cleanup ununsed files and comments

This commit is contained in:
Guillaume Raffy 2019-10-04 12:27:25 +02:00
parent 1c44113747
commit 61f6d9aeba
3 changed files with 0 additions and 339 deletions

4
Jenkinsfile vendored
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@ -8,10 +8,6 @@ pipeline {
sh './scripts/cleanup.bash'
sh './scripts/install_fiji.bash'
sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app install'
// sh 'export FIJI_ROOT_PATH=$(pwd)/Fiji.app; ./scripts/install_ij_opencv.bash'
// 'export FIJI_ROOT_PATH=$(pwd)/Fiji.app; ./scripts/install_lipase_in_fiji.bash'
// echo 'Create or update the virtual Python environment'
// sh '/bin/bash ./src/CI/CI.bash -i ci_venv'
}
}
stage('Testing the package...') {

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@ -1,311 +0,0 @@
#!/bin/bash
if [ $FIJI_ROOT_PATH = '' ]
then
echo "please define the location of Fiji via the FIJI_ROOT_PATH environment variable"
return 1
fi
# function get_fiji_root_path()
# {
# if [ $FIJI_ROOT_PATH != '' ]
# then
# echo $FIJI_ROOT_PATH
# return
# fi
# local fiji_root_path=''
# case $(hostname) in
# 'pr079234.spm.univ-rennes1.fr') # simpa-macbook2
# fiji_root_path='/Applications/Fiji.app'
# ;;
# 'pr079180.spm.univ-rennes1.fr') # graffy-ws2
# fiji_root_path='~/soft/Fiji.app'
# ;;
# *)
# case $(whoami) in
# 'jenkins-agent')
# fiji_root_path="$(pwd)"
# ;;
# esac
# ;;
# esac
# echo "$fiji_root_path"
# }
function ensure_maven_in_installed()
{
sudo port install maven32
sudo port select --set maven maven32
}
function accept_maven_scijava_org_certificate()
{
# fixes (using the nice description in https://commandlinefanatic.com/cgi-bin/showarticle.cgi?article=art032) the following error when executing "mvn -Dimagej.app.directory=/Applications/Fiji.app"
# [INFO] ------------------------------------------------------------------------
# [ERROR] Failed to execute goal on project example-script-collection: Could not resolve dependencies for project org.scijava:example-script-collection:jar:0.1.0-SNAPSHOT: Failed to collect dependencies at net.imagej:imagej:jar:2.0.0-rc-71: Failed to read artifact descriptor for net.imagej:imagej:jar:2.0.0-rc-71: Could not transfer artifact net.imagej:imagej:pom:2.0.0-rc-71 from/to scijava.public (https://maven.scijava.org/content/groups/public): sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target -> [Help 1]
# [ERROR]
# [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
local java_home=$(/usr/libexec/java_home)
#[1]graffy@pr079234:~/toto/example-script-collection[15:43:02]>/usr/libexec/java_home
#/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home
local jre_home="$java_home/jre"
