226 lines
8.9 KiB
Bash
226 lines
8.9 KiB
Bash
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#!/bin/bash
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FIJI_ROOT_PATH='/Applications/Fiji.app'
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function ensure_maven_in_installed()
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{
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sudo port install maven32
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sudo port select --set maven maven32
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}
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function accept_maven_scijava_org_certificate()
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{
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# fixes (using the nice description in https://commandlinefanatic.com/cgi-bin/showarticle.cgi?article=art032) the following error when executing "mvn -Dimagej.app.directory=/Applications/Fiji.app"
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# [INFO] ------------------------------------------------------------------------
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# [ERROR] Failed to execute goal on project example-script-collection: Could not resolve dependencies for project org.scijava:example-script-collection:jar:0.1.0-SNAPSHOT: Failed to collect dependencies at net.imagej:imagej:jar:2.0.0-rc-71: Failed to read artifact descriptor for net.imagej:imagej:jar:2.0.0-rc-71: Could not transfer artifact net.imagej:imagej:pom:2.0.0-rc-71 from/to scijava.public (https://maven.scijava.org/content/groups/public): sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target -> [Help 1]
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# [ERROR]
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# [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
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local java_home=$(/usr/libexec/java_home)
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#[1]graffy@pr079234:~/toto/example-script-collection[15:43:02]>/usr/libexec/java_home
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#/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home
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local jre_home="$java_home/jre"
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keytool -list -keystore $jre_home/lib/security/cacerts
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# just press enter on the password prompt
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# [1]graffy@pr079234:~/toto/example-script-collection[15:44:43]>keytool -list -keystore /Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre/lib/security/cacerts
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# Enter keystore password:
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# ***************** WARNING WARNING WARNING *****************
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# * The integrity of the information stored in your keystore *
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# * has NOT been verified! In order to verify its integrity, *
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# * you must provide your keystore password. *
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# ***************** WARNING WARNING WARNING *****************
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# Keystore type: JKS
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# Keystore provider: SUN
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# Your keystore contains 93 entries
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# digicertassuredidrootca, Apr 16, 2008, trustedCertEntry,
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# Certificate fingerprint (SHA1): 05:63:B8:63:0D:62:D7:5A:BB:C8:AB:1E:4B:DF:B5:A8:99:B2:4D:43
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# ...
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# godaddyrootg2ca, Jul 19, 2014, trustedCertEntry,
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# Certificate fingerprint (SHA1): 47:BE:AB:C9:22:EA:E8:0E:78:78:34:62:A7:9F:45:C2:54:FD:E6:8B
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keytool -printcert -rfc -sslserver maven.scijava.org
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# [1]graffy@pr079234:~/toto/example-script-collection[16:06:05]>keytool -printcert -rfc -sslserver maven.scijava.org
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# -----BEGIN CERTIFICATE-----
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# MIIFWDCCBECgAwIBAgISA7zwf4Rs4UhVp5fLyHh58bjtMA0GCSqGSIb3DQEBCwUAMEoxCzAJBgNV
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# ...
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# Ob5k02cDAcqlcJqIzqhxANh7UDoLw7h36hBnyIHDMbMMkfrtgMv5WSa0DZ2mZf63P6iYGUmr5dtz
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# ciAu0w==
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# -----END CERTIFICATE-----
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# -----BEGIN CERTIFICATE-----
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# MIIFWDCCBECgAwIBAgISA7zwf4Rs4UhVp5fLyHh58bjtMA0GCSqGSIb3DQEBCwUAMEoxCzAJBgNV
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# ...
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# Ob5k02cDAcqlcJqIzqhxANh7UDoLw7h36hBnyIHDMbMMkfrtgMv5WSa0DZ2mZf63P6iYGUmr5dtz
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# ciAu0w==
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# -----END CERTIFICATE-----
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# -----BEGIN CERTIFICATE-----
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# MIIEkjCCA3qgAwIBAgIQCgFBQgAAAVOFc2oLheynCDANBgkqhkiG9w0BAQsFADA/MSQwIgYDVQQK
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# ...
