Merge pull request #295 from mariux64/add-cron-scripts

libexec_cron: Import sbin scripts from projects

install.sh

@@ -257,6 +257,9 @@ install_data misc_etc_files/modprobe.d/ixgbe_sfp.conf     "$DESTDIR$sysconfdir/m
 install_exec forensics/mxvmem                             "$DESTDIR$usr_bindir/mxvmem"
 install_data misc_systemd_units/sshd.service              "$DESTDIR$systemdunitdir/sshd.service"
 install_data misc_systemd_units/pacbio-sshd.service       "$DESTDIR$systemdunitdir/pacbio-sshd.service"
+for f in libexec_cron/*; do
+    install_exec "$f"                                     "$DESTDIR$usr_exec_prefix/libexec/cron/$(basename "$f")"
+done
 
 postinstall
 exit

libexec_cron/prj_FlowCytometryLab_fix-users.pl

@@ -0,0 +1,56 @@
+#! /usr/bin/perl
+
+use strict;
+
+
+sub scandir {
+	my ($dirname)=@_;
+	opendir my $dir,$dirname or die "$dirname: $!\n";
+	return sort grep !/^\./,readdir $dir;
+}
+
+my $sts=0;
+
+my @DIRS=scandir('/project/FlowCytometryLab/');
+
+for my $name (sort @DIRS) {
+	$name eq 'home' and next;
+	my $d="/project/FlowCytometryLab/$name";
+	lstat $d or die "$d: $!\n";
+	-d _ or next;
+	if (my $uid=getpwnam($name)) {
+		my @f1=lstat _;
+		unless (chdir($d)) {
+			warn "$d: $!\n";
+			$sts=1;
+			next;
+		}
+		my @f2=lstat '.';
+		unless ($f1[0] == $f2[0] && $f1[1]==$f2[1]) {
+			warn "$d: won't work on replaced directory\n";
+			$sts=1;
+			next;
+		}
+		system 'find','.',
+			'-type','d',
+			'-not','-user',$uid,
+			'-ls',
+			'-exec','chown',$uid,'{}',';',
+			and $sts=1;
+		system 'find','.',
+			'-type','f',
+			'-links','1',
+			'-not','-user',$uid,
+			'-ls',
+			'-exec','chown',$uid,'{}',';',
+			and $sts=1;
+		if ( ($f2[2] & 07777) != 02770) {
+			system 'chmod','02770','.' and $sts=1;
+		}
+	} else {
+		getpwnam("O$name") and next;
+		warn "$name: no such user\n";
+		$sts=1;
+	}
+}
+exit $sts;

libexec_cron/prj_ag_schulz_images_purge_trash.sh

@@ -0,0 +1,13 @@
+#! /bin/bash
+set -x
+shopt -s nullglob
+cd /project/ag_schulz_images/
+for D in .Trash-[0-9]*;do
+	find "$D" -not -type d -ctime +3 -exec rm {} \;
+	find "$D" -type d -exec rmdir {} \; 2>/dev/null || true
+done
+cd /project/ag_schulz_images_bkp/
+for D in .Trash-[0-9]*;do
+	find "$D" -not -type d -ctime +3 -exec rm {} \;
+	find "$D" -type d -exec rmdir {} \; 2>/dev/null || true
+done

libexec_cron/prj_ag_schulz_purge_trash.sh

@@ -0,0 +1,8 @@
+#! /bin/bash
+set -x
+shopt -s nullglob
+cd /project/ag_schulz/
+for D in .Trash-[0-9]*;do
+	find "$D" -not -type d -ctime +3 -exec rm {} \;
+	find "$D" -type d -exec rmdir {} \; 2>/dev/null || true
+done

libexec_cron/prj_agsgpa_purge_trash.sh

@@ -0,0 +1,8 @@
+#! /bin/bash
+set -x
+shopt -s nullglob
+cd /project/agsgpa/
+for D in .Trash-[0-9]*;do
+	find "$D" -not -type d -ctime +3 -exec rm {} \;
+	find "$D" -type d -exec rmdir {} \; 2>/dev/null || true
+done

libexec_cron/prj_communication_cleanperm.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+P=/project/communication
+G=commugrp
+[ ! -d ${P}/home ] && exit 1
+
+LOG=${P}/home/cron/cleanperm.sh.log
+NOTHOME="-not -regex ${P}/home/?.*"
+date >>${LOG}
+find ${P}/ -type d -not -perm -2771 ${NOTHOME} -exec chmod -v 2771 {} ';' >>$LOG 2>&1
+find ${P}/ -type f -perm -u+x   -not -perm -g+x                   ${NOTHOME} -exec chmod -v ug+x,o-rw    {} ';' >>$LOG 2>&1
+find ${P}/ -type f -perm -u+rw  -not -perm -g+rw  -not -perm /u=x ${NOTHOME} -exec chmod -v ug+rw,o-rw   {} ';' >>$LOG 2>&1
+find ${P}/ -type f -perm -u+rwx -not -perm -g+rwx                 ${NOTHOME} -exec chmod -v ug+rwx,o-rwx {} ';' >>$LOG 2>&1
+find ${P}/ -not -group ${G} -ls -exec chgrp -v ${G} {} ';' >>$LOG 2>&1

