys |
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import time |
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import bson |
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import gridfs |
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import pymongo |
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import sacred.optional as opt |
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from pymongo.errors import AutoReconnect, InvalidDocument, DuplicateKeyError |
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from sacred.commandline_options import CommandLineOption |
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from sacred.dependencies import get_digest |
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from sacred.observers.base import RunObserver |
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from sacred.serializer import flatten |
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from sacred.utils import ObserverError |
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DEFAULT_MONGO_PRIORITY = 30 |
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def force_valid_bson_key(key): |
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key = str(key) |
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if key.startswith('$'): |
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key = '@' + key[1:] |
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key = key.replace('.', ',') |
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return key |
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def force_bson_encodeable(obj): |
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if isinstance(obj, dict): |
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try: |
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bson.BSON.encode(obj, check_keys=True) |
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return obj |
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except bson.InvalidDocument: |
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return {force_valid_bson_key(k): force_bson_encodeable(v) |
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for k, v in obj.items()} |
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elif opt.has_numpy and isinstance(obj, opt.np.ndarray): |
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return obj |
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else: |
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try: |
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bson.BSON.encode({'dict_just_for_testing': obj}) |
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return obj |
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except bson.InvalidDocument: |
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return str(obj) |
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class MongoObserver(RunObserver): |
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COLLECTION_NAME_BLACKLIST = {'fs.files', 'fs.chunks', '_properties', |
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'system.indexes', 'seach_space'} |
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VERSION = 'MongoObserver-0.7.0' |
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@staticmethod |
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def create(url='localhost', db_name='sacred', collection='runs', |
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overwrite=None, priority=DEFAULT_MONGO_PRIORITY, **kwargs): |
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client = pymongo.MongoClient(url, **kwargs) |
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database = client[db_name] |
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if collection in MongoObserver.COLLECTION_NAME_BLACKLIST: |
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raise KeyError('Collection name "{}" is reserved. ' |
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'Please use a different one.'.format(collection)) |
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runs_collection = database[collection] |
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metrics_collection = database["metrics"] |
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fs = gridfs.GridFS(database) |
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return MongoObserver(runs_collection, |
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fs, overwrite=overwrite, |
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metrics_collection=metrics_collection, |
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priority=priority) |
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def __init__(self, runs_collection, |
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fs, overwrite=None, metrics_collection=None, |
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priority=DEFAULT_MONGO_PRIORITY): |
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self.runs = runs_collection |
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self.metrics = metrics_collection |
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self.fs = fs |
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self.overwrite = overwrite |
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self.run_entry = None |
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self.priority = priority |
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def queued_event(self, ex_info, command, queue_time, config, meta_info, |
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_id): |
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if self.overwrite is not None: |
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raise RuntimeError("Can't overwrite with QUEUED run.") |
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self.run_entry = { |
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'experiment': dict(ex_info), |
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'command': command, |
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'config': flatten(config), |
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'meta': meta_info, |
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'status': 'QUEUED' |
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} |
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# set ID if given |
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if _id is not None: |
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self.run_entry['_id'] = _id |
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# save sources |
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self.run_entry['experiment']['sources'] = self.save_sources(ex_info) |
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self.insert() |
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return self.run_entry['_id'] |
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def started_event(self, ex_info, command, host_info, start_time, config, |
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meta_info, _id): |
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if self.overwrite is None: |
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self.run_entry = {'_id': _id} |
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else: |
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if self.run_entry is not None: |
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raise RuntimeError("Cannot overwrite more than once!") |
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# sanity checks |
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if self.overwrite['experiment']['sources'] != ex_info['sources']: |
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raise RuntimeError("Sources don't match") |
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self.run_entry = self.overwrite |
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self.run_entry.update({ |
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'experiment': dict(ex_info), |
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'format': self.VERSION, |
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'command': command, |