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# TZ+sOPAveyxindmjkW8lGy+QsRlGPfZ+G6Z6h7mjem0Y+iWlkYcV4PIWL1iwBi8saCbGS5jN2p8M
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# +X+Q7UNKEkROb3N6KOqkqm57TH2H3eDJAkSnh6/DNFu0Qg==
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# -----END CERTIFICATE-----
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# split output into:
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# - /tmp/cert1.pem
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# - /tmp/cert2.pem
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# - /tmp/cert3.pem
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keytool -importcert -file /tmp/cert1.pem -keystore $jre_home/lib/security/cacerts
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# password : changeit
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# [1]graffy@pr079234:~/toto/example-script-collection[17:12:30]>sudo keytool -importcert -file /tmp/cert1.pem -keystore $jre_home/lib/security/cacerts
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# Password:
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# Sorry, try again.
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# Password:
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# Enter keystore password:
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# Owner: CN=maven.imagej.net
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# Issuer: CN=Let's Encrypt Authority X3, O=Let's Encrypt, C=US
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# Serial number: 3bcf07f846ce14855a797cbc87879f1b8ed
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# Valid from: Sat Aug 17 07:39:53 CEST 2019 until: Fri Nov 15 06:39:53 CET 2019
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# Certificate fingerprints:
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# MD5: 05:B4:5A:31:AE:1F:36:71:0E:24:FB:0F:72:AE:BD:BD
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# SHA1: E5:3E:B0:CC:8E:D0:C6:A3:EF:2F:42:93:45:60:82:C2:1B:A3:BD:F3
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# SHA256: 74:3C:C7:2C:E6:C5:FE:9F:79:F5:F7:9D:7E:2A:4F:C9:BA:51:A0:88:95:1C:FC:15:8D:DC:EC:B0:99:BD:0E:61
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# Signature algorithm name: SHA256withRSA
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# Version: 3
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# Extensions:
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# #1: ObjectId: 1.3.6.1.4.1.11129.2.4.2 Criticality=false
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# 0000: 04 81 F2 00 F0 00 76 00 74 7E DA 83 31 AD 33 10 ......v.t...1.3.
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# 0010: 91 21 9C CE 25 4F 42 70 C2 BF FD 5E 42 20 08 C6 .!..%OBp...^B ..
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# 0020: 37 35 79 E6 10 7B CC 56 00 00 01 6C 9E 4D C8 C6 75y....V...l.M..
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# 0030: 00 00 04 03 00 47 30 45 02 20 1C DB D8 F3 9D 77 .....G0E. .....w
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# 0040: 48 BB B3 D7 0E 50 C4 0F C0 DF 65 94 A7 C4 23 E2 H....P....e...#.
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# 0050: 19 C3 88 4D 8D 6D D9 82 D3 BA 02 21 00 AC CC 93 ...M.m.....!....
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# 0060: BE 28 59 5C 2E BC A0 8E 36 4D 23 FB 1D 4B 0F FE .(Y\....6M#..K..
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# 0070: F4 38 9F C6 D1 13 53 91 62 25 0F C9 71 00 76 00 .8....S.b%..q.v.
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# 0080: 29 3C 51 96 54 C8 39 65 BA AA 50 FC 58 07 D4 B7 )<Q.T.9e..P.X...
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# 0090: 6F BF 58 7A 29 72 DC A4 C3 0C F4 E5 45 47 F4 78 o.Xz)r......EG.x
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# 00A0: 00 00 01 6C 9E 4D CA AD 00 00 04 03 00 47 30 45 ...l.M.......G0E
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# 00B0: 02 20 5B D4 50 BC 32 89 32 C4 33 EB 5B 30 3F 25 . [.P.2.2.3.[0?%
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# 00C0: F0 7C A6 D4 8A F7 8B AB 55 3A 54 6D F9 2E C9 DE ........U:Tm....
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# 00D0: D3 4B 02 21 00 8C A8 8B D3 38 20 38 A1 BB 37 B3 .K.!.....8 8..7.
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# 00E0: EE 3A 38 17 82 16 D3 1C E0 30 95 C4 E7 F7 8A 26 .:8......0.....&
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# 00F0: 62 B7 BC AF DF b....