libexec_cron/prj_it_cleanperm.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+[ ! -d /project/it/home ] && exit 1
+LOG=/project/it/cron/cleanperm.sh.log
+NOTHOME="-not -regex /project/it/home/?.*"
+date >>${LOG}
+find /project/it/ -type d -not -perm -2771 ${NOTHOME} -exec chmod -v 2771 {} ';' >>$LOG 2>&1
+find /project/it/ -type f -perm -u+x   -not -perm -g+x                   ${NOTHOME} -exec chmod -v ug+x,o-rw    {} ';' >>$LOG 2>&1
+find /project/it/ -type f -perm -u+rw  -not -perm -g+rw  -not -perm /u=x ${NOTHOME} -exec chmod -v ug+rw,o-rw   {} ';' >>$LOG 2>&1
+find /project/it/ -type f -perm -u+rwx -not -perm -g+rwx                 ${NOTHOME} -exec chmod -v ug+rwx,o-rwx {} ';' >>$LOG 2>&1
+find /project/it/EDV-Bestellungen/ -type f -not -perm -o+r -exec chmod -v o+r {} ';' >>$LOG 2>&1
+find /project/it/ -not -group edv -ls -exec chgrp -v edv {} ';' >>$LOG 2>&1

libexec_cron/prj_meissner_external_fastq_autoarchive.pl

@@ -0,0 +1,43 @@
+#! /usr/bin/perl
+use strict;
+use warnings;
+use File::Find;
+
+our $PROJECT_PATH = '/project/meissner_external_fastq/';
+our $PROJECT_RAW_PATH = '/amd/furoncles/M/MG000/project/meissner_external_fastq';
+
+chdir $PROJECT_RAW_PATH or die "$PROJECT_RAW_PATH: $!\n";
+
+my @f1 = lstat $PROJECT_PATH or die "$PROJECT_PATH: $!\n";
+my @f2 = lstat $PROJECT_RAW_PATH or die "$PROJECT_RAW_PATH: $!\n";
+
+$f1[0] == $f2[0] && $f1[1] == $f2[1] or die "paths $PROJECT_PATH doeesn't match $PROJECT_RAW_PATH. Has the project been moved?\”";
+
+my $twoweeksago = time - 2*7*24*60*60;
+print "twoweeksago:",scalar(localtime($twoweeksago)),"\n";
+
+my  $done = 0;
+for my $folder (<RUN_*>) {
+    -d $folder or next;
+    -e "$folder/$folder.is-archived-on-tape.log" and next;
+    my $mtime = 0;
+    find (
+        sub {
+            my @f = lstat $_ or die "$File::Find::name: $!\n";
+            $f[9] > $mtime and $mtime = $f[9];
+            $f[10] > $mtime and $mtime = $f[10];
+        },
+        $folder
+    );
+    print "mtime of folder $folder is ",scalar(localtime($mtime)),"\n";
+    if ($mtime < $twoweeksago) {
+        system "/project/admin/tools/archiver.pl", $folder and exit 1;
+        rename "$folder.is-archived-on-tape.log", "$folder/$folder.is-archived-on-tape.log"
+            or die "rename $folder.is-archived-on-tape.log to $folder/$folder.is-archived-on-tape.log: $!\n";
+        $done++;
+        if ($done >= 2) {
+            print "limit of max 2 archives per day reached\n";
+            exit;
+        }
+    }
+}

libexec_cron/prj_minion_archiver.pl

@@ -0,0 +1,77 @@
+#! /usr/bin/perl
+use strict;
+use warnings;
+
+sub lock_or_exit {
+	open our $LOCKFD,'>>','/run/lock/minion-archive' or die "/run/lock/minion-archive: $!\n";
+	unless (flock $LOCKFD,6) {  # LOCK_EX+LOCK_NB
+		$!!=11 and die "$!\n";
+		warn "already running\n";
+		exit;
+	}
+}
+
+sub scandir {
+	my ($dirname)=@_;
+	opendir my $dir,$dirname or die "$dirname: $!\n";
+	return sort grep !/^\./,readdir $dir;
+}
+
+sub find_dh_pattern {
+	my ($dh,$pattern)=@_;
+	while(my $fn=readdir $dh) {
+		return $1 if $fn=~$pattern;
+	}
+	return undef;
+}
+
+sub warn0 {
+	warn @_;
+	return 0;
+}
+
+sub archive {
+	my ($id)=@_;
+	my $minionpath="/project/minion/raw/$id";
+	lstat $minionpath or return warn0("$minionpath: $!\n");
+	-l _ or return warn0("$minionpath: not a symbolic link\n");
+	my $target=readlink($minionpath) or die "$minionpath: $!\n";
+	$target=~s#/+$##;
+	my $miniondatapath="/project/miniondata/raw/$id";
+	$target eq $miniondatapath or return warn0("$minionpath: invalid target $target\n");
+	my ($dev1,$ino1)=lstat $target or return warn0("$target: $!\n");
+	-d _ or return warn0("$target: not a directory\n");
+	my $fullpath="/amd/mercwithamouth/M/M8026/project/miniondata/raw/$id";
+	my ($dev2,$ino2)=lstat $fullpath or die "$fullpath: $!\n";
+	unless ($dev1==$dev2 && $ino1==$ino2) {
+		die "$fullpath not the same as $target\n";
+	}
+	-e "$fullpath.is-archived-on-tape.log" and die "$fullpath.is-archived-on-tape.log already exists\n";
+	warn "archive $fullpath\n";
+	system '/project/admin/tools/archiver.pl',$fullpath and exit 1;
+	system 'mv',"$fullpath.is-archived-on-tape.log","/project/minion/archive/$id.ARCHIVE_COMPLETED" and exit 1;
+	unlink("/project/minion/archive/$id.ARCHIVE_REQUESTED") or die "/project/minion/archive/$id.ARCHIVE_REQUESTED: $!\n";
+	return 1;
+}
+
+lock_or_exit();
+chdir '/project/minion/archive' or die "/project/minion/archive: $!\n";
+
+while (1) {
+	my $progress;
+	my $errors;
+
+	opendir my $dh,'.';
+	while (my $id=find_dh_pattern($dh,qr/^(.+)\.ARCHIVE_REQUESTED$/)) {
+		redo unless -e "$id.ARCHIVE_REQUESTED";    #  Operator changed his mind?
+		if (archive($id)) {
+			$progress++;
+		} else {
+			$errors++;
+		}
+	}
+	unless ($progress) {
+		exit($errors ? 1 : 0);
+	}
+	sleep 5;
+}

