kentutils: add v455, v460, v464, v465 + package updates (#44413)
This addresses a few issues in the kentutils package: - Issue #44372 - Cleaning up formattting and styles - Removing old versions that are not avaialble anymore - Removing newer versions that are also not available anymore - The installer does not install the static libs that are expected by packages that depend on kentutils - There are conflicts and less-than-desirable dependencies that can be addressed via variants Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
This commit is contained in:
Teague Sterling
GitHub
parent
a2e4fb6b95
commit
dcf13af459
@ -0,0 +1,13 @@
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diff --git a/jksql.c.orig b/jksql.c
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index bf38b3b..69b2c42 100644
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--- a/kent/src/hg/lib/jksql.c
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+++ b/kent/src/hg/lib/jksql.c
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@@ -1129,7 +1129,7 @@ mysql_options(conn, MYSQL_OPT_LOCAL_INFILE, NULL);
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if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0"))
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{
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#if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000
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- mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED);
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+ mysql_options(conn, MYSQL_OPT_SSL_MODE, (void*) SSL_MODE_REQUIRED);
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#else
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my_bool flag = TRUE;
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mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag);
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@ -0,0 +1,13 @@
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diff --git a/kent/src/inc/common.mk.orig b/kent/src/inc/common.mk
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index 83803ad..8c90e3a 100644
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--- a/kent/src/inc/common.mk
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+++ b/kent/src/inc/common.mk
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@@ -226,6 +226,8 @@ ifeq (${ZLIB},)
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ZLIB=-lz
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endif
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+MYSQLLIBS := $(subst -lzlib,, ${MYSQLLIBS})
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+
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# on hgwdev, use the static libraries
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ifeq (${IS_HGWDEV},yes)
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FULLWARN = yes
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@ -3,39 +3,154 @@
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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from spack.package import *
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class Kentutils(MakefilePackage):
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"""Jim Kent command line bioinformatic utilities"""
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"""
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Jim Kent command line bioinformatic utilities and libraries
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This bundles a custom version of htslib, but can be overridden with ~htslib.
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Consider adding the ^mysql+client_only dependency to avoid building all mysql/mariadb.
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"""
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homepage = "https://genome.cse.ucsc.edu/"
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url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v453.src.tgz"
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version("459", sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb")
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# The above archive only goes back to v305. v302 is left for now but deprecated. Suggest
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# this is dropped on next update (v302 is from 2014!) and the `requires()` removed.
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maintainers("teaguesterling")
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version("465", sha256="eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0")
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version("464", sha256="24e20fe68e2a2894d802c87662f69a62f71b3c15fafb2e4d6c3c425c63638bb2")
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version("460", sha256="b955e56ee880074521ef1ab1371491f47e66dc6fdd93b05328386dd675a635fa")
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version("455", sha256="e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db")
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# This version isn't present in the archive any more
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# Might be worth changing url to: https://github.com/ucscGenomeBrowser/kent-core/tags/...
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version(
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"302.1",
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commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9",
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git="https://github.com/ENCODE-DCC/kentUtils.git",
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"459",
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sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb",
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deprecated=True,
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)
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depends_on("libpng")
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depends_on("openssl")
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depends_on("uuid")
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depends_on("mariadb")
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depends_on("zlib-api")
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depends_on("freetype")
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depends_on("libiconv")
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# The bundled version of kentlib has some custom changes that are used by parts of
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# kentlib. See https://github.com/spack/spack/pull/44501#issuecomment-2162789410
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# for some additional details. A built-in version SHOULD work for most things though.
