Changeset: 4f417118508e for MonetDB URL: https://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=4f417118508e Added Files: clients/mapilib/mapi_prompt.h clients/mapilib/mapi_querytype.h sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_00.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_01.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_02.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_03.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_04.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_05.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_06.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_07.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_09.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_10.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_11.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_12.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_13.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_16.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_17.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_18.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_19.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_20.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_21.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_23.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_24.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_25.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_26.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_27.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_28.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_29.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_30.sql sql/backends/monet5/UDF/pyapi3/Tests/pyapi3_32.sql sql/backends/monet5/UDF/pyapi3/Tests/pyloader3_01.sql sql/backends/monet5/UDF/pyapi3/Tests/pyloader3_02.sql sql/backends/monet5/UDF/pyapi3/Tests/pyloader3_05.sql sql/backends/monet5/UDF/pyapi3/connection.h sql/backends/monet5/UDF/pyapi3/conversion.h sql/backends/monet5/UDF/pyapi3/convert_loops.h sql/backends/monet5/UDF/pyapi3/emit.h sql/backends/monet5/UDF/pyapi3/formatinput.h sql/backends/monet5/UDF/pyapi3/pyapi.h sql/backends/monet5/UDF/pyapi3/pyheader.h sql/backends/monet5/UDF/pyapi3/pytypes.h sql/backends/monet5/UDF/pyapi3/type_conversion.h sql/backends/monet5/UDF/pyapi3/undef.h sql/backends/monet5/UDF/pyapi3/unicode.h sql/test/BugTracker-2020/Tests/ifthenelse-crash.Bug-6815.sql sql/test/BugTracker-2020/Tests/ifthenelse-crash.Bug-6815.stable.err sql/test/BugTracker-2020/Tests/ifthenelse-crash.Bug-6815.stable.out sql/test/analytics/Tests/analytics14.sql sql/test/analytics/Tests/analytics14.stable.err sql/test/analytics/Tests/analytics14.stable.out sql/test/analytics/Tests/analytics15.sql sql/test/analytics/Tests/analytics15.stable.err sql/test/analytics/Tests/analytics15.stable.out sql/test/analytics/Tests/analytics16.sql sql/test/analytics/Tests/analytics16.stable.err sql/test/analytics/Tests/analytics16.stable.out sql/test/analytics/Tests/analytics17.sql sql/test/analytics/Tests/analytics17.stable.err sql/test/analytics/Tests/analytics17.stable.out Removed Files: clients/examples/python/mclient-python2.py debian/libmonetdb5-server-bam.install debian/monetdb-python2.install sql/backends/monet5/Tests/createorreplace.sql sql/backends/monet5/Tests/createorreplace.stable.err sql/backends/monet5/Tests/createorreplace.stable.out sql/backends/monet5/Tests/pyapi00.sql sql/backends/monet5/Tests/pyapi00.stable.err sql/backends/monet5/Tests/pyapi00.stable.out sql/backends/monet5/Tests/pyapi01.sql sql/backends/monet5/Tests/pyapi01.stable.err sql/backends/monet5/Tests/pyapi01.stable.out sql/backends/monet5/Tests/pyapi02.sql sql/backends/monet5/Tests/pyapi02.stable.err sql/backends/monet5/Tests/pyapi02.stable.out sql/backends/monet5/Tests/pyapi03.sql sql/backends/monet5/Tests/pyapi03.stable.err sql/backends/monet5/Tests/pyapi03.stable.out sql/backends/monet5/Tests/pyapi04.sql sql/backends/monet5/Tests/pyapi04.stable.err sql/backends/monet5/Tests/pyapi04.stable.out sql/backends/monet5/Tests/pyapi05.sql 