Mercurial > repos > shellac > guppy_basecaller

comparison env/bin/sdbadmin @ 5:9b1c78e6ba9c draft default tip

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"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
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4:79f47841a781 5:9b1c78e6ba9c
1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
2 # Copyright (c) 2009 Chris Moyer http://kopertop.blogspot.com/
3 #
4 # Permission is hereby granted, free of charge, to any person obtaining a
5 # copy of this software and associated documentation files (the
6 # "Software"), to deal in the Software without restriction, including
7 # without limitation the rights to use, copy, modify, merge, publish, dis-
8 # tribute, sublicense, and/or sell copies of the Software, and to permit
9 # persons to whom the Software is furnished to do so, subject to the fol-
10 # lowing conditions:
11 #
12 # The above copyright notice and this permission notice shall be included
13 # in all copies or substantial portions of the Software.
14 #
15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
21
22 #
23 # Tools to dump and recover an SDB domain
24 #
25 VERSION = "%prog version 1.0"
26 import boto
27 import time
28 from boto import sdb
29 from boto.compat import json
30
31 def choice_input(options, default=None, title=None):
32 """
33 Choice input
34 """
35 if title == None:
36 title = "Please choose"
37 print title
38 objects = []
39 for n, obj in enumerate(options):
40 print "%s: %s" % (n, obj)
41 objects.append(obj)
42 choice = int(raw_input(">>> "))
43 try:
44 choice = objects[choice]
45 except:
46 choice = default
47 return choice
48
49 def confirm(message="Are you sure?"):
50 choice = raw_input("%s [yN] " % message)
51 return choice and len(choice) > 0 and choice[0].lower() == "y"
52
53
54 def dump_db(domain, file_name, use_json=False, sort_attributes=False):
55 """
56 Dump SDB domain to file
57 """
58 f = open(file_name, "w")
59 if use_json:
60 for item in domain:
61 data = {"name": item.name, "attributes": item}
62 print >> f, json.dumps(data, sort_keys=sort_attributes)
63 else:
64 doc = domain.to_xml(f)
65
66 def empty_db(domain):
67 """
68 Remove all entries from domain
69 """
70 for item in domain:
71 item.delete()
72
73 def load_db(domain, file, use_json=False):
74 """
75 Load a domain from a file, this doesn't overwrite any existing
76 data in the file so if you want to do a full recovery and restore
77 you need to call empty_db before calling this
78
79 :param domain: The SDB Domain object to load to
80 :param file: The File to load the DB from
81 """
82 if use_json:
83 for line in file.readlines():
84 if line:
85 data = json.loads(line)
86 item = domain.new_item(data['name'])
87 item.update(data['attributes'])
88 item.save()
89
90 else:
91 domain.from_xml(file)
92
93 def check_valid_region(conn, region):
94 if conn is None:
95 print 'Invalid region (%s)' % region
96 sys.exit(1)
97
98 def create_db(domain_name, region_name):
99 """Create a new DB
100
101 :param domain: Name of the domain to create
102 :type domain: str
103 """
104 sdb = boto.sdb.connect_to_region(region_name)
105 check_valid_region(sdb, region_name)
106 return sdb.create_domain(domain_name)
107
108 if __name__ == "__main__":
109 from optparse import OptionParser
110 parser = OptionParser(version=VERSION, usage="Usage: %prog [--dump|--load|--empty|--list|-l] [options]")
111
112 # Commands
113 parser.add_option("--dump", help="Dump domain to file", dest="dump", default=False, action="store_true")
114 parser.add_option("--load", help="Load domain contents from file", dest="load", default=False, action="store_true")
115 parser.add_option("--empty", help="Empty all contents of domain", dest="empty", default=False, action="store_true")
116 parser.add_option("-l", "--list", help="List All domains", dest="list", default=False, action="store_true")
117 parser.add_option("-c", "--create", help="Create domain", dest="create", default=False, action="store_true")
118
119 parser.add_option("-a", "--all-domains", help="Operate on all domains", action="store_true", default=False, dest="all_domains")
120 if json:
121 parser.add_option("-j", "--use-json", help="Load/Store as JSON instead of XML", action="store_true", default=False, dest="json")
122 parser.add_option("-s", "--sort-attibutes", help="Sort the element attributes", action="store_true", default=False, dest="sort_attributes")
123 parser.add_option("-d", "--domain", help="Do functions on domain (may be more then one)", action="append", dest="domains")
124 parser.add_option("-f", "--file", help="Input/Output file we're operating on", dest="file_name")
125 parser.add_option("-r", "--region", help="Region (e.g. us-east-1[default] or eu-west-1)", default="us-east-1", dest="region_name")
126 (options, args) = parser.parse_args()
127
128 if options.create:
129 for domain_name in options.domains:
130 create_db(domain_name, options.region_name)
131 exit()
132
133 sdb = boto.sdb.connect_to_region(options.region_name)
134 check_valid_region(sdb, options.region_name)
135 if options.list:
136 for db in sdb.get_all_domains():
137 print db
138 exit()
139
140 if not options.dump and not options.load and not options.empty:
141 parser.print_help()
142 exit()
143
144
145
146
147 #
148 # Setup
149 #
150 if options.domains:
151 domains = []
152 for domain_name in options.domains:
153 domains.append(sdb.get_domain(domain_name))
154 elif options.all_domains:
155 domains = sdb.get_all_domains()
156 else:
157 domains = [choice_input(options=sdb.get_all_domains(), title="No domain specified, please choose one")]
158
159
160 #
161 # Execute the commands
162 #
163 stime = time.time()
164 if options.empty:
165 if confirm("WARNING!!! Are you sure you want to empty the following domains?: %s" % domains):
166 stime = time.time()
167 for domain in domains:
168 print "--------> Emptying %s <--------" % domain.name
169 empty_db(domain)
170 else:
171 print "Canceling operations"
172 exit()
173
174 if options.dump:
175 for domain in domains:
176 print "--------> Dumping %s <---------" % domain.name
177 if options.file_name:
178 file_name = options.file_name
179 else:
180 file_name = "%s.db" % domain.name
181 dump_db(domain, file_name, options.json, options.sort_attributes)
182
183 if options.load:
184 for domain in domains:
185 print "---------> Loading %s <----------" % domain.name
186 if options.file_name:
187 file_name = options.file_name
188 else:
189 file_name = "%s.db" % domain.name
190 load_db(domain, open(file_name, "rb"), options.json)
191
192
193 total_time = round(time.time() - stime, 2)
194 print "--------> Finished in %s <--------" % total_time