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variant(
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"builtin_htslib",
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default=False,
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description="Build with bundled htslib (using an external htslib may lead to errors)",
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sticky=True,
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)
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requires("%gcc", when="@302.1")
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with default_args(type=("build", "link", "run")):
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depends_on("libpng")
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depends_on("openssl")
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depends_on("uuid")
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depends_on("mysql-client")
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depends_on("zlib-api")
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depends_on("freetype")
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depends_on("libiconv")
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depends_on("htslib+pic", when="~builtin_htslib")
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# The bgzip.c bug present in other packages is present in kent/src/htslib/bgzf.c
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# Conflicting line: assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
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# We can patch this by removing the assertion, but there are still performance issues
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# See: https://github.com/samtools/htslib/issues/1257
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conflicts("zlib-ng")
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# Does not add a link to mysql_config, which is required for compilation
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conflicts("mariadb-c-client")
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# MySQL pointer/integer conversion issue (https://github.com/ucscGenomeBrowser/kent/pull/87)
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patch("fix-mysql-options-gcc13.patch", when="%gcc@13: ^mysql")
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# MySQL build flags from `mysql_config` are not compatible with Spack's method of building
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# and includes zlib when it's not needed/available, leading to a linking failure.
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patch("mysql-zlib-workaround.patch", when="%gcc ^mysql")
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def flag_handler(self, name, flags):
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if name == "ldflags":
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if name == "cflags":
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flags.append(self.compiler.cc_pic_flag)
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elif name == "ldflags":
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flags.append(f'{self.spec["libiconv"].libs.ld_flags}')
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return (flags, None, None)
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@property
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def machtype(self):
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# This is hard-coded in the Makefile and included here for reference
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# and to make it adjustable if we need to adjust this in the future
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return "local"
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@property
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def headers(self):
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headers = []
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headers.extend(find_headers("*", self.prefix.inc, recursive=True))
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if self.spec.satisfies("+builtin_htslib"):
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headers.extend(find_headers("*", self.prefix.htslib, recursive=True))
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return HeaderList(headers)
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@property
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def libs(self):
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return LibraryList([join_path(self.prefix, lib) for lib in self.local_libs])
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@property
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def local_libs(self):
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libs = [
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f"lib/{self.machtype}/jkweb.a",
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f"lib/{self.machtype}/jkOwnLib.a",
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f"lib/{self.machtype}/jkhgap.a",
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f"lib/{self.machtype}/jkhgapcgi.a",
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f"hg/altSplice/lib/{self.machtype}/libSpliceGraph.a",
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]
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if self.spec.satisfies("+builtin_htslib"):
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libs.append("htslib/libhts.a")
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return LibraryList(libs)
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@property
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def lib_dir(self):
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return join_path(self.prefix.lib, self.machtype)
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@property
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def htslib_include_dir(self):
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if self.spec.satisfies("~builtin_htslib"):
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# If we're not using the bundled version, just defer to htslib
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return self.spec["htslib"].prefix.include
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else:
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# In the event we're using the bundled htslib, the htslib
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# headers live in a different part of the installed tree
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return self.prefix.htslib
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# Packages that link to kentlib (and potential, htslib) often have
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# idiosyncratic ways of setting up their includes and linker paths.
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# Having these paths available will make things cleaner downstream.
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def setup_dependent_package(self, module, dep_spec):
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setattr(module, "kentutils_include_dir", self.prefix.inc)
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setattr(module, "kentutils_lib_dir", self.lib_dir)
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setattr(module, "kentutils_htslib_include_dir", self.htslib_include_dir)
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def install_libs_from_stage(self, spec, prefix):
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# Dependent packages expect things in the source tree, but we don't
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# want to copy all of the compilation artifacts in so we'll do them
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# manually instead of leaving the build directory around
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src_prefix = "kent/src"
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def install_kent(path, tree):
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src = join_path(src_prefix, path)
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dest = join_path(prefix, path)
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mkdirp(os.path.dirname(dest))
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if tree:
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install_tree(src, dest)
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else:
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install(src, dest)
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install_kent("inc", tree=True)
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if spec.satisfies("+builtin_htslib"):
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install_kent("htslib/htslib", tree=True)
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for lib in self.local_libs:
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install_kent(lib, tree=False)
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def install(self, spec, prefix):
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install_tree("bin", prefix.bin)
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self.install_libs_from_stage(spec, prefix)
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