Merge branch 'master' of ssh://github.com/EUDAT-B2SAFE/B2SAFE-core

b2safe.config

@@ -1,16 +1,24 @@
 #directory of the iRODS installation
+#for irods3 it is, typically, /home/user/iRODS
+#for irods4 it is, typically, /var/lib/irods/iRODS
 IRODS_DIR: /var/lib/irods/iRODS
 
 #directory of the iRODS configuration files
+#for irods3 it is, typically, /home/user/iRODS/server/config/reConfigs 
+#for irods4 it is, typically, /etc/irods
 IRODS_CONF_DIR: /etc/irods
 
 #directory of the iRODS server configuration file (server.config)
+#for irods3 it is, typically, /home/user/iRODS/server/config 
+#for irods4 it is, typically, /etc/irods
 IRODS_SERVER_CONF_DIR: /etc/irods
 
 #directory of the source package downloaded via git
 SOURCE_DIR: /var/lib/irods/B2SAFE-core
 
 #directory of iRODS module configuration files
+#for irods3 it is, typically, /home/user/b2safe-core
+#for irods4 it is, typically, /etc/irods/b2safe-core
 CONF_DIR: /etc/irods/b2safe-core
 
 #default iRODS resource
@@ -20,6 +28,8 @@ DEFAULT_RESOURCE: demoResc
 CRED_STORE_TYPE: os
 
 #path to the credentials file for EPIC
+#for irods3 it is, typically, /home/user/b2safe-core/credentials
+#for irods4 it is, typically, /etc/irods/b2safe-core/credentials
 CRED_FILE_PATH: /etc/irods/b2safe-core/credentials
 
 #iRODS server id in the form <protocol>://<server_name>:<irods_port> 
@@ -42,6 +52,8 @@ USERS: *
 LOG_LEVEL: DEBUG
 
 #directory of the B2SAFE log files
+#for irods3 it is, typically, /home/user/b2safe-core/log
+#for irods4 it is, typically, /etc/irods/b2safe-core/log
 LOG_DIR: /etc/irods/b2safe-core/log
 
 #shared iRODS collection to store command files

b2safe_install.py

@@ -206,7 +206,14 @@ def check(strr, fname):
           + BACK).lower()
     chk = inpt(inp)
 
-stat(SOURCE_DIR)
+try:
+    subprocess.check_call(["stat", SOURCE_DIR])
+except subprocess.CalledProcessError:
+    print RED + BOLD + 'Directory ' + SOURCE_DIR + ' does not exist.' \
+          'Please, check the SOURCE_DIR in 2safe.config. ' \
+          'It should point to the place where you have downloaded ' \
+          'the git repository' + BACK
+    exit()
 
 try:
     subprocess.call(["cp", "-r"] + glob.glob(os.path.join(SOURCE_DIR \
@@ -238,7 +245,7 @@ def check(strr, fname):
 symlink(SOURCE_DIR + "/rulebase/local.re", \
         IRODS_CONF_DIR + "/euloc.re", \
         IRODS_CONF_DIR + "/euloc.re")
-
+        
 print '3. edit <irods>/server/config/server.config and append '\
 ',eudat,eurepl,eupids,eucerr,euloc'\
 ',to reRuleSet (make sure to include the comma and no spaces)'
@@ -267,7 +274,20 @@ def check(strr, fname):
             line1 = line.replace("replication","eurepl")
             line1 = line1.replace("pid-service","eupids")
             line1 = line1.replace("catchError","eucerr")
+            line1 = line1.replace(",eudat-authZ-filters","")
+            line1 = line1.replace("eudat-authZ-filters,","")
+            line1 = line1.replace(",authZ","")
+            line1 = line1.replace("authZ,","")
             line1 = line1.replace("local","euloc")
+            line1 = line1.replace(",integritycheck","")
+            line1 = line1.replace("integritycheck,","")
+            destination.write(line1)
+        elif (line.find('euaf') > -1) or \
+(line.find('euint') > -1):
+            line1 = line.replace(",euaf","")
+            line1 = line1.replace("euaf,","")
+            line1 = line1.replace(",euint","")
+            line1 = line1.replace("euint,","")
             destination.write(line1)
         else:
             destination.write(line)
@@ -521,7 +541,7 @@ def check(strr, fname):
     else:
         subprocess.call(["mkdir", LOG_DIR])
 else:
-    print RED + BOLD + 'Directory ' + LOG_DIR + ' exists. \n'
+    print RED + BOLD + 'Directory ' + LOG_DIR + ' exists. \n' + BACK
 
 filename = CONF_DIR + "/log.manager.conf"
 try:

install.txt

@@ -21,34 +21,27 @@ Enable the module
 
 Automatically:
 
