source: trunk/config/dist/base.config @ 7518

Last change on this file since 7518 was 7518, checked in by Nicklas Nordborg, 4 years ago

References #2130: Upgrade 3-rd party libraries

Updated MySQL JDBC driver to version 8.0.13. The main driver class has changed so this requires a configuration change in base.config: db.driver = com.mysql.cj.jdbc.Driver.

They have also changed the default value for nullCatalogMeansCurrent from true to false, which is affecting the installation since it will check and try to create things in other databases than what is specified in the connection URL. I think we have to update our code so that we always supply the current database name instead of null

  • Property svn:eol-style set to LF
  • Property svn:keywords set to Id
File size: 11.7 KB
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1# $Id: base.config 7518 2018-11-05 12:09:42Z 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# MySQL
29# -----
30db.dialect          = org.hibernate.dialect.MySQL5InnoDBDialect
31db.driver           = com.mysql.cj.jdbc.Driver
32db.url              = jdbc:mysql://localhost/base2?characterEncoding=UTF-8&useCursorFetch=true&defaultFetchSize=100&useServerPrepStmts=true&nullCatalogMeansCurrent=true
33db.dynamic.catalog  = base2dynamic
34db.queries          = /mysql-queries.xml
35#export.max.items    = 20000
36
37# --------
38# Postgres
39# --------
40#db.dialect          = org.hibernate.dialect.PostgreSQL9Dialect
41#db.driver           = org.postgresql.Driver
42#db.url              = jdbc:postgresql:base2
43#db.dynamic.schema   = dynamic
44#db.queries          = /postgres-queries.xml
45
46# -------------
47# Common to all
48# -------------
49db.username            = base2user
50db.password            = password
51db.extended-properties = /extended-properties.xml
52db.raw-data-types      = /raw-data-types.xml
53db.batch-size          = 50
54# Number of hours between cleanup of unused items in the database
55# Set to 0 to disable (recommended for job agents)
56db.cleanup.interval    = 24
57
58
59# ======================
60# Authentication section
61# ======================
62
63# If extra information such as address, email, phone, etc. should
64# be synchronized or not from external authentication managers
65#auth.synchronize    = 0
66
67# If passwords should be cached locally or not to allow
68# fallback to internal authentication when external authentication
69# system is not responding
70#auth.cachepasswords = 0
71
72# Number of days to cache passwords locally
73#auth.daystocache    = 0
74
75
76# ==========================
77# Internal job queue section
78# ==========================
79# If the internal job queue should be enabled or not
80jobqueue.internal.enabled            = true
81
82# Signal receiver class for sending signals to running jobs (to abort them)
83jobqueue.internal.signalreceiver.class = net.sf.basedb.core.signal.LocalSignalReceiver
84jobqueue.internal.signalreceiver.init  = jobqueue:0
85
86# If plugins with useInteralJobQueue = false should be executed or not
87jobqueue.internal.runallplugins      = false
88
89# The maximum thread priority for any thread executing a plug-in
90#jobqueue.internal.maxthreadpriority  = 4
91
92# Number of seconds between checks to the job queue
93jobqueue.internal.checkinterval      = 30
94
95# NOTE! A quick job may use threads from any of the "slower" pools
96# if there is place for another thread
97# Number of threads to reserved for jobs that takes < 1 minute to execute
98jobqueue.internal.shortest.threads   = 1
99#jobqueue.internal.shortest.threadpriority = 4
100
101# Number of threads to reserved for jobs that takes < 10 minutes to execute
102jobqueue.internal.short.threads      = 1
103#jobqueue.internal.short.threadpriority = 4
104
105# Number of threads to reserved for jobs that takes < 1 hour to execute
106jobqueue.internal.medium.threads     = 2
107#jobqueue.internal.medium.threadpriority = 3
108
109# Number of threads to reserved for jobs that takes > 1 hour to execute
110jobqueue.internal.long.threads       = 4
111#jobqueue.internal.long.threadpriority = 3
112
113# ==========================
114# External job agent section
115# ==========================
116
117# Number of seconds to cache information from a job agent before it
118# is reloaded. The default value is 60 seconds.
119agent.maxage=60
120
121# The timeout in milliseconds to use when connecting to job agents to
122# get information. The default value is 1000 milliseconds.
123agent.connection.timeout=1000
124
125
126# =========================
127# Secondary storage section
128# =========================
129# The classname of the driver; leave empty to disable secondary storage
130# secondary.storage.driver   = net.sf.basedb.core.InternalStorageController
131
132# Initialisation options to the seconday storage controller
133# The internal implementation wants a path to the secondary directory
134# secondary.storage.init     = /usr/local/base2/secondary
135
136# The interval (in seconds) between checks for new files to move
137# secondary.storage.interval = 3600
138
139# Comma-separated list of time values (hours:minutes) when the controller
140# should be executed; overrides the interval setting if present
141# secondary.storage.time = 18:15,07:30
142
143# =========================
144# Change history section
145# =========================
146
147# Change history for items can be logged with the help of extensions.
148# BASE ships with a built-in extension that log changes to the database.
149# This is disabled by default, but can be enabled through the web
150# interface: Adminstrate -> Plug-ins & extensions -> Overview
151
152# If the "Change history" tab should be visible in the web interface
153# or not. It is hidden by default.
154# changelog.show-in-web = true
155
156# If DB logger should log detailed information about which properties
157# that has been updated (default: false)
158# changelog.dblogger.detailed-properties = true
159
160# If the DB logger should log the old property values when they
161# are modified (default: false; ingored unless 'detailed-properties'
162# is enabled).
163# changelog.dblogger.old-property-values = true
164
165
166# ==========================
167# SMTP server section
168# ==========================
169
170# SMTP server for outgoing mail. If not specified,
171# mail sending and 2-factor login will be disabled
172# mail.server.host
