source: branches/3.18-stable/config/dist/base.config @ 7938

Last change on this file since 7938 was 7822, checked in by Nicklas Nordborg, 18 months ago

References #2214: Upgrade Hibernate and other 3-rd party components

Updated MySQL JDBC driver to 8.0.19. The 8.0.20 was also tested but there seems to be an issue with Date parameters in some queries: https://bugs.mysql.com/bug.php?id=99713

I have also changed the default configuration to use MySQL 8.

There was an issue with the TestChangeHistory.test_list_by_user() that sometimes worked and sometimes failed. The most likely reason is the filter on the current time which could be affected by rounding milliseconds up/down, so the timestamp used for filtering was modified by -1 second.

  • Property svn:eol-style set to LF
  • Property svn:keywords set to Id
File size: 10.9 KB
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1# $Id: base.config 7822 2020-06-08 11:32:37Z nicklas $
2#
3# Copyright (C) 2006 Nicklas Nordborg
4# Copyright (C) 2007 Nicklas Nordborg, Martin Svensson
5#
6# This file is part of BASE - BioArray Software Environment.
7# Available at http://base.thep.lu.se/
8#
9# BASE is free software; you can redistribute it and/or
10# modify it under the terms of the GNU General Public License
11# as published by the Free Software Foundation; either version 3
12# of the License, or (at your option) any later version.
13#
14# BASE is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with BASE. If not, see <http://www.gnu.org/licenses/>.
21# ----------------------------------------
22
23# =======================
24# Database driver section
25# =======================
26
27# ----------------------
28# Postgres (recommended)
29# ----------------------
30db.dialect          = org.hibernate.dialect.PostgreSQL9Dialect
31db.url              = jdbc:postgresql:base2
32db.dynamic.schema   = dynamic
33db.queries          = /postgres-queries.xml
34
35# -----
36# MySQL
37# -----
38# db.dialect          = org.hibernate.dialect.MySQL8Dialect
39# db.url              = jdbc:mysql://localhost/base2?characterEncoding=UTF-8&useCursorFetch=true&defaultFetchSize=100&useServerPrepStmts=true&sslMode=DISABLED
40# db.dynamic.catalog  = base2dynamic
41# db.queries          = /mysql-queries.xml
42
43
44# -------------
45# Common to all
46# -------------
47db.username            = base2user
48db.password            = password
49db.extended-properties = /extended-properties.xml
50db.raw-data-types      = /raw-data-types.xml
51db.batch-size          = 50
52# Number of hours between cleanup of unused items in the database
53# Set to 0 to disable (recommended for job agents)
54db.cleanup.interval    = 24
55
56
57# ======================
58# Authentication section
59# ======================
60
61# If extra information such as address, email, phone, etc. should
62# be synchronized or not from external authentication managers
63#auth.synchronize    = 0
64
65# If passwords should be cached locally or not to allow
66# fallback to internal authentication when external authentication
67# system is not responding
68#auth.cachepasswords = 0
69
70# Number of days to cache passwords locally
71#auth.daystocache    = 0
72
73
74# ==========================
75# Internal job queue section
76# ==========================
77# If the internal job queue should be enabled or not
78jobqueue.internal.enabled            = true
79
80# Signal receiver class for sending signals to running jobs (to abort them)
81jobqueue.internal.signalreceiver.class = net.sf.basedb.core.signal.LocalSignalReceiver
82jobqueue.internal.signalreceiver.init  = jobqueue:0
83
84# If plugins with useInteralJobQueue = false should be executed or not
85jobqueue.internal.runallplugins      = false
86
87# The maximum thread priority for any thread executing a plug-in
88#jobqueue.internal.maxthreadpriority  = 4
89
90# Number of seconds between checks to the job queue
91jobqueue.internal.checkinterval      = 30
92
93# NOTE! A quick job may use threads from any of the "slower" pools
94# if there is place for another thread
95# Number of threads to reserved for jobs that takes < 1 minute to execute
96jobqueue.internal.shortest.threads   = 1
97#jobqueue.internal.shortest.threadpriority = 4
98
99# Number of threads to reserved for jobs that takes < 10 minutes to execute
100jobqueue.internal.short.threads      = 1
101#jobqueue.internal.short.threadpriority = 4
102
103# Number of threads to reserved for jobs that takes < 1 hour to execute
104jobqueue.internal.medium.threads     = 2
105#jobqueue.internal.medium.threadpriority = 3
106
107# Number of threads to reserved for jobs that takes > 1 hour to execute
108jobqueue.internal.long.threads       = 4
109#jobqueue.internal.long.threadpriority = 3
110
111# ==========================
112# External job agent section
113# ==========================
114
115# Number of seconds to cache information from a job agent before it
116# is reloaded. The default value is 60 seconds.
117agent.maxage=60
118
119# The timeout in milliseconds to use when connecting to job agents to
120# get information. The default value is 1000 milliseconds.
121agent.connection.timeout=1000
122
123
124# =========================
125# Change history section
126# =========================
127
128# Change history for items can be logged with the help of extensions.
129# BASE ships with a built-in extension that log changes to the database.
130# This is disabled by default, but can be enabled through the web
131# interface: Adminstrate -> Plug-ins & extensions -> Overview
132
133# If the "Change history" tab should be visible in the web interface
134# or not. It is hidden by default.
135# changelog.show-in-web = true
136
137# If DB logger should log detailed information about which properties
138# that has been updated (default: false)
139# changelog.dblogger.detailed-properties = true
140
141# If the DB logger should log the old property values when they
142# are modified (default: false; ingored unless 'detailed-properties'
143# is enabled).
144# changelog.dblogger.old-property-values = true
145
146
147# ==========================
148# SMTP server section
149# ==========================
150
151# SMTP server for outgoing mail. If not specified,
152# mail sending and 2-factor login will be disabled
153# mail.server.host
154
155# The port number the SMTP server is listening on. If not