libexec_cron/prj_owlmayerUnpublishedData_archiver.pl

@@ -0,0 +1,75 @@
+#! /usr/bin/perl
+use strict;
+use warnings;
+
+sub lock_or_exit {
+	open our $LOCKFD,'>>','/run/lock/mayer-minion-archive' or die "/run/lock/mayer-minion-archive: $!\n";
+	unless (flock $LOCKFD,6) {  # LOCK_EX+LOCK_NB
+		$!!=11 and die "$!\n";
+		warn "already running\n";
+		exit;
+	}
+}
+
+sub scandir {
+	my ($dirname)=@_;
+	opendir my $dir,$dirname or die "$dirname: $!\n";
+	return sort grep !/^\./,readdir $dir;
+}
+
+sub find_dh_pattern {
+	my ($dh,$pattern)=@_;
+	while(my $fn=readdir $dh) {
+		return $1 if $fn=~$pattern;
+	}
+	return undef;
+}
+
+sub warn0 {
+	warn @_;
+	return 0;
+}
+
+sub archive {
+	my ($id)=@_;
+	my $miniondatapath="/project/owlmayerMinion/raw/$id";
+	lstat $miniondatapath or return warn0("$miniondatapath: $!\n");
+
+	my ($dev1,$ino1)=lstat $miniondatapath or return warn0("$miniondatapath: $!\n");
+	-d _ or return warn0("$miniondatapath: not a directory\n");
+	my $fullpath="/amd/snugglebites/M/M8033/project/owlmayerMinion/raw/$id";
+	my ($dev2,$ino2)=lstat $fullpath or die "$fullpath: $!\n";
+	unless ($dev1==$dev2 && $ino1==$ino2) {
+		die "$fullpath not the same as $miniondatapath\n";
+	}
+	-e "$fullpath.is-archived-on-tape.log" and die "$fullpath.is-archived-on-tape.log already exists\n";
+	-e "$id.is-archived-on-tape.log" and die "$id.is-archived-on-tape.log already exists\n";
+	warn "archive $fullpath\n";
+	system '/project/admin/tools/archiver.pl',$fullpath and exit 1;
+	system 'mv',"$fullpath.is-archived-on-tape.log","./" and exit 1;
+	unlink("$id.ARCHIVE_REQUESTED") or die "$id.ARCHIVE_REQUESTED: $!\n";
+	system 'chmod','-R','a-w',$fullpath;
+	return 1;
+}
+
+lock_or_exit();
+chdir '/project/owlmayerUnpublishedData/archive' or die "/project/owlmayerUnpublishedData/archive: $!\n";
+
+while (1) {
+	my $progress;
+	my $errors;
+
+	opendir my $dh,'.';
+	while (my $id=find_dh_pattern($dh,qr/^(.+)\.ARCHIVE_REQUESTED$/)) {
+		redo unless -e "$id.ARCHIVE_REQUESTED";    #  Operator changed his mind?
+		if (archive($id)) {
+			$progress++;
+		} else {
+			$errors++;
+		}
+	}
+	unless ($progress) {
+		exit($errors ? 1 : 0);
+	}
+	sleep 5;
+}

libexec_cron/prj_owlmayerUnpublishedData_purge_trash.sh

@@ -0,0 +1,8 @@
+#! /bin/bash
+set -x
+shopt -s nullglob
+cd /project/owlmayerUnpublishedData/
+for D in .Trash-[0-9]*;do
+	find "$D" -not -type d -ctime +3 -exec rm {} \;
+	find "$D" -type d -exec rmdir {} \; 2>/dev/null || true
+done