173
174# The port number the SMTP server is listening on. If not
175# specified the default port is used (25 or 465 if ssl is enabled)
176# mail.server.port = 25
177
178# A flag to enable SSL encryption
179# mail.server.ssl = 0
180
181# A flag to enable TLS encryption
182# mail.server.tls = 0
183
184# Email to use in the "From" address. If not specified,
185# mail sending will be disabled
186# mail.from.email = noreply@mail.yourdomain
187
188# Name to use in the "From" address. If not specified,
189# a default value is created automatically using the
190# host name of the BASE server.
191# mail.from.name
192
193
194# =======================
195# Plug-ins and extensions
196# =======================
197
198# The path to the directory where external plugins are installed
199plugins.dir=/usr/local/base2/plugins
200
201# Set this flag to disable all external extensions
202extensions.disabled = false
203
204
205# ===============
206# General section
207# ===============
208
209# Title that is displayed in the browser tab. Use $VERSION to include
210# the current BASE version and $SERVER to include the server name.
211app.title = BASE $VERSION @ $SERVER
212
213# The path to the directory where uploaded files are stored
214userfiles = /usr/local/base2/files
215
216# Number of minutes to keep permission information for the logged
217# in user in memory before it is reloaded from the database.
218permission.timeout = 10
219
220# Number of minutes to keep SessionControl object in the cache
221# after the last use
222cache.timeout = 20
223
224# If the static cache should be disabled or enabled
225# Disabling the static cache may reduce performance for
226# certain operations
227cache.static.disabled = false
228
229# Timeout (in days) for items in the static cache
230# Items that hasn't been accessed in the configured amount of
231# of time will be removed from the cache
232cache.static.max-age = 30
233
234#Overwrite the existing help texts when updating the program
235helptext.update = true
236
237# Set to 1 to disable auto-compression of uploaded files
238autocompress.disable = 0
239
240# Locale settings are used to customize gui text and labels
241# locale.language =
242# locale.country =
243# locacle.variant =
244
245# The default character set that will be used to parse text files that
246# hasn't specified a character set. The default value for this setting
247# is ISO-8859-1.
248#
249# defaultCharset = ISO-8859-1
250
251# A comma-separated list of the most commonly used character sets for text
252# files. This list is used to order selection lists so that the common values
253# are listed at the top of the list.
254#
255# commonCharsets = UTF-8,US-ASCII,ISO-8859-1
256
257# A regular expression that used to filter character sets that are not used
258# in order to keep the selection list shorter. If no value is specified all
259# character sets are included. The standard setting will filter out all
260# character sets starting with 'x-' or 'IBM'. Character sets that are specified
261# in the commonCharsets setting are never filtered.
262#
263ignoreCharsets = ((x|X)\-|IBM).*
264
265# ===================
266# Geolocation section
267# ===================
268
269# URL to the 'ipstack' (previously 'freegeoip') server. Use {IP} as a
270# placeholder for the IP address. The service should return a JSON
271# data object. Before it can be used you need to register and receive
272# an API key. See https://ipstack.com/ for more information.
273# Replace [API_KEY] in the URL below and uncomment the setting to
274# activate geolocation lookup.
275# geolocation.freegeoip = http://api.ipstack.com/{IP}?access_key=[API_KEY]&output=json
276
277# A template URL for displaying a map with a marker on a specified location
278# Use {LAT} and {LONG} as placeholders for the latitude and longitude
279# If no template is specified map links will not be created. The default
280# configuration use OpenStreetMap, or you can switch to Google Maps or
281# some other map provide that supports a latitude/longitude location.
282geolocation.maptemplate = https://www.openstreetmap.org/?mlat={LAT}&mlon={LONG}#map=11/{LAT}/{LONG}
283# geolocation.maptemplate = https://www.google.com/maps/search/?api=1&query={LAT},{LONG}
284
285# ===============
286# SSL section
287# ===============
288# Configuration settings for supporting file access via https.
289# Changes are only needed if authentication is needed or if, for example,
290# files are stored on servers with self-signed certificates.
291
292# ssl.context.protocol = TLS
293# ssl.context.provider =
294# ssl.keystore.file =
295# ssl.keystore.password =
296# ssl.keystore.type = JKS
297# ssl.keystore.algorithm = SunX509
298# ssl.keystore.provider =
299# ssl.truststore.file = <java-home>/jre/lib/security/cacerts
300# ssl.truststore.password = changeit
301# ssl.truststore.type = JKS
302# ssl.truststore.algorithm = PKIX
303# ssl.truststore.provider =
304
305# ===================
306# Migration section
307# ===================
308# Configuration settings that are related to migrating a BASE
309# installation on a MySQL database to a PostgreSQL database.
310# See documentation for more information.
311
312# Enable this flag to compress the exported data. This may increase
313# performance if disks are slow.
314# migrate.export.compress = 0
315
316# The number of rows that should be fetched at the same time from
317# the database. Increasing this value may give better performance
318# but requires more memory.
319# migrate.export.fetch-size = 20000
320
321# Enable this flag to issue an SQL statment for statistical
322# analysis of the imported data before continuing with the next table.
323# Disabling this may result in very poor performance.
324# migrate.import.analyze = 1
325
326# Enable this flag to drop the primary key of a table before importing
327# data to it. This may increase the performance. The primary key is
328# re-created after the data has been imported.
329# migrate.import.drop-primary-key = 1
330
331# Enable this flag to drop unique constraints and indexes before importing
332# data. This may increase the performance. The constraints and indexes
333# are re-created after the data has been imported. NOTE! Foreign key
334# constraints are not affected by this flag, since they must always be dropped.
335# migrate.import.drop-constraints = 1
336
337
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