-1.1. enable the module in "<irods>/modules/B2SAFE/info.txt"
-     If a previous version of the module is present, disable it before to install the new one, in "<irods>/
-     modules/OLD_MODULE/info.txt" (if the directory name is the same, change it)
-
-1.2. rerun the irodssetup script
-
-Manually:
-
-1.1. <irods>/scripts/configure --enable-B2SAFE
-     If a previous version of the module is present, disable it before to install the new one (if the directory  
-     name is the same, change it):
-     <irods>/scripts/configure --disable-OLD_MODULE --enable-B2SAFE
-1.2. make clean
-1.3. make
-1.4 <irods>/irodsctl restart
+0. download the git repository 
+   from https://github.com/EUDAT-B2SAFE/B2SAFE-core/releases
 
+1. copy source conf dir (/whre_you_have_downloaded/B2SAFE-core/conf) 
+   to the future config directory    of the b2safe module 
+   (for irods4: /etc/irods/b2safe-core; for irods3: /home/user/b2safe-core)
 
 2. create a symbolic link to the eudat rulebase
-  cd <irods>
-  ln -s <absolute-irods-path>/modules/B2SAFE/rulebase/*.re ./server/config/reConfigs/*.re
+  for irods3: ln -s /whre_you_have_downloaded/B2SAFE-core/rulebase/*.re <irods>/server/config/reConfigs/*.re
+  for irods4: ln -s /whre_you_have_downloaded/B2SAFE-core/rulebase/*.re /etc/irods/*.re
+
   replacing the jolly character "*" with each file name available in the directory "rulebase".
 
-3. edit <irods>/server/config/server.config and append to "reRuleSet" the list of ruleset file names written 
+3. edit <irods>/server/config/server.config (irods3) or /etc/irods/server.config (irods4)
+   and append to "reRuleSet" the list of ruleset file names written 
    in a single line and without the suffix".re", in this way ",filename1,filename2,filename3 ..."  
 	(make sure to include the comma and no spaces)
 
 4. configure iRODS hooks.
-	edit the <irods>/server/config/reConfigs/core.re file and add the following two acPostProcForPutHooks:
+	edit the <irods>/server/config/reConfigs/core.re (irods3) or /etc/irods/core.re (irods4) file 
+	and add the following two acPostProcForPutHooks:
 
 	acPostProcForPut {
         	ON($objPath like "\*.replicate") {
@@ -61,30 +54,40 @@ Manually:
        	 	}
 	}
 
-5. properly configure the default resource in <irods>/server/config/reConfigs/core.re
+5. properly configure the default resource in <irods>/server/config/reConfigs/core.re (irods3) 
+   or /etc/irods/core.re (irods4)
 
 6.1 install the python scripts
-	cd <irods>
-        ln -s <absolute-irods-path>/modules/B2SAFE/cmd/* ./server/bin/cmd/
+   for irods3: <irods_dir> is usually /home/user/iRODS
+   for irods4: <irods_dir> is usually /var/lib/irods/iRODS
+   ln -s /whre_you_have_downloaded/B2SAFE-core/cmd/* <irods_dir>/server/bin/cmd/
         check permissions on the scripts and make sure they are executable by the irods user
             e.g.chmod u+x cmd/*
 
-6.2 update the "getEpicApiParameters" rule in "./server/config/reConfigs/local.re"
-    - Configure the credential storage type: "os": stored on the local filesystem or "irods": stored on de irods namespace.
+6.2 update the "getEpicApiParameters" rule in "./server/config/reConfigs/euloc.re" (irods3)
+    or /etc/irods/euloc.re (irods4)
+    - Configure the credential storage type: "os": stored on the local filesystem 
+      or "irods": stored on de irods namespace.
     - Set the path to the credentials file
-    - set the correct serverID to include the fully qualified hostname. For instance: "irods://node.domain.com:1247"
-    - Set the proper values in the credentials file (see ./cmd/credentials_example for an example)
-6.3 update the "getAuthZParameters" rule in "./server/config/reConfigs/local.re"
-    - Set the proper values in modules/B2SAFE/cmd/authz.map.json
-6.4 update the "getLogParameters" rule in "./server/config/reConfigs/local.re"
-    - Set the proper values in modules/B2SAFE/cmd/log.manager.conf
+    - set the correct serverID to include the fully qualified hostname. 
+      For instance: "irods://node.domain.com:1247"
+    - Set the proper values in the credentials file 
+      (see /whre_you_have_downloaded/B2SAFE-core/cmd/credentials_example for an example)
+
+6.3 update the "getAuthZParameters" rule in "./server/config/reConfigs/euloc.re" (irods3)
+    or /etc/irods/euloc.re (irods4)
+    - Set the proper values in <irods>/server/bin/cmd/authz.map.json
+
+6.4 update the "getLogParameters" rule in "./server/config/reConfigs/euloc.re" (irods3)
+    or /etc/irods/euloc.re (irods4)
+    - Set the proper values in <irods>/server/bin/cmd/log.manager.conf
 
-7. create a shared space in all zones as configured in the eudat.re rulebase getSharedCollection function.
-        - defaults to "<zone>/replicate"
-        - make sure all users involved in the replication can write in this collection.
+7. create a shared space in all zones (local and remote), for example: "<zone>/replicate".
+    Grant all users involved in the replication write access to this collection.
 