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sql/test/mapi/Tests/python3_dbapi.SQL.sh sql/test/merge-partitions/Tests/All sql/test/mergetables/Tests/All sql/test/miscellaneous/Tests/groupby_error.sql sql/test/miscellaneous/Tests/groupby_error.stable.out sql/test/pg_regress/Tests/interval.stable.out sql/test/pg_regress/Tests/interval.stable.out.int128 sql/test/subquery/Tests/correlated.stable.err sql/test/subquery/Tests/correlated.stable.out sql/test/subquery/Tests/subquery3.sql sql/test/subquery/Tests/subquery3.stable.err sql/test/subquery/Tests/subquery3.stable.out sql/test/sys-schema/Tests/All sql/test/sys-schema/Tests/systemfunctions.stable.out sql/test/sys-schema/Tests/systemfunctions.stable.out.int128 sql/test/testdb-upgrade-chain-hge/Tests/upgrade.stable.out.int128 sql/test/testdb-upgrade-chain/Tests/upgrade.stable.out sql/test/testdb-upgrade-chain/Tests/upgrade.stable.out.32bit sql/test/testdb-upgrade-chain/Tests/upgrade.stable.out.int128 sql/test/testdb-upgrade-hge/Tests/upgrade.stable.out.int128 sql/test/testdb-upgrade/Tests/upgrade.stable.out sql/test/testdb-upgrade/Tests/upgrade.stable.out.32bit sql/test/testdb-upgrade/Tests/upgrade.stable.out.int128 testing/Mfilter.py testing/Mtest.py.in tools/merovingian/daemon/forkmserver.c tools/mserver/Makefile.ag tools/mserver/mserver5.1.in tools/mserver/mserver5.c Branch: compactprofiler Log Message:
Merge with default branch. diffs (truncated from 291310 to 300 lines): diff --git a/ChangeLog b/ChangeLog --- a/ChangeLog +++ b/ChangeLog @@ -1,6 +1,9 @@ # ChangeLog file for devel # This file is updated with Maddlog +* Thu Jan 30 2020 Sjoerd Mullender <sjo...@acm.org> +- Removed support for bam and sam files. + * Fri Dec 6 2019 Panagiotis Koutsourakis <kutsu...@monetdbsolutions.com> - Added mserver5 option (--set raw_strings=true|false) and monetdb database property (raw_strings=yes|no) to control interpretation diff --git a/MonetDB.spec b/MonetDB.spec --- a/MonetDB.spec +++ b/MonetDB.spec @@ -66,16 +66,6 @@ %endif %endif -%if %{?rhel:0}%{!?rhel:1} -# By default create the MonetDB-bam-MonetDB5 package. -# Note that the samtools-devel RPM is not available on RedHat -# Enterprise Linux and derivatives, even with EPEL availabe. -# (Actually, at the moment of writing, samtools-devel is available in -# EPEL for RHEL 6, but not for RHEL 7. We don't make the distinction -# here and just not build the MonetDB-bam-MonetDB5 RPM.) -%bcond_without samtools -%endif - # By default use PCRE for the implementation of the SQL LIKE and ILIKE # operators. Otherwise the POSIX regex functions are used. %bcond_without pcre @@ -85,14 +75,9 @@ %bcond_without rintegration %endif -# On Fedora <= 30 and RHEL 7, create the MonetDB-python2 package. -# On RHEL 6, numpy is too old. -%if 0%{?rhel} == 7 || %{!?fedora:1000}%{?fedora} <= 30 -%bcond_without py2integration -%endif -%if %{?rhel:0}%{!?rhel:1} -# On RHEL 6, Python 3 is too old, and on RHEL 7, the default Python 3 -# is too old (in both cases 3.4). +%if 0%{?rhel} >= 7 || 0%{?fedora} > 0 +# On RHEL 6, Python 3 is too old. On RHEL 7, Python 3 was too old +# when RHEL 7 was released, but now it is ok. %bcond_without py3integration %endif @@ -156,18 +141,6 @@ BuildRequires: readline-devel BuildRequires: unixODBC-devel # BuildRequires: uriparser-devel BuildRequires: pkgconfig(zlib) -%if %{with samtools} -BuildRequires: samtools-devel -%endif -%if %{with py2integration} -BuildRequires: python-devel -%if %{?rhel:1}%{!?rhel:0} -# RedHat Enterprise Linux calls it simply numpy -BuildRequires: numpy -%else -BuildRequires: python2-numpy -%endif -%endif %if %{with py3integration} BuildRequires: python3-devel >= 3.5 BuildRequires: python3-numpy @@ -313,7 +286,7 @@ This package contains the files needed t %defattr(-,root,root) %dir %{_includedir}/monetdb %{_libdir}/libmapi.so -%{_includedir}/monetdb/mapi.h +%{_includedir}/monetdb/mapi*.h %{_libdir}/pkgconfig/monetdb-mapi.pc %package client-odbc @@ -439,29 +412,6 @@ This package contains support for readin %{_libdir}/monetdb5/lib_lidar.so %endif -%if %{with samtools} -%package bam-MonetDB5 -Summary: MonetDB5 SQL interface to the bam library -Group: Applications/Databases -Requires: MonetDB5-server%{?