Merge pull request #76 from oliveralka/update/SIRIUS490

[Udpate] SIRIUS to version 4.9.0
OpenMS · Jul 13, 2021 · 52b731c · 52b731c
2 parents c0f58d4 + e0035a6
commit 52b731c
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Showing 188 changed files with 102 additions and 33 deletions.
diff --git a/All/Sirius/app/FTAlignmentTool-4.6.0.jar b/All/Sirius/app/FTAlignmentTool-4.6.0.jar
diff --git a/All/Sirius/app/FastTreeAlign-4.6.0.jar b/All/Sirius/app/FastTreeAlign-4.6.0.jar
diff --git a/All/Sirius/app/annotations-4.6.0.jar b/All/Sirius/app/annotations-4.6.0.jar
diff --git a/All/Sirius/app/blob-storage-4.6.0.jar b/All/Sirius/app/blob-storage-4.6.0.jar
diff --git a/All/Sirius/app/canopus_predict_oss-1.6.0.jar b/All/Sirius/app/canopus_predict_oss-1.6.0.jar
diff --git a/All/Sirius/app/chemdb_file_oss-1.6.0.jar b/All/Sirius/app/chemdb_file_oss-1.6.0.jar
diff --git a/All/Sirius/app/chemdb_rest_oss-1.6.0.jar b/All/Sirius/app/chemdb_rest_oss-1.6.0.jar
diff --git a/All/Sirius/app/chemdb_sql_oss-1.6.0.jar b/All/Sirius/app/chemdb_sql_oss-1.6.0.jar
diff --git a/All/Sirius/app/chemdb_utils_oss-1.6.0.jar b/All/Sirius/app/chemdb_utils_oss-1.6.0.jar
diff --git a/All/Sirius/app/chemical_db_oss-1.6.0.jar b/All/Sirius/app/chemical_db_oss-1.6.0.jar
diff --git a/All/Sirius/app/chemistry_base-4.6.0.jar b/All/Sirius/app/chemistry_base-4.6.0.jar
diff --git a/All/Sirius/app/confidence_score_predict_oss-1.6.0.jar b/All/Sirius/app/confidence_score_predict_oss-1.6.0.jar
diff --git a/All/Sirius/app/error_reporter_oss-1.6.0.jar b/All/Sirius/app/error_reporter_oss-1.6.0.jar
diff --git a/All/Sirius/app/fingerblast_oss-1.6.0.jar b/All/Sirius/app/fingerblast_oss-1.6.0.jar
diff --git a/All/Sirius/app/fingerid_base_oss-1.6.0.jar b/All/Sirius/app/fingerid_base_oss-1.6.0.jar
diff --git a/All/Sirius/app/fingerid_project_space_oss-1.6.0.jar b/All/Sirius/app/fingerid_project_space_oss-1.6.0.jar
diff --git a/All/Sirius/app/fingerprint_pvalues_oss-1.6.0.jar b/All/Sirius/app/fingerprint_pvalues_oss-1.6.0.jar
diff --git a/All/Sirius/app/fingerprinter_oss-1.6.0.jar b/All/Sirius/app/fingerprinter_oss-1.6.0.jar
diff --git a/All/Sirius/app/fragmentation_tree_construction-4.6.0.jar b/All/Sirius/app/fragmentation_tree_construction-4.6.0.jar
diff --git a/All/Sirius/app/ft_cplex-4.6.0.jar b/All/Sirius/app/ft_cplex-4.6.0.jar
diff --git a/All/Sirius/app/ft_gurobi-4.6.0.jar b/All/Sirius/app/ft_gurobi-4.6.0.jar
diff --git a/All/Sirius/app/gibbs_sampling-4.6.0.jar b/All/Sirius/app/gibbs_sampling-4.6.0.jar
diff --git a/All/Sirius/app/google-cloud-support-4.6.0.jar b/All/Sirius/app/google-cloud-support-4.6.0.jar
diff --git a/All/Sirius/app/io-4.6.0.jar b/All/Sirius/app/io-4.6.0.jar
diff --git a/All/Sirius/app/isotope_pattern_analysis-4.6.0.jar b/All/Sirius/app/isotope_pattern_analysis-4.6.0.jar
diff --git a/All/Sirius/app/jjobs-core-0.9.20-SNAPSHOT.jar b/All/Sirius/app/jjobs-core-0.9.20-SNAPSHOT.jar
diff --git a/All/Sirius/app/lcms-4.6.0.jar b/All/Sirius/app/lcms-4.6.0.jar
diff --git a/All/Sirius/app/mass_decomposer-4.6.0.jar b/All/Sirius/app/mass_decomposer-4.6.0.jar
diff --git a/All/Sirius/app/passatutto-4.6.0.jar b/All/Sirius/app/passatutto-4.6.0.jar
diff --git a/All/Sirius/app/passatutto_project_space-4.6.0.jar b/All/Sirius/app/passatutto_project_space-4.6.0.jar
diff --git a/All/Sirius/app/preprocessing-4.6.0.jar b/All/Sirius/app/preprocessing-4.6.0.jar
diff --git a/All/Sirius/app/quality_assessment-4.6.0.jar b/All/Sirius/app/quality_assessment-4.6.0.jar
diff --git a/All/Sirius/app/rest_client_oss-1.6.0.jar b/All/Sirius/app/rest_client_oss-1.6.0.jar
diff --git a/All/Sirius/app/rest_core_oss-1.6.0.jar b/All/Sirius/app/rest_core_oss-1.6.0.jar
diff --git a/All/Sirius/app/sirius.cfg b/All/Sirius/app/sirius.cfg
@@ -1,5 +1,5 @@
 [Application]
-app.classpath=$APPDIR/sirius_cli-4.8.2.jar
+app.classpath=$APPDIR/sirius_cli-4.9.0.jar
 app.mainclass=de.unijena.bioinf.ms.frontend.SiriusCLIApplication
 app.classpath=$APPDIR/FTAlignmentTool-4.6.0.jar
 app.classpath=$APPDIR/FastTreeAlign-4.6.0.jar