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# #2: ObjectId: 1.3.6.1.5.5.7.1.1 Criticality=false
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# AuthorityInfoAccess [
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# [
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# accessMethod: ocsp
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# accessLocation: URIName: http://ocsp.int-x3.letsencrypt.org
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# ,
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# accessMethod: caIssuers
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# accessLocation: URIName: http://cert.int-x3.letsencrypt.org/
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# ]
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# ]
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# #3: ObjectId: 2.5.29.35 Criticality=false
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# AuthorityKeyIdentifier [
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# KeyIdentifier [
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# 0000: A8 4A 6A 63 04 7D DD BA E6 D1 39 B7 A6 45 65 EF .Jjc......9..Ee.
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# 0010: F3 A8 EC A1 ....
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# ]
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# ]
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# #4: ObjectId: 2.5.29.19 Criticality=true
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# BasicConstraints:[
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# CA:false
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# PathLen: undefined
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# ]
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# #5: ObjectId: 2.5.29.32 Criticality=false
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# CertificatePolicies [
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# [CertificatePolicyId: [2.23.140.1.2.1]
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# [] ]
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# [CertificatePolicyId: [1.3.6.1.4.1.44947.1.1.1]
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# [PolicyQualifierInfo: [
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# qualifierID: 1.3.6.1.5.5.7.2.1
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# qualifier: 0000: 16 1A 68 74 74 70 3A 2F 2F 63 70 73 2E 6C 65 74 ..http://cps.let
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# 0010: 73 65 6E 63 72 79 70 74 2E 6F 72 67 sencrypt.org
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# ]] ]
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# ]
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# #6: ObjectId: 2.5.29.37 Criticality=false
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# ExtendedKeyUsages [
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# serverAuth
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# clientAuth
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# ]
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# #7: ObjectId: 2.5.29.15 Criticality=true
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# KeyUsage [
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# DigitalSignature
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# Key_Encipherment
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# ]
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# #8: ObjectId: 2.5.29.17 Criticality=false
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# SubjectAlternativeName [
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# DNSName: maven.imagej.net
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# ]
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# #9: ObjectId: 2.5.29.14 Criticality=false
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# SubjectKeyIdentifier [
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# KeyIdentifier [
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# 0000: 63 09 5F EA C5 C8 7D 24 DD 2B 11 71 BB FB F6 F9 c._....$.+.q....
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# 0010: 6F 7C BD 0A o...
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# ]
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# ]
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# Trust this certificate? [no]: yes
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# Certificate was added to keystore
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#> mykey, Sep 20, 2019, trustedCertEntry,
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#> Certificate fingerprint (SHA1): E5:3E:B0:CC:8E:D0:C6:A3:EF:2F:42:93:45:60:82:C2:1B:A3:BD:F3
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#export MAVEN_OPTS="-Xmx512m -Djavax.net.ssl.trustStore=trust.jks \
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# -Djavax.net.ssl.trustStorePassword= \
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# -Djavax.net.ssl.keyStore=/tmp/cert1.pem \
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# -Djavax.net.ssl.keyStoreType=pem
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}
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function create_test_jar()
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{
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git clone https://github.com/imagej/example-script-collection.git
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pushd example-script-collection
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rm -R src/test/java
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ensure_maven_in_installed
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accept_maven_scijava_org_certificate
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mvn -Dimagej.app.directory=/Applications/Fiji.app
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popd
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}
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function install_lipase_libs_in_fiji()
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{
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# https://imagej.net/Jython_Scripting
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mkdir -p "$FIJI_ROOT_PATH/jars/Lib"
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# cp -R ./src/* "$FIJI_ROOT_PATH/jars/Lib"
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pushd src
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find ./lipase -name "*.py" > /tmp/files.txt
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jar cvf $FIJI_ROOT_PATH/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar @/tmp/files.txt
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popd
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}
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function install_lipase_in_fiji()
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{
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install_lipase_libs_in_fiji
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mkdir -p $FIJI_ROOT_PATH/plugins/Ipr
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rsync -a ./src/ij-plugins/Ipr/ $FIJI_ROOT_PATH/plugins/Ipr/
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}
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install_lipase_in_fiji
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