_isa} = %{version}-%{release} - -%description bam-MonetDB5 -MonetDB is a database management system that is developed from a -main-memory perspective with use of a fully decomposed storage model, -automatic index management, extensibility of data types and search -accelerators. It also has an SQL front end. - -This package contains the interface to load and query BAM (binary -version of Sequence Alignment/Map) data. - -%files bam-MonetDB5 -%defattr(-,root,root) -%{_libdir}/monetdb5/autoload/*_bam.mal -%{_libdir}/monetdb5/createdb/*_bam.sql -%{_libdir}/monetdb5/bam.mal -%{_libdir}/monetdb5/lib_bam.so -%endif - %if %{with rintegration} %package R Summary: Integration of MonetDB and R, allowing use of R from within SQL @@ -488,32 +438,6 @@ install it. %{_libdir}/monetdb5/lib_rapi.so %endif -%if %{with py2integration} -%package python2 -Summary: Integration of MonetDB and Python, allowing use of Python from within SQL -Group: Applications/Databases -Requires: MonetDB-SQL-server5%{?_isa} = %{version}-%{release} - -%description python2 -MonetDB is a database management system that is developed from a -main-memory perspective with use of a fully decomposed storage model, -automatic index management, extensibility of data types and search -accelerators. It also has an SQL front end. - -This package contains the interface to use the Python language from -within SQL queries. This package is for Python 2. - -NOTE: INSTALLING THIS PACKAGE OPENS UP SECURITY ISSUES. If you don't -know how this package affects the security of your system, do not -install it. - -%files python2 -%defattr(-,root,root) -%{_libdir}/monetdb5/pyapi.* -%{_libdir}/monetdb5/autoload/*_pyapi.mal -%{_libdir}/monetdb5/lib_pyapi.so -%endif - %if %{with py3integration} %package python3 Summary: Integration of MonetDB and Python, allowing use of Python from within SQL @@ -614,9 +538,6 @@ exit 0 %if %{with lidar} %exclude %{_libdir}/monetdb5/lidar.mal %endif -%if %{with py2integration} -%exclude %{_libdir}/monetdb5/pyapi.mal -%endif %if %{with py3integration} %exclude %{_libdir}/monetdb5/pyapi3.mal %endif @@ -635,9 +556,6 @@ exit 0 %if %{with lidar} %exclude %{_libdir}/monetdb5/autoload/*_lidar.mal %endif -%if %{with py2integration} -%exclude %{_libdir}/monetdb5/autoload/*_pyapi.mal -%endif %if %{with py3integration} %exclude %{_libdir}/monetdb5/autoload/*_pyapi3.mal %endif @@ -646,10 +564,6 @@ exit 0 %endif %exclude %{_libdir}/monetdb5/autoload/??_sql*.mal %{_libdir}/monetdb5/autoload/*.mal -%if %{with samtools} -%exclude %{_libdir}/monetdb5/bam.mal -%exclude %{_libdir}/monetdb5/autoload/*_bam.mal -%endif %{_libdir}/monetdb5/lib_capi.so %{_libdir}/monetdb5/lib_generator.so %{_libdir}/monetdb5/lib_udf.so @@ -753,9 +667,6 @@ use SQL with MonetDB, you will need to i %if %{with lidar} %exclude %{_libdir}/monetdb5/createdb/*_lidar.sql %endif -%if %{with samtools} -%exclude %{_libdir}/monetdb5/createdb/*_bam.sql -%endif %{_libdir}/monetdb5/createdb/*.sql %{_libdir}/monetdb5/sql*.mal %if %{with hugeint} @@ -939,7 +850,6 @@ export CFLAGS --enable-netcdf=no \ --enable-odbc=yes \ --enable-profiler=no \ - --enable-py2integration=%{?with_py2integration:yes}%{!?with_py2integration:no} \ --enable-py3integration=%{?with_py3integration:yes}%{!?with_py3integration:no} \ --enable-rintegration=%{?with_rintegration:yes}%{!?with_rintegration:no} \ --enable-sanitizer=no \ @@ -958,11 +868,9 @@ export CFLAGS --with-openssl=yes \ --with-proj=no \ --with-pthread=yes \ - --with-python2=%{?with_py2integration:yes}%{!?with_py2integration:no} \ --with-python3=yes \ --with-readline=yes \ --with-regex=%{?with_pcre:PCRE}%{!?with_pcre:POSIX} \ - --with-samtools=%{?with_samtools:yes}%{!?with_samtools:no} \ --with-snappy=no \ --with-unixodbc=yes \ --with-uuid=yes \ diff --git a/NT/mksqlwxs.py b/NT/mksqlwxs.py --- a/NT/mksqlwxs.py +++ b/NT/mksqlwxs.py @@ -51,7 +51,6 @@ def main(): extend = [] debug = [] geom = [] - pyapi2 = [] pyapi3 = [] print(r'<?xml version="1.0"?