1[LMDB_CACHE]
2; Path to the file where an LMDB si2csi cache file is located
3; If not provided then no cache will be used.
4dbfile_si2csi=
5;dbfile_si2csi=/data/PSG/cache/si2csi.db
6; Path to the file where an LMDB bioseq_info cache file is located
7; If not provided then no cache will be used.
8dbfile_bioseq_info=
9;dbfile_bioseq_info=/data/PSG/cache/bioseq_info.db
10; Path to the file where an LMDB blob_prop cache file is located
11; If not provided then no cache will be used.
12dbfile_blob_prop=
13;dbfile_blob_prop=/data/PSG/cache/blob_prop.db
14
15
16[AUTO_EXCLUDE]
17; Cache size per client.
18; 0 - means it is disabled.
19; Default: 1000
20max_cache_size=1000
21
22; The percentage of the records to purge (of max_cache_size; 0 <= int <= 100)
23; Default: 20
24purge_percentage=20
25
26; Client inactivity purge timeout, seconds, integer.
27; Used for garbage collecting
28; Default: 60
29inactivity_purge_timeout=60
30
31
32[SERVER]
33; HTTP port (1...65534)
34; No default. If port is not specified or is out of range the server
35; will not start
36port=@PORT@
37
38; Number of HTTP workers (1...100)
39; Default: 32
40workers=32
41
42; Listener backlog (5...2048)
43; Default: 256
44backlog=256
45
46; Max number of connections (5...65000)
47; Default: 4096
48maxconn=4096
49
50; Operation timeout in milliseconds
51; Default: 30000
52optimeout=30000
53
54; Max Cassandra operation retries
55; Default: 1
56maxretries=1
57
58; Affects request start/request stop
59; Does not affect PSG_INFO, PSG_ERROR etc
60log=true
61
62; Cassandra root keyspace which is used for discovering the sat to keyspace
63; mapping as well as the location of the SI2CSI and BIOSEQ_INFO tables
64; Default: sat_info
65root_keyspace=sat_info
66
67; In most cases the blobs are not split because they are... just too small to
68; be split. So, in the spirit of the "slim" purpose such original blobs should
69; be sent to the client.
70; Default: 10KB
71slim_max_blob_size=10KB
72
73; Max number of hops allowed.
74; It must be an integer > 0.
75; Default: 2
76max_hops=2
77
78
79[ADMIN]
80; Authorization token for the shutdown request.
81; If provided then the URL shutdown request must have the corresponding
82; auth_token parameter to be authorized.
83; If not provided then any URL shutdown request will be authorized.
84; Both, clear text and encrypted text are supported. If it is impossible to
85; decrypt the value, then the value is treated as a clear text
86auth_token=
87
88
89
90[STATISTICS]
91; The statistics for the blob retrieving timing is collected depending on
92; the blob sizes in separate bins. The first bin covers the range of sizes
93; from 0 till small_blob_size inclusive. Then the ranges will start from the
94; power of 2.
95; Default: 16
96small_blob_size=16
97
98; Min time value (microseconds)
99; Default: 1
100min=1
101
102; Max time value (microseconds)
103; Default: 16 * 1024 * 1024
104max=16777216
105
106; Number of bins
107; Default: 24
108n_bins=24
109
110; Scale type
111; can be "log" or "linear"
112; Default: log
113type=log
114
115; Histogram rotation time interval (tick), in seconds.
116; Must be an integer greater than zero.
117; Default (also a fallback on bad value):  10
118tick_span = 10
119
120[CASSANDRA_DB]
121; default: false
122cassandralog=false
123
124; Connection timeout in ms
125; Default: 30000
126ctimeout=30000
127
128; Query timeout in ms
129; Default: 5000
130qtimeout=5000
131
132; Data namespace
133; Default: empty string
134namespace=
135
136; Fallback read consistency
137; Default: false
138fallbackrdconsistency=false
139
140; Lower down consistency of BD write operations if local quorum cannot be achieved
141; 0 - default cassandra driver behavior
142; Default: 0
143fallbackwriteconsistency=0
144
145; Load balancing policy. Accepted values are: DCAware, RoundRobin
146; Default: DCAware
147loadbalancing=DCAware
148
149; Enables TokenAware routing
150; Default: true
151tokenaware=true
152
153; Enables LatencyAware routing
154; Default: true
155latencyaware=true
156
157; Number of io threads to async processing (1...32)
158; Basically it is how many blob chunks are requested simultaneously per request.