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'host': dict(host_info), |
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'start_time': start_time, |
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'config': flatten(config), |
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'meta': meta_info, |
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'status': 'RUNNING', |
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'resources': [], |
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'artifacts': [], |
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'captured_out': '', |
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'info': {}, |
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'heartbeat': None |
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}) |
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# save sources |
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self.run_entry['experiment']['sources'] = self.save_sources(ex_info) |
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self.insert() |
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return self.run_entry['_id'] |
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def heartbeat_event(self, info, captured_out, beat_time, result): |
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self.run_entry['info'] = flatten(info) |
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self.run_entry['captured_out'] = captured_out |
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self.run_entry['heartbeat'] = beat_time |
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self.run_entry['result'] = result |
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self.save() |
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def completed_event(self, stop_time, result): |
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self.run_entry['stop_time'] = stop_time |
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self.run_entry['result'] = flatten(result) |
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self.run_entry['status'] = 'COMPLETED' |
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self.final_save(attempts=10) |
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def interrupted_event(self, interrupt_time, status): |
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self.run_entry['stop_time'] = interrupt_time |
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self.run_entry['status'] = status |
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self.final_save(attempts=3) |
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def failed_event(self, fail_time, fail_trace): |
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self.run_entry['stop_time'] = fail_time |
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self.run_entry['status'] = 'FAILED' |
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self.run_entry['fail_trace'] = fail_trace |
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self.final_save(attempts=1) |
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def resource_event(self, filename): |
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if self.fs.exists(filename=filename): |
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md5hash = get_digest(filename) |
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if self.fs.exists(filename=filename, md5=md5hash): |
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resource = (filename, md5hash) |
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if resource not in self.run_entry['resources']: |
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self.run_entry['resources'].append(resource) |
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self.save() |
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return |
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with open(filename, 'rb') as f: |
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file_id = self.fs.put(f, filename=filename) |
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md5hash = self.fs.get(file_id).md5 |
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self.run_entry['resources'].append((filename, md5hash)) |
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self.save() |
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def artifact_event(self, name, filename): |
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with open(filename, 'rb') as f: |
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run_id = self.run_entry['_id'] |
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db_filename = 'artifact://{}/{}/{}'.format(self.runs.name, run_id, |
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name) |
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file_id = self.fs.put(f, filename=db_filename) |
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self.run_entry['artifacts'].append({'name': name, |
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'file_id': file_id}) |
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self.save() |
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def log_metrics(self, metrics_by_name, info): |
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"""Store new measurements to the database. |
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Take measurements and store them into |
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the metrics collection in the database. |
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Additionally, reference the metrics |
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in the info["metrics"] dictionary. |
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""" |
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if self.metrics is None: |
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# If, for whatever reason, the metrics collection has not been set |
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# do not try to save there anything |
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return |
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for key in metrics_by_name: |
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query = {"run_id": self.run_entry['_id'], |
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"name": key} |
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push = {"steps": {"$each": metrics_by_name[key]["steps"]}, |
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"values": {"$each": metrics_by_name[key]["values"]}, |
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"timestamps": {"$each": metrics_by_name[key]["timestamps"]} |
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} |
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update = {"$push": push} |
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result = self.metrics.update_one(query, update, upsert=True) |
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if result.upserted_id is not None: |
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# This is the first time we are storing this metric |
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info.setdefault("metrics", []) \ |
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.append({"name": key, "id": str(result.upserted_id)}) |
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def insert(self): |
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if self.overwrite: |
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return self.save() |
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autoinc_key = self.run_entry.get('_id') is None |
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while True: |
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if autoinc_key: |
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c = self.runs.find({}, {'_id': 1}) |
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c = c.sort('_id', pymongo.DESCENDING).limit(1) |
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self.run_entry['_id'] = c.next()['_id'] + 1 if c.count() else 1 |
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try: |
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self.runs.insert_one(self.run_entry) |