keytool -list -keystore $jre_home/lib/security/cacerts
# just press enter on the password prompt
# [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
# Enter keystore password:
# ***************** WARNING WARNING WARNING *****************
# * The integrity of the information stored in your keystore *
# * has NOT been verified! In order to verify its integrity, *
# * you must provide your keystore password. *
# ***************** WARNING WARNING WARNING *****************
# Keystore type: JKS
# Keystore provider: SUN
# Your keystore contains 93 entries
# digicertassuredidrootca, Apr 16, 2008, trustedCertEntry,
# Certificate fingerprint (SHA1): 05:63:B8:63:0D:62:D7:5A:BB:C8:AB:1E:4B:DF:B5:A8:99:B2:4D:43
# ...
# godaddyrootg2ca, Jul 19, 2014, trustedCertEntry,
# Certificate fingerprint (SHA1): 47:BE:AB:C9:22:EA:E8:0E:78:78:34:62:A7:9F:45:C2:54:FD:E6:8B
keytool -printcert -rfc -sslserver maven.scijava.org
# [1]graffy@pr079234:~/toto/example-script-collection[16:06:05]>keytool -printcert -rfc -sslserver maven.scijava.org
# -----BEGIN CERTIFICATE-----
# MIIFWDCCBECgAwIBAgISA7zwf4Rs4UhVp5fLyHh58bjtMA0GCSqGSIb3DQEBCwUAMEoxCzAJBgNV
# ...
# Ob5k02cDAcqlcJqIzqhxANh7UDoLw7h36hBnyIHDMbMMkfrtgMv5WSa0DZ2mZf63P6iYGUmr5dtz
# ciAu0w==
# -----END CERTIFICATE-----
# -----BEGIN CERTIFICATE-----
# MIIFWDCCBECgAwIBAgISA7zwf4Rs4UhVp5fLyHh58bjtMA0GCSqGSIb3DQEBCwUAMEoxCzAJBgNV
# ...
# Ob5k02cDAcqlcJqIzqhxANh7UDoLw7h36hBnyIHDMbMMkfrtgMv5WSa0DZ2mZf63P6iYGUmr5dtz
# ciAu0w==
# -----END CERTIFICATE-----
# -----BEGIN CERTIFICATE-----
# MIIEkjCCA3qgAwIBAgIQCgFBQgAAAVOFc2oLheynCDANBgkqhkiG9w0BAQsFADA/MSQwIgYDVQQK
# ...
# TZ+sOPAveyxindmjkW8lGy+QsRlGPfZ+G6Z6h7mjem0Y+iWlkYcV4PIWL1iwBi8saCbGS5jN2p8M
# +X+Q7UNKEkROb3N6KOqkqm57TH2H3eDJAkSnh6/DNFu0Qg==
# -----END CERTIFICATE-----
# split output into:
# - /tmp/cert1.pem
# - /tmp/cert2.pem
# - /tmp/cert3.pem
keytool -importcert -file /tmp/cert1.pem -keystore $jre_home/lib/security/cacerts
# password : changeit
# [1]graffy@pr079234:~/toto/example-script-collection[17:12:30]>sudo keytool -importcert -file /tmp/cert1.pem -keystore $jre_home/lib/security/cacerts