159; For example, if a blob with 100 chunks is requested then 4 select statements
160; will be created and maintained simultaneously.
161; Default: 4
162numthreadsio=4
163
164; Number of connections per node (1...8)
165; Default: 2
166numconnperhost=2
167
168; Maximum count of connections per node (1...8)
169; Default: 4
170maxconnperhost=4
171
172; TCP keep-alive the initial delay in seconds
173; Default: 0
174keepalive=0
175
176; Cassandra password file and a section where credentials are stored
177; Default: empty, i.e. no user/password combination is used.
178;password_file=/home/dmitrie1/.ssh/cass.ini
179;password_section=BIGDATAPROD_RO
180
181
182; LBSM name or a list of host[:port] items (',' or ' ' separated).
183; If the value has neither ' ', nor ',' nor ':' then it is treated as a
184; load balancer name. The load balancer resolved host ports are are sorted
185; in accordance with their rates.
186; The list of host[:port] items, regardless where it came from - directly from
187; a parameter value or from a load balancer - is analyzed further. The
188; analizis checks that if ports are provided then they are the same. If the
189; port is provided then it is used for the Cassandra cluster. If no ports are
190; provided then the Cassandra driver uses its default one.
191;service=localhost:9042
192;service=idtest111:9042
193;service=idtest214:9042
194service=ID_CASS_TEST
195;service=idtest111,idtest112,idtest114,idtest211,idtest212,idtest213,idtest214
196;service=idstore11,idstore12,idstore13,idstore14,idstore15,idstore16,idstore17,idstore18
197
198
199[DEBUG]
200; If set to true then psg will respond to TEST/io URL sending back up to
201; 1000000000 bytes
202psg_allow_io_test=false
203
204DIAG_POST_LEVEL=Error
205;DIAG_POST_LEVEL=Warning
206;DIAG_POST_LEVEL=Info
207
208; Tracing is independent from the diag post level
209; To switch on tracing use diag_trace set to something (true, on, etc)
210; To switch off tracing comment out diag_trace
211; By some reasons diag_trace type is string, not boolean and it is checked for
212; non emptyness
213;diag_trace=true
214
215
216[COUNTERS]
217; Each value in this section is for overwriting the server default metrics
218; names and descriptions. The format is as follows:
219; MetricID=<Metric name>:::<Metric description>
220; e.g.
221; LookupLmdbBlobPropFound=BLOB props found in LMDB:::Time required to find BLOB props in LMDB
222; The metric names and descriptions are used by the GRID Dashboard
223
224
225[CASSANDRA_PROCESSOR]
226; Enable/disable all Cassandra/LMDB processors if not explicitly specified
227; in the URL parameters.
228; Default: enabled (enabled=true)
229enabled=true
230
231
232[HEALTH]
233; The seq_id which is resolved in cache only when /health or /deep-health URL is requested
234; Default: gi|2
235test_seq_id=gi|2
236
237; Ignore/do not ignore test seq_id resolution errors
238; Default: true (ignore errors)
239test_seq_id_ignore_error=true
240
241[SSL]
242; If enabled then the server will work over https.
243; Note: certificate and private key files must be provided if switched on
244; Default: false
245ssl_enable=false
246
247; Path to the certificate file. Must be provided for https.
248; Default: no default
249ssl_cert_file="/export/home/satskyse/psg/ssl/130.14.24.194.crt"
250
251; Path to the private key file. Must be provided for https.
252; Default: no default
253ssl_key_file="/export/home/satskyse/psg/ssl/130.14.24.194.key"
254
255; SSL ciphers. Optional
256; Default: "TLSv1.2:!NULL-SHA256"
257; NOTE: NLM requires hardening security so weak ciphers are not allowed. For
258;       example, SSLv2, SSLv3, TLS1 and TLS1.1 must not be used.
259ssl_ciphers=""
260
261