 8.0.1 change "#!/usr/bin/env python" in the python scripts in modules/B2SAFE/cmd/ to your python installation
-8.0.2 install httplib2, simplejson, lxml, defusedxml, and pylint:
+
+8.0.2 install httplib2, simplejson, lxml, defusedxml,  queuelib, and pylint:
 	httplib2
 	download from http://code.google.com/p/httplib2
 	python setup.py install
@@ -97,15 +100,25 @@ Manually:
         pip install defusedxml
         apt-get install pylint
         yum install pylint
+
+    queuelib
+    download from https://pypi.python.org/pypi/queuelib
+    python setup.py install
 
-8.1 test the epic api interaction by running the "./cmd/epicclient.py test" script manually and with "iexecmd epicclient.py"
-8.2 test the replication by changing and triggering "replicate.r" rule in <irods>/modules/B2SAFE/rules
+8.1 test the epic api interaction by running 
+    "./cmd/epicclient.py <os_or_irods> <path_to_credentials> test" script manually 
+    and with "iexecmd epicclient.py"
+
+8.2 test the module by changing and triggering rules in <irods>/modules/B2SAFE/rules
+    For example, eudatRepl.r to replicate a data set. See the hints inside the rule.
 
 DATACENTER only:
 
-it is necessary to configure the authz.map.json file in order to allow user to execute rules, which calls external scripts (see documentation).
+it is necessary to configure the <irods>/server/bin/cmd/authz.map.json file 
+in order to allow user to execute rules, which calls external scripts (see documentation).
 
-it is necessary to configure the log.manager.conf file in order to enable the logging system (see documentation).
+it is necessary to configure the <irods>/server/bin/cmd/log.manager.conf file 
+in order to enable the logging system (see documentation).
 
 *** Command files ***
 

packaging/create_deb_package.sh

@@ -11,9 +11,11 @@ RPM_BUILD_ROOT="${HOME}/debbuild/"
 RPM_SOURCE_DIR=$B2SAFEHOME
 PRODUCT="irods-eudat-b2safe"
 IRODS_PACKAGE_DIR=`grep -i _irodsPackage ${PRODUCT}.spec | head -n 1 | awk '{print $3}'`
-# retrieve parameters from spec file. So we only have to update the spec file.
-VERSION=`grep -i "^Version:" ${PRODUCT}.spec  | awk '{print $2}'`
-RELEASE=`grep -i "^Release:" ${PRODUCT}.spec  | awk '{print $2}'`
+# retrieve parameters from local.re in tree
+MAJOR_VERS=`grep "^\s*\*major_version" $B2SAFEHOME/rulebase/local.re | awk -F\" '{print $2}'`
+MINOR_VERS=`grep "^\s*\*minor_version" $B2SAFEHOME/rulebase/local.re | awk -F\" '{print $2}'`
+VERSION="${MAJOR_VERS}.${MINOR_VERS}"
+RELEASE=`grep "^\s*\*sub_version" $B2SAFEHOME/rulebase/local.re | awk -F\" '{print $2}'`
 PACKAGE="${PRODUCT}_${VERSION}-${RELEASE}"
 
 if [ "$USERNAME" = "root" ]

packaging/create_rpm_package.sh

@@ -30,7 +30,16 @@ else
 	echo '%_topdir %(echo $HOME)/rpmbuild' > ~/.rpmmacros
 fi
 
+# find directory where we are executing:
+ABSOLUTE_PATH=$(cd `dirname "${BASH_SOURCE[0]}"` && pwd)
+
+#extract major_version, minor_version and subversion from local.re in tree
+MAJOR_VERS=`grep "^\s*\*major_version" $ABSOLUTE_PATH/../rulebase/local.re | awk -F\" '{print $2}'`
+MINOR_VERS=`grep "^\s*\*minor_version" $ABSOLUTE_PATH/../rulebase/local.re | awk -F\" '{print $2}'`
+SUB_VERS=`grep "^\s*\*sub_version" $ABSOLUTE_PATH/../rulebase/local.re | awk -F\" '{print $2}'`
+VERSION="${MAJOR_VERS}.${MINOR_VERS}"
+
 # build rpm
-rpmbuild -ba irods-eudat-b2safe.spec
+rpmbuild -ba --define "_version $VERSION" --define "_release $SUB_VERS" irods-eudat-b2safe.spec
 
 # done..