# Password:
# Sorry, try again.
# Password:
# Enter keystore password:
# Owner: CN=maven.imagej.net
# Issuer: CN=Let's Encrypt Authority X3, O=Let's Encrypt, C=US
# Serial number: 3bcf07f846ce14855a797cbc87879f1b8ed
# Valid from: Sat Aug 17 07:39:53 CEST 2019 until: Fri Nov 15 06:39:53 CET 2019
# Certificate fingerprints:
# MD5: 05:B4:5A:31:AE:1F:36:71:0E:24:FB:0F:72:AE:BD:BD
# SHA1: E5:3E:B0:CC:8E:D0:C6:A3:EF:2F:42:93:45:60:82:C2:1B:A3:BD:F3
# 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
# Signature algorithm name: SHA256withRSA
# Version: 3
# Extensions:
# #1: ObjectId: 1.3.6.1.4.1.11129.2.4.2 Criticality=false
# 0000: 04 81 F2 00 F0 00 76 00 74 7E DA 83 31 AD 33 10 ......v.t...1.3.
# 0010: 91 21 9C CE 25 4F 42 70 C2 BF FD 5E 42 20 08 C6 .!..%OBp...^B ..
# 0020: 37 35 79 E6 10 7B CC 56 00 00 01 6C 9E 4D C8 C6 75y....V...l.M..
# 0030: 00 00 04 03 00 47 30 45 02 20 1C DB D8 F3 9D 77 .....G0E. .....w
# 0040: 48 BB B3 D7 0E 50 C4 0F C0 DF 65 94 A7 C4 23 E2 H....P....e...#.
# 0050: 19 C3 88 4D 8D 6D D9 82 D3 BA 02 21 00 AC CC 93 ...M.m.....!....
# 0060: BE 28 59 5C 2E BC A0 8E 36 4D 23 FB 1D 4B 0F FE .(Y\....6M#..K..
# 0070: F4 38 9F C6 D1 13 53 91 62 25 0F C9 71 00 76 00 .8....S.b%..q.v.
# 0080: 29 3C 51 96 54 C8 39 65 BA AA 50 FC 58 07 D4 B7 )<Q.T.9e..P.X...
# 0090: 6F BF 58 7A 29 72 DC A4 C3 0C F4 E5 45 47 F4 78 o.Xz)r......EG.x
# 00A0: 00 00 01 6C 9E 4D CA AD 00 00 04 03 00 47 30 45 ...l.M.......G0E
# 00B0: 02 20 5B D4 50 BC 32 89 32 C4 33 EB 5B 30 3F 25 . [.P.2.2.3.[0?%
# 00C0: F0 7C A6 D4 8A F7 8B AB 55 3A 54 6D F9 2E C9 DE ........U:Tm....
# 00D0: D3 4B 02 21 00 8C A8 8B D3 38 20 38 A1 BB 37 B3 .K.!.....8 8..7.
# 00E0: EE 3A 38 17 82 16 D3 1C E0 30 95 C4 E7 F7 8A 26 .:8......0.....&
# 00F0: 62 B7 BC AF DF b....
# #2: ObjectId: 1.3.6.1.5.5.7.1.1 Criticality=false
# AuthorityInfoAccess [
# [
# accessMethod: ocsp
# accessLocation: URIName: http://ocsp.int-x3.letsencrypt.org
# ,
# accessMethod: caIssuers
# accessLocation: URIName: http://cert.int-x3.letsencrypt.org/
# ]
# ]
# #3: ObjectId: 2.5.29.35 Criticality=false
# AuthorityKeyIdentifier [
# KeyIdentifier [
# 0000: A8 4A 6A 63 04 7D DD BA E6 D1 39 B7 A6 45 65 EF .Jjc......9..Ee.
# 0010: F3 A8 EC A1 ....
# ]
# ]
# #4: ObjectId: 2.5.29.19 Criticality=true
# BasicConstraints:[
# CA:false
# PathLen: undefined
# ]
# #5: ObjectId: 2.5.29.32 Criticality=false
# CertificatePolicies [
# [CertificatePolicyId: [2.23.140.1.2.1]
# [] ]
# [CertificatePolicyId: [1.3.6.1.4.1.44947.1.1.1]
# [PolicyQualifierInfo: [
# qualifierID: 1.3.6.1.5.5.7.2.1
# qualifier: 0000: 16 1A 68 74 74 70 3A 2F 2F 63 70 73 2E 6C 65 74 ..http://cps.let
# 0010: 73 65 6E 63 72 79 70 74 2E 6F 72 67 sencrypt.org
# ]] ]
# ]
# #6: ObjectId: 2.5.29.37 Criticality=false
# ExtendedKeyUsages [
# serverAuth
# clientAuth
# ]
# #7: ObjectId: 2.5.29.15 Criticality=true
# KeyUsage [
# DigitalSignature
# Key_Encipherment
# ]
# #8: ObjectId: 2.5.29.17 Criticality=false
# SubjectAlternativeName [
# DNSName: maven.imagej.net
# ]
# #9: ObjectId: 2.5.29.14 Criticality=false
# SubjectKeyIdentifier [
# KeyIdentifier [
# 0000: 63 09 5F EA C5 C8 7D 24 DD 2B 11 71 BB FB F6 F9 c._....$.+.q....
# 0010: 6F 7C BD 0A o...
# ]
# ]
# Trust this certificate? [no]: yes
# Certificate was added to keystore
#> mykey, Sep 20, 2019, trustedCertEntry,
#> Certificate fingerprint (SHA1): E5:3E:B0:CC:8E:D0:C6:A3:EF:2F:42:93:45:60:82:C2:1B:A3:BD:F3
#export MAVEN_OPTS="-Xmx512m -Djavax.net.ssl.trustStore=trust.jks \
# -Djavax.net.ssl.trustStorePassword= \
# -Djavax.net.ssl.keyStore=/tmp/cert1.pem \
# -Djavax.net.ssl.keyStoreType=pem
}
function create_test_jar()