156# specified the default port is used (25 or 465 if ssl is enabled)
157# mail.server.port = 25
158
159# A flag to enable SSL encryption
160# mail.server.ssl = 0
161
162# A flag to enable TLS encryption
163# mail.server.tls = 0
164
165# Email to use in the "From" address. If not specified,
166# mail sending will be disabled
167# mail.from.email = noreply@mail.yourdomain
168
169# Name to use in the "From" address. If not specified,
170# a default value is created automatically using the
171# host name of the BASE server.
172# mail.from.name
173
174
175# =======================
176# Plug-ins and extensions
177# =======================
178
179# The path to the directory where external plugins are installed
180plugins.dir=/usr/local/base2/plugins
181
182# Set this flag to disable all external extensions
183extensions.disabled = false
184
185
186# ===============
187# General section
188# ===============
189
190# Title that is displayed in the browser tab. Use $VERSION to include
191# the current BASE version and $SERVER to include the server name.
192app.title = BASE $VERSION @ $SERVER
193
194# The path to the directory where uploaded files are stored
195userfiles = /usr/local/base2/files
196
197# Number of minutes to keep permission information for the logged
198# in user in memory before it is reloaded from the database.
199permission.timeout = 10
200
201# Number of minutes to keep SessionControl object in the cache
202# after the last use
203cache.timeout = 20
204
205# If the static cache should be disabled or enabled
206# Disabling the static cache may reduce performance for
207# certain operations
208cache.static.disabled = false
209
210# Timeout (in days) for items in the static cache
211# Items that hasn't been accessed in the configured amount of
212# of time will be removed from the cache
213cache.static.max-age = 30
214
215#Overwrite the existing help texts when updating the program
216helptext.update = true
217
218# Set to 1 to disable auto-compression of uploaded files
219autocompress.disable = 0
220
221# Locale settings are used to customize gui text and labels
222# locale.language =
223# locale.country =
224# locacle.variant =
225
226# The default character set that will be used to parse text files that
227# hasn't specified a character set. The default value for this setting
228# is ISO-8859-1.
229#
230# defaultCharset = ISO-8859-1
231
232# A comma-separated list of the most commonly used character sets for text
233# files. This list is used to order selection lists so that the common values
234# are listed at the top of the list.
235#
236# commonCharsets = UTF-8,US-ASCII,ISO-8859-1
237
238# A regular expression that used to filter character sets that are not used
239# in order to keep the selection list shorter. If no value is specified all
240# character sets are included. The standard setting will filter out all
241# character sets starting with 'x-' or 'IBM'. Character sets that are specified
242# in the commonCharsets setting are never filtered.
243#
244ignoreCharsets = ((x|X)\-|IBM).*
245
246# ===================
247# Geolocation section
248# ===================
249
250# URL to the 'ipstack' (previously 'freegeoip') server. Use {IP} as a
251# placeholder for the IP address. The service should return a JSON
252# data object. Before it can be used you need to register and receive
253# an API key. See https://ipstack.com/ for more information.
254# Replace [API_KEY] in the URL below and uncomment the setting to
255# activate geolocation lookup.
256# geolocation.freegeoip = http://api.ipstack.com/{IP}?access_key=[API_KEY]&output=json
257
258# A template URL for displaying a map with a marker on a specified location
259# Use {LAT} and {LONG} as placeholders for the latitude and longitude
260# If no template is specified map links will not be created. The default
261# configuration use OpenStreetMap, or you can switch to Google Maps or
262# some other map provide that supports a latitude/longitude location.
263geolocation.maptemplate = https://www.openstreetmap.org/?mlat={LAT}&mlon={LONG}#map=11/{LAT}/{LONG}
264# geolocation.maptemplate = https://www.google.com/maps/search/?api=1&query={LAT},{LONG}
265
266# ===============
267# SSL section
268# ===============
269# Configuration settings for supporting file access via https.
270# Changes are only needed if authentication is needed or if, for example,
271# files are stored on servers with self-signed certificates.
272
273# ssl.context.protocol = TLS
274# ssl.context.provider =
275# ssl.keystore.file =
276# ssl.keystore.password =
277# ssl.keystore.type = JKS
278# ssl.keystore.algorithm = SunX509
279# ssl.keystore.provider =
280# ssl.truststore.file = <java-home>/jre/lib/security/cacerts
281# ssl.truststore.password = changeit
282# ssl.truststore.type = JKS
283# ssl.truststore.algorithm = PKIX
284# ssl.truststore.provider =
285
286# ===================
287# Migration section
288# ===================
289# Configuration settings that are related to migrating a BASE
290# installation on a MySQL database to a PostgreSQL database.
291# See documentation for more information.
292
293# Enable this flag to compress the exported data. This may increase
294# performance if disks are slow.
295# migrate.export.compress = 0
296
297# The number of rows that should be fetched at the same time from
298# the database. Increasing this value may give better performance
299# but requires more memory.
300# migrate.export.fetch-size = 20000
301
302# Enable this flag to issue an SQL statment for statistical
303# analysis of the imported data before continuing with the next table.
304# Disabling this may result in very poor performance.
305# migrate.import.analyze = 1
306
307# Enable this flag to drop the primary key of a table before importing
308# data to it. This may increase the performance. The primary key is
309# re-created after the data has been imported.
310# migrate.import.drop-primary-key = 1
311
312# Enable this flag to drop unique constraints and indexes before importing
313# data. This may increase the performance. The constraints and indexes
314# are re-created after the data has been imported. NOTE! Foreign key
315# constraints are not affected by this flag, since they must always be dropped.
316# migrate.import.drop-constraints = 1
317
318
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