>') print(r'<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">') @@ -85,14 +84,6 @@ def main(): print(r' <FileSearch Id="CheckFile3" Name="geom.mal"/>') print(r' </DirectorySearch>') print(r' </Property>') - print(r' <Property Id="PYAPI2EXISTS">') - print(r' <DirectorySearch Id="CheckFileDir4" Path="[INSTALLDIR]" Depth="0">') - print(r' <FileSearch Id="CheckFile4" Name="pyapi_locatepython.bat"/>') - print(r' </DirectorySearch>') - print(r' <DirectorySearch Id="CheckFileDir42" Path="[INSTALLDIR]" Depth="0">') - print(r' <FileSearch Id="CheckFile42" Name="pyapi_locatepython2.bat"/>') - print(r' </DirectorySearch>') - print(r' </Property>') print(r' <Property Id="PYAPI3EXISTS">') print(r' <DirectorySearch Id="CheckFileDir5" Path="[INSTALLDIR]" Depth="0">') print(r' <FileSearch Id="CheckFile5" Name="pyapi_locatepython3.bat"/>') @@ -181,8 +172,6 @@ def main(): [r'lib\monetdb5\autoload\{}'.format(x) for x in sorted(filter(lambda x: x.endswith('.mal') and ('geom' not in x) and ('pyapi' not in x) and ('opt_sql_append' not in x), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))]) id = comp(geom, id, 18, [r'lib\monetdb5\autoload\{}'.format(x) for x in sorted(filter(lambda x: x.endswith('.mal') and ('geom' in x), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))]) - id = comp(pyapi2, id, 18, - [r'lib\monetdb5\autoload\{}'.format(x) for x in sorted(filter(lambda x: x.endswith('_pyapi.mal'), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))]) id = comp(pyapi3, id, 18, [r'lib\monetdb5\autoload\{}'.format(x) for x in sorted(filter(lambda x: x.endswith('_pyapi3.mal'), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))]) print(r' </Directory>') @@ -202,9 +191,6 @@ def main(): [r'lib\monetdb5\{}'.format(x) for x in sorted(filter(lambda x: x.endswith('.mal') and ('geom' in x), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5'))))]) id = comp(geom, id, 16, [r'lib\monetdb5\{}'.format(x) for x in sorted(filter(lambda x: x.startswith('lib_') and (x.endswith('.dll') or x.endswith('.pdb')) and ('geom' in x), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5'))))]) - id = comp(pyapi2, id, 16, - [r'lib\monetdb5\pyapi.mal', - r'lib\monetdb5\lib_pyapi.dll']) id = comp(pyapi3, id, 16, [r'lib\monetdb5\pyapi3.mal', r'lib\monetdb5\lib_pyapi3.dll']) @@ -240,8 +226,6 @@ def main(): r'M5server.bat', r'msqldump.bat', r'stethoscope.bat']) - id = comp(pyapi2, id, 12, - [r'pyapi_locatepython2.bat']) id = comp(pyapi3, id, 12, [r'pyapi_locatepython3.bat']) id = comp(features, id, 12, @@ -272,11 +256,6 @@ def main(): print(r' <ComponentRef Id="{}"/>'.format(f)) print(r' <MergeRef Id="VCRedist"/>') print(r' </Feature>') - print(r' <Feature Id="PyAPI2" Level="1000" AllowAdvertise="no" Absent="allow" Title="Include embedded Python 2" Description="Files required for using embedded Python 2.">') - for f in pyapi2: - print(r' <ComponentRef Id="{}"/>'.format(f)) - print(r' <Condition Level="1">PYAPI2EXISTS</Condition>') - print(r' </Feature>') print(r' <Feature Id="PyAPI3" Level="1000" AllowAdvertise="no" Absent="allow" Title="Include embedded Python 3" Description="Files required for using embedded Python 3.">') for f in pyapi3: print(r' <ComponentRef Id="{}"/>'.format(f)) diff --git a/NT/monetdb_config.h.in b/NT/monetdb_config.h.in --- a/NT/monetdb_config.h.in +++ b/NT/monetdb_config.h.in @@ -112,18 +112,6 @@ /* there is something very similar to asctime_r on Windows: */ #define asctime_r(t,b,s) asctime_s(b,s,t) -/* Define to 1 if you have the <bam/bam.h> header file. */ -/* #undef HAVE_BAM_BAM_H */ - -/* Define to 1 if you have the <bam/bgzf.h> header file. */ -/* #undef HAVE_BAM_BGZF_H */ - -/* Define to 1 if you have the <bam/kstring.h> header file. */ -/* #undef HAVE_BAM_KSTRING_H */ - -/* Define to 1 if you have the <bam/sam.h> header file. */ -/* #undef HAVE_BAM_SAM_H */ - /* Define to 1 if you have the `cbrt' function. */ #define HAVE_CBRT 1 @@ -258,9 +246,6 @@ /* #undef HAVE_LIBPTHREAD */ /* Define if we can link to python */ -/* #undef HAVE_LIBPY2 */ - -/* Define if we can link to python */ /* #undef HAVE_LIBPY3 */ _______________________________________________ checkin-list mailing list checkin-list@monetdb.org https://www.monetdb.org/mailman/listinfo/checkin-list