diff --git a/science/Makefile b/science/Makefile index e043cab1c2b9..a1eeff45bed3 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,373 +1,374 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-FAdist SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += apbs SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += code_saturne SUBDIR += colt SUBDIR += conduit SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += crf++ SUBDIR += csvtk SUBDIR += dakota SUBDIR += dalton SUBDIR += dcl SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dvc SUBDIR += eccodes SUBDIR += elk SUBDIR += elmerfem SUBDIR += epte SUBDIR += erd SUBDIR += ergo SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fastjet SUBDIR += fisicalab SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += hepmc3 SUBDIR += highfive SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kim-api SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmsym SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openkim-models SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin SUBDIR += orthanc + SUBDIR += orthanc-mysql SUBDIR += orthanc-webviewer SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += packmol SUBDIR += pagmo2 SUBDIR += paje SUBDIR += pcmsolver SUBDIR += phonopy SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PubChemPy SUBDIR += py-PyFR SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-access SUBDIR += py-asdf SUBDIR += py-ase SUBDIR += py-avogadrolibs SUBDIR += py-cdo SUBDIR += py-chainer SUBDIR += py-chainer-chemistry SUBDIR += py-chempy SUBDIR += py-cirq-aqt SUBDIR += py-cirq-core SUBDIR += py-cirq-google SUBDIR += py-cirq-ionq SUBDIR += py-cirq-pasqal SUBDIR += py-coards SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-eccodes SUBDIR += py-esda SUBDIR += py-geolinks SUBDIR += py-geomet SUBDIR += py-geometer SUBDIR += py-geometric SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5json SUBDIR += py-h5py SUBDIR += py-hiphive SUBDIR += py-inequality SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-liac-arff SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nibabel SUBDIR += py-nilearn SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-rmsd SUBDIR += py-ruffus SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-optimize SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-tobler SUBDIR += py-veusz SUBDIR += pybrain SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += scidavis SUBDIR += segyio SUBDIR += shelxle SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simbody SUBDIR += simgrid SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += tfel-edf SUBDIR += thermofun SUBDIR += tinker SUBDIR += udunits SUBDIR += v_sim SUBDIR += vipster SUBDIR += vmd SUBDIR += voro++ SUBDIR += votca SUBDIR += wannier90 SUBDIR += wwplot SUBDIR += wxmacmolplt SUBDIR += xcfun SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xtb SUBDIR += yoda .include diff --git a/science/orthanc-mysql/Makefile b/science/orthanc-mysql/Makefile new file mode 100644 index 000000000000..c63b5c716eb9 --- /dev/null +++ b/science/orthanc-mysql/Makefile @@ -0,0 +1,48 @@ +# Created by: maintainer.freebsd@xpoundit.com + +PORTNAME= orthanc-mysql +DISTVERSION= 4.0 +CATEGORIES= science +MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/plugin-mysql/:main \ + https://www.orthanc-server.com/downloads/get.php?path=/orthanc/:framework \ + https://orthanc.osimis.io/ThirdPartyDownloads/:thirdparty +DISTFILES= OrthancMySQL-${PORTVERSION}.tar.gz:main \ + Orthanc-1.9.3.tar.gz:framework \ + e2fsprogs-1.44.5.tar.gz:thirdparty +DIST_SUBDIR= orthanc +EXTRACT_ONLY= OrthancMySQL-${PORTVERSION}.tar.gz + +MAINTAINER= maintainer.freebsd@xpoundit.com +COMMENT= Orthanc plugin to use MySQL/MariaDB for indexing or storage + +LICENSE= AGPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc +LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ + libcurl.so:ftp/curl \ + libgdcmCommon.so:devel/gdcm \ + libjsoncpp.so:devel/jsoncpp \ + libpugixml.so:textproc/pugixml +RUN_DEPENDS= Orthanc:science/orthanc + +USES= cmake localbase mysql:client python:build ssl +USE_LDCONFIG= yes + +WRKSRC= ${WRKDIR}/OrthancMySQL-${PORTVERSION} +CMAKE_SOURCE_PATH= ${WRKSRC}/MySQL +CMAKE_OFF= DBUILD_UNIT_TESTS USE_SYSTEM_ORTHANC_SDK USE_SYSTEM_UUID +CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-1.9.3/OrthancFramework/Sources \ + -DORTHANC_FRAMEWORK_SOURCE=path +CXXFLAGS+= -I${LOCALBASE}/include -DNDEBUG +CFLAGS+= -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG + +PLIST_SUB= DISTVERSION=${DISTVERSION} + +post-extract: + ${MKDIR} ${WRKSRC}/MySQL/ThirdPartyDownloads + ${CP} ${DISTDIR}/${DIST_SUBDIR}/e2fsprogs-1.44.5.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads + ${CP} ${DISTDIR}/${DIST_SUBDIR}/Orthanc-1.9.3.tar.gz ${WRKSRC}/MySQL/ThirdPartyDownloads + ${TAR} -C ${WRKSRC}/MySQL/ThirdPartyDownloads -xf ${WRKSRC}/MySQL/ThirdPartyDownloads/Orthanc-1.9.3.tar.gz + +.include diff --git a/science/orthanc-mysql/distinfo b/science/orthanc-mysql/distinfo new file mode 100644 index 000000000000..23cc7032cd8b --- /dev/null +++ b/science/orthanc-mysql/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1620905033 +SHA256 (orthanc/OrthancMySQL-4.0.tar.gz) = 9420b7d3293768778fc4f60cc7d72c0e15c1287bead98f6c3a9beddf6865a09a +SIZE (orthanc/OrthancMySQL-4.0.tar.gz) = 318342 +SHA256 (orthanc/Orthanc-1.9.3.tar.gz) = 41cc35a3d15ecb0d7b834e8e28a740cc4ffa1f333c019a764228d60e96608960 +SIZE (orthanc/Orthanc-1.9.3.tar.gz) = 1818313 +SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc +SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 diff --git a/science/orthanc-mysql/pkg-descr b/science/orthanc-mysql/pkg-descr new file mode 100644 index 000000000000..d05cb690085d --- /dev/null +++ b/science/orthanc-mysql/pkg-descr @@ -0,0 +1,5 @@ +Orthanc-mysql is an Orthanc plugin that replaces the default SQLite +engine of Orthanc with a MySQL back-end. The plugin is compatible +with MariaDB as well. + +WWW: https://www.orthanc-server.com/static.php?page=mysql diff --git a/science/orthanc-mysql/pkg-plist b/science/orthanc-mysql/pkg-plist new file mode 100644 index 000000000000..5e9be4387fa3 --- /dev/null +++ b/science/orthanc-mysql/pkg-plist @@ -0,0 +1,4 @@ +share/orthanc/plugins/libOrthancMySQLIndex.so +share/orthanc/plugins/libOrthancMySQLIndex.so.%%DISTVERSION%% +share/orthanc/plugins/libOrthancMySQLStorage.so +share/orthanc/plugins/libOrthancMySQLStorage.so.%%DISTVERSION%%