diff --git a/All/Sirius/app/sirius_api-4.6.0.jar b/All/Sirius/app/sirius_api-4.6.0.jar
diff --git a/All/Sirius/app/sirius_cli-4.8.2.jar → All/Sirius/app/sirius_cli-4.9.0.jar b/All/Sirius/app/sirius_cli-4.8.2.jar → All/Sirius/app/sirius_cli-4.9.0.jar
diff --git a/All/Sirius/app/sirius_isotopes-4.6.0.jar b/All/Sirius/app/sirius_isotopes-4.6.0.jar
diff --git a/All/Sirius/app/sirius_project_space-4.6.0.jar b/All/Sirius/app/sirius_project_space-4.6.0.jar
diff --git a/All/Sirius/app/sirius_web_client-1.6.0.jar b/All/Sirius/app/sirius_web_client-1.6.0.jar
diff --git a/All/Sirius/app/spectral_alignment-4.6.0.jar b/All/Sirius/app/spectral_alignment-4.6.0.jar
diff --git a/All/Sirius/app/tree_motif_search-4.6.0.jar b/All/Sirius/app/tree_motif_search-4.6.0.jar
diff --git a/All/Sirius/app/utils-4.6.0.jar b/All/Sirius/app/utils-4.6.0.jar
diff --git a/All/Sirius/manual-4.8.2-manual.pdf b/All/Sirius/manual-4.8.2-manual.pdf
diff --git a/Linux/64bit/Sirius/lib/native/libglpk.so.40 b/Linux/64bit/Sirius/lib/native/libglpk.so.40
diff --git a/Linux/64bit/Sirius/lib/native/libglpk_java.so b/Linux/64bit/Sirius/lib/native/libglpk_java.so
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/jaotc b/Linux/64bit/Sirius/lib/runtime/bin/jaotc
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/java b/Linux/64bit/Sirius/lib/runtime/bin/java
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/jfr b/Linux/64bit/Sirius/lib/runtime/bin/jfr
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/jrunscript b/Linux/64bit/Sirius/lib/runtime/bin/jrunscript
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/keytool b/Linux/64bit/Sirius/lib/runtime/bin/keytool
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/rmid b/Linux/64bit/Sirius/lib/runtime/bin/rmid
diff --git a/Linux/64bit/Sirius/lib/runtime/bin/rmiregistry b/Linux/64bit/Sirius/lib/runtime/bin/rmiregistry
diff --git a/Linux/64bit/Sirius/lib/runtime/conf/security/java.security b/Linux/64bit/Sirius/lib/runtime/conf/security/java.security
@@ -730,8 +730,8 @@ jdk.jar.disabledAlgorithms=MD2, MD5, RSA keySize < 1024, \
 # Example:
 #   jdk.tls.disabledAlgorithms=MD5, SSLv3, DSA, RSA keySize < 2048, \
 #       rsa_pkcs1_sha1, secp224r1
-jdk.tls.disabledAlgorithms=SSLv3, RC4, DES, MD5withRSA, DH keySize < 1024, \
-    EC keySize < 224, 3DES_EDE_CBC, anon, NULL, \
+jdk.tls.disabledAlgorithms=SSLv3, TLSv1, TLSv1.1, RC4, DES, MD5withRSA, \
+    DH keySize < 1024, EC keySize < 224, 3DES_EDE_CBC, anon, NULL, \
     include jdk.disabled.namedCurves
 
 #
@@ -1309,3 +1309,26 @@ jdk.io.permissionsUseCanonicalPath=false
 # System value prevails. The default value of the property is "false".
 #
 #jdk.security.allowNonCaAnchor=true
+
+#
+# JNDI Object Factories Filter
+#
+# This filter is used by the JNDI runtime to control the set of object factory classes
+# which will be allowed to instantiate objects from object references returned by
+# naming/directory systems. The factory class named by the reference instance will be
+# matched against this filter. The filter property supports pattern-based filter syntax
+# with the same format as jdk.serialFilter.
+#
+# Each pattern is matched against the factory class name to allow or disallow it's
+# instantiation. The access to a factory class is allowed unless the filter returns
+# REJECTED.
+#
+# Note: This property is currently used by the JDK Reference implementation.
+# It is not guaranteed to be examined and used by other implementations.
+#
+# If the system property jdk.jndi.object.factoriesFilter is also specified, it supersedes
+# the security property value defined here. The default value of the property is "*".
+#
+# The default pattern value allows any object factory class specified by the reference
+# instance to recreate the referenced object.
+#jdk.jndi.object.factoriesFilter=*
diff --git a/Linux/64bit/Sirius/lib/runtime/legal/java.desktop/freetype.md b/Linux/64bit/Sirius/lib/runtime/legal/java.desktop/freetype.md
@@ -1,4 +1,4 @@
-## The FreeType Project: Freetype v2.10.1
+## The FreeType Project: Freetype v2.10.2
 
 
 ### FreeType Notice

diff --git a/Linux/64bit/Sirius/lib/runtime/legal/java.desktop/lcms.md b/Linux/64bit/Sirius/lib/runtime/legal/java.desktop/lcms.md
@@ -1,10 +1,10 @@
-## Little Color Management System (LCMS) v2.9
+## Little Color Management System (LCMS) v2.11
 
 ### LCMS License
 <pre>
 
 Little Color Management System
-Copyright (c) 1998-2011 Marti Maria Saguer
+Copyright (c) 1998-2020 Marti Maria Saguer
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the "Software"),