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except InvalidDocument: |
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raise ObserverError('Run contained an unserializable entry.' |
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'(most likely in the info)') |
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except DuplicateKeyError: |
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if not autoinc_key: |
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raise |
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return |
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def save(self): |
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try: |
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self.runs.replace_one({'_id': self.run_entry['_id']}, |
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self.run_entry) |
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except AutoReconnect: |
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pass # just wait for the next save |
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except InvalidDocument: |
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raise ObserverError('Run contained an unserializable entry.' |
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'(most likely in the info)') |
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def final_save(self, attempts): |
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for i in range(attempts): |
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try: |
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self.runs.save(self.run_entry) |
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return |
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except AutoReconnect: |
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if i < attempts - 1: |
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time.sleep(1) |
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except InvalidDocument: |
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self.run_entry = force_bson_encodeable(self.run_entry) |
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print("Warning: Some of the entries of the run were not " |
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"BSON-serializable!\n They have been altered such that " |
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"they can be stored, but you should fix your experiment!" |
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"Most likely it is either the 'info' or the 'result'.", |
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file=sys.stderr) |
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from tempfile import NamedTemporaryFile |
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with NamedTemporaryFile(suffix='.pickle', delete=False, |
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prefix='sacred_mongo_fail_') as f: |
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pickle.dump(self.run_entry, f) |
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print("Warning: saving to MongoDB failed! " |
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"Stored experiment entry in '{}'".format(f.name), |
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file=sys.stderr) |
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def save_sources(self, ex_info): |
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base_dir = ex_info['base_dir'] |
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source_info = [] |
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for source_name, md5 in ex_info['sources']: |
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abs_path = os.path.join(base_dir, source_name) |
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file = self.fs.find_one({'filename': abs_path, 'md5': md5}) |
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if file: |
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_id = file._id |
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else: |
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with open(abs_path, 'rb') as f: |
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_id = self.fs.put(f, filename=abs_path) |
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source_info.append([source_name, _id]) |
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return source_info |
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def __eq__(self, other): |
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if isinstance(other, MongoObserver): |
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return self.runs == other.runs |
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return False |
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def __ne__(self, other): |
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return not self.__eq__(other) |
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class MongoDbOption(CommandLineOption): |
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"""Add a MongoDB Observer to the experiment.""" |
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arg = 'DB' |
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arg_description = "Database specification. Can be " \ |
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"[host:port:]db_name[.collection][!priority]" |
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DB_NAME_PATTERN = r"[_A-Za-z][0-9A-Za-z#%&'()+\-;=@\[\]^_{}.]{0,63}" |
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HOSTNAME_PATTERN = \ |
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r"(?=.{1,255}$)" \ |
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r"[0-9A-Za-z](?:(?:[0-9A-Za-z]|-){0,61}[0-9A-Za-z])?" \ |
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r"(?:\.[0-9A-Za-z](?:(?:[0-9A-Za-z]|-){0,61}[0-9A-Za-z])?)*" \ |
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r"\.?" |
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URL_PATTERN = "(?:" + HOSTNAME_PATTERN + ")" + ":" + "(?:[0-9]{1,5})" |
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PRIORITY_PATTERN = "(?P<priority>!-?\d+)?" |
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DB_NAME = re.compile("^" + DB_NAME_PATTERN + PRIORITY_PATTERN + "$") |
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|
URL = re.compile("^" + URL_PATTERN + PRIORITY_PATTERN + "$") |
|
305
|
|
|
URL_DB_NAME = re.compile("^(?P<url>" + URL_PATTERN + ")" + ":" + |
|
306
|
|
|
"(?P<db_name>" + DB_NAME_PATTERN + ")" + |
|
307
|
|
|
PRIORITY_PATTERN + "$") |
|
308
|
|
|
|
|
309
|
|
|
@classmethod |
|
310
|
|
|
def apply(cls, args, run): |
|
311
|
|
|
url, db_name, collection, priority = cls.parse_mongo_db_arg(args) |
|
312
|
|
|
if collection: |
|
313
|
|
|
mongo = MongoObserver.create(db_name=db_name, url=url, |
|
314
|
|
|
collection=collection, |
|
315
|
|
|
priority=priority) |
|
316
|
|
|
else: |
|
317
|
|
|
mongo = MongoObserver.create(db_name=db_name, url=url, |
|
318
|
|
|
priority=priority) |
|
319
|
|
|
|
|
320
|
|
|
run.observers.append(mongo) |
|
321
|
|
|
|
|
322
|
|
|
@classmethod |
|
323
|
|
|
def parse_mongo_db_arg(cls, mongo_db): |
|
324
|
|
|
def get_priority(pattern): |
|
325
|
|
|
prio_str = pattern.match(mongo_db).group('priority') |
|
326
|
|
|
if prio_str is None: |
|
327
|
|
|
return DEFAULT_MONGO_PRIORITY |
|
328
|
|
|
else: |
|
329
|
|
|
return int(prio_str[1:]) |
|
330
|
|
|
|
|
331
|
|
|
if cls.DB_NAME.match(mongo_db): |
|
332
|
|
|
db_name, _, collection = mongo_db.partition('.') |
|
333
|
|
|
return ('localhost:27017', db_name, collection, |
|
334
|
|
|
get_priority(cls.DB_NAME)) |
|
335
|
|
|
elif cls.URL.match(mongo_db): |
|
336
|
|
|
return mongo_db, 'sacred', '', get_priority(cls.URL) |
|
337
|
|
|
elif cls.URL_DB_NAME.match(mongo_db): |
|
338
|
|
|
match = cls.URL_DB_NAME.match(mongo_db) |
|
339
|
|
|
db_name, _, collection = match.group('db_name').partition('.') |
|
340
|
|
|
return (match.group('url'), db_name, collection, |
|
341
|
|
|
get_priority(cls.URL_DB_NAME)) |
|
342
|
|
|
else: |
|
343
|
|
|
raise ValueError('mongo_db argument must have the form "db_name" ' |
|
344
|
|
|
'or "host:port[:db_name]" but was {}' |
|
345
|
|
|
.format(mongo_db)) |
|
346
|
|
|
|