{
git clone https://github.com/imagej/example-script-collection.git
pushd example-script-collection
rm -R src/test/java
ensure_maven_in_installed
accept_maven_scijava_org_certificate
mvn -Dimagej.app.directory=/Applications/Fiji.app
# on ubuntu :
# [WARNING] Rule 2: org.apache.maven.plugins.enforcer.RequireJavaVersion failed with message:
# Detected JDK Version: 11.0.4 is not in the allowed range [1.8.0-101,1.8.9999].
# [INFO] ------------------------------------------------------------------------
# [INFO] BUILD FAILURE
# [INFO] ------------------------------------------------------------------------
# [INFO] Total time: 06:03 min
# [INFO] Finished at: 2019-09-23T16:57:17+02:00
# [INFO] ------------------------------------------------------------------------
# [ERROR] Failed to execute goal org.apache.maven.plugins:maven-enforcer-plugin:1.4.1:enforce (enforce-rules) on project example-script-collection: Some Enforcer rules have failed. Look above for specific messages explaining why the rule failed. -> [Help 1]
popd
}
function ensure_ij_opencv_plugin_is_installed()
{
# enable IJ-OpenCV-plugins site because it's disabled by default
# graffy@graffy-ws2:~$ zcat /home/graffy/soft/Fiji.app/db.xml.gz | grep IJ-Op | grep -v "jar" | grep -v "<plu"
# <disabled-update-site name="IJ-OpenCV-plugins" url="https://sites.imagej.net/IJ-OpenCV/" official="true" description="Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV." timestamp="20190819101544"/>
# graffy@graffy-ws2:~$ history | less
# graffy@graffy-ws2:~$ ~/soft/Fiji.app/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/
# Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
# Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
# Done: Checksummer
# graffy@graffy-ws2:~$ zcat /home/graffy/soft/Fiji.app/db.xml.gz | grep IJ-Op | grep -v "jar" | grep -v "<plu"
# <update-site name="IJ-OpenCV-plugins" url="https://sites.imagej.net/IJ-OpenCV/" official="true" description="Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV." timestamp="20190819101544"/>
$FIJI_ROOT_PATH/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/
# then apply an update to download and install IJ-OpenCV-plugins :
# jars/IJ-OpenCV.jar
# jars/javacv.far
# jars/opencv-linux-x86.jar
# jars/opencv-linux-x86_64.jar
# jars/opencv-macosx-x86_64.jar
# jars/opencv-windows-x86.jar
# jars/opencv-windows-x86_64.jar
# jars/opencv.jar
# lib/haarcascade_frontalface_alt.xml
# graffy@graffy-ws2:~$ ~/soft/Fiji.app/ImageJ-linux64 --update update
# Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
# Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
# Done: Checksummer
# Done: Downloading...
# Done: Downloading...
$FIJI_ROOT_PATH/ImageJ-linux64 --update update
}
function install_lipase_libs_in_fiji()
{
# https://imagej.net/Jython_Scripting
mkdir -p "$FIJI_ROOT_PATH/jars/Lib"
# cp -R ./src/* "$FIJI_ROOT_PATH/jars/Lib"
pushd src
find ./lipase -name "*.py" > /tmp/files.txt
jar cvf $FIJI_ROOT_PATH/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar @/tmp/files.txt
popd
}
function install_lipase_in_fiji()
{
# lipase plugins require IJ-OpenCV-plugins
ensure_ij_opencv_plugin_is_installed
install_lipase_libs_in_fiji
mkdir -p $FIJI_ROOT_PATH/plugins/Ipr
rsync -a ./src/ij-plugins/Ipr/ $FIJI_ROOT_PATH/plugins/Ipr/
}
install_lipase_in_fiji

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@ -1,24 +0,0 @@
#!/bin/bash
FIJI_EXE_PATH=''
RAW_IMAGES_ROOT_PATH=''
LIPASE_SRC_ROOT_PATH="$(pwd)/src"
case "$(uname)" in
'Linux')
FIJI_EXE_PATH='./Fiji.app/ImageJ-linux64'
RAW_IMAGES_ROOT_PATH='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images'
;;
'Darwin')
FIJI_EXE_PATH='/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx'
RAW_IMAGES_ROOT_PATH='/Users/graffy/work/lipase/raw-images'
;;
*)
echo "unhandled operating system : $(uname)"
exit 1
esac
"$FIJI_EXE_PATH" --ij2 --headless --run './tests/test0001.py' "raw_images_root_path='$RAW_IMAGES_ROOT_PATH'"
# on macosx : /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './test0001.py'
# /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './tests/test0001.py' "lipase_src_root_path='$(pwd)',raw_images_root_path='/Users/graffy/ownCloud/ipr/lipase/raw-images'"
ERROR_CODE=$?
echo "Fiji 's return code : $ERROR_CODE"
ERROR_CODE=$(cat '/tmp/test_result.txt')
exit $ERROR_CODE