forked from broadgsa/gatk-protected
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ant-bridge.sh
executable file
·173 lines (130 loc) · 6.26 KB
/
ant-bridge.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
#!/bin/sh
mvn_args="verify"
mvn_properties=
mvn_clean=
unknown_args=
property_regex='-D(.*)=(.*)'
unit_test_regex='.*UnitTest'
post_script=
run_type="run"
for arg in "${@}" ; do
if [[ "${arg}" == "dry" ]] ; then
run_type="dry"
elif [[ "${arg}" == "clean" ]] ; then
mvn_clean="clean"
mvn_args=
elif [[ "${arg}" =~ ${property_regex} ]] ; then
property_name=${BASH_REMATCH[1]}
property_value=${BASH_REMATCH[2]}
if [[ "${property_name}" == "single" ]] ; then
test_property="test"
test_disabled="it.test"
if [[ ! "${property_value}" =~ ${unit_test_regex} ]] ; then
test_property="it.test"
test_disabled="test"
fi
mvn_properties="${mvn_properties} -D${test_disabled}=disabled -D${test_property}=${property_value}"
elif [[ "${property_name}" == "test.debug.port" ]] ; then
mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
mvn_properties="${mvn_properties} -Dmaven.failsafe.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
elif [[ "${property_name}" == "test.default.maxmemory" ]] ; then
mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
else
unknown_args="${unknown_args} \"${arg}\""
fi
else
if [[ "${arg}" != "dist" && "${mvn_args}" != "" && "${mvn_args}" != "verify" ]] ; then
echo "Sorry, this script does not currently support mixing targets." >&2
exit 1
elif [[ "${arg}" == "dist" ]] ; then
mvn_args="verify"
elif [[ "${arg}" == "gatk" ]] ; then
mvn_args="verify '-P!queue'"
elif [[ "${arg}" == "test.compile" ]] ; then
mvn_args="test-compile"
elif [[ "${arg}" == "gatkdocs" ]] ; then
local_repo="sitetemprepo"
mvn_args="install -Dmaven.repo.local=${local_repo} -Ddisable.queue && mvn site -Dmaven.repo.local=${local_repo} -Ddisable.queue"
elif [[ "${arg}" == "package.gatk.full" ]] ; then
mvn_args="package '-P!private,!queue'"
elif [[ "${arg}" == "package.gatk.all" ]] ; then
mvn_args="package '-P!queue'"
elif [[ "${arg}" == "package.queue.full" ]] ; then
mvn_args="package '-P!private'"
elif [[ "${arg}" == "package.queue.all" ]] ; then
mvn_args="package"
# elif [[ "${arg}" == "release.gatk.full" ]] ; then
# mvn_args="package '-P!private,!queue'"
# post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
# elif [[ "${arg}" == "release.queue.full" ]] ; then
# mvn_args="package '-P!private'"
# post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
elif [[ "${arg}" == "build-picard-private" ]] ; then
mvn_args="mvn install -f private/picard-maven/pom.xml"
# TODO: clover support
# see ant and maven docs for clover:
# https://confluence.atlassian.com/display/CLOVER/1.+QuickStart+Guide
# https://confluence.atlassian.com/display/CLOVER/Clover-for-Maven+2+and+3+User%27s+Guide
#
#elif [[ "${arg}" == "clover.report" ]] ; then
# mvn_args=...
#
#elif [[ "${arg}" == "with.clover" ]] ; then
# mvn_args=...
# TODO: This runs *all* commit tests, including the few on Queue.
elif [[ "${arg}" == "gatkfull.binary.release.tests" ]] ; then
local_repo="sitetemprepo"
mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
mvn_args="${mvn_args} -Dgatk.packagetests.enabled=true"
mvn_args="${mvn_args} -Dgatk.packagecommittests.skipped=false"
# TODO: This runs only the queue tests (full, non-dry run), but not the commit tests for Queue.
elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
local_repo="sitetemprepo"
mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
mvn_args="${mvn_args} -Dgatk.packagetests.enabled=true"
mvn_args="${mvn_args} -Dgatk.packagequeuetests.skipped=false"
mvn_args="${mvn_args} -Dgatk.queuetests.run=true"
elif [[ "${arg}" == "committests" ]] ; then
mvn_args="verify -Dgatk.committests.skipped=false"
elif [[ "${arg}" == "test" ]] ; then
mvn_args="test -Dgatk.unittests.skipped=false"
elif [[ "${arg}" == "unittest" ]] ; then
mvn_args="test -Dgatk.unittests.skipped=false"
elif [[ "${arg}" == "integrationtest" ]] ; then
mvn_args="verify -Dgatk.integrationtests.skipped=false"
elif [[ "${arg}" == "largescaletest" ]] ; then
mvn_args="verify -Dgatk.largescaletests.skipped=false"
elif [[ "${arg}" == "knowledgebasetest" ]] ; then
mvn_args="verify -Dgatk.knowledgebasetests.skipped=false"
elif [[ "${arg}" == "queuetest" ]] ; then
mvn_args="verify -Dgatk.queuetests.skipped=false"
elif [[ "${arg}" == "queuetestrun" ]] ; then
mvn_args="verify -Dgatk.queuetests.skipped=false -Dgatk.queuetests.run=true"
elif [[ "${arg}" == "fasttest" ]] ; then
mvn_args="verify -Dgatk.committests.skipped=false -pl private/gatk-tools-private -am -Dresource.bundle.skip=true"
else
unknown_args="${unknown_args} \"${arg}\""
fi
fi
done
mvn_cmd=
if [[ "${mvn_clean}" != "" ]] ; then
if [[ "${mvn_args}" != "" ]] ; then
mvn_cmd="mvn ${mvn_clean} && mvn ${mvn_args}"
else
mvn_cmd="mvn ${mvn_clean}"
fi
else
mvn_cmd="mvn ${mvn_args}"
fi
if [[ "${unknown_args}" != "" ]] ; then
echo "Unrecognized arguments:${unknown_args}" >&2
else
echo "Equivalent maven command"
echo "${mvn_cmd}${mvn_properties}${post_script}"
if [[ "${run_type}" != "dry" ]] ; then
sh -c "${mvn_cmd}${mvn_properties}${post_script}"
fi
fi