DataFrameDimension

.appveyor.ctest

@@ -30,7 +30,6 @@ ctest_start(Continuous)
 ctest_configure()
 ctest_build()
 ctest_test(RETURN_VALUE tests_ret)
-ctest_submit()
 
 if(NOT tests_ret EQUAL 0)
   message(FATAL_ERROR "Test had failures!")

.gitignore

@@ -10,6 +10,9 @@ Makefile.conf
 # ingore documentation
 doc/html
 docs/_build
+docs/api
+docs/api_doc/html
+docs/api_doc/xml
 
 # ignore hdf5 files
 *.hdf

.travis.ctest

@@ -47,8 +47,6 @@ if(GCOV AND $ENV{CXX} MATCHES "g\\+\\+")
   ctest_coverage()
 endif()
 
-ctest_submit()
-
 if(NOT tests_ret EQUAL 0)
   message(FATAL_ERROR "Test had failures!")
 endif()

.travis.yml

@@ -28,6 +28,10 @@ matrix:
       env: FS_BACKEND=OFF DOCKERFILE=ub1804
 
 addons:
+  apt:
+    update: true
+    packages:
+      - lcov
   homebrew:
     packages:
       - cmake
@@ -45,7 +49,7 @@ cache:
     - $HOME/Library/Caches/Homebrew
 
 before_install:
-  - if [[ "$CXX" == "gcc" ]];
+  - if [[ "$TRAVIS_COMPILER" == "gcc" ]];
     then
        export CC=gcc;
        export CXX=g++;
@@ -77,8 +81,9 @@ script:
     fi
 
 after_success:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$FS_BACKEND" == "OFF" ]]; then
-      lcov -q --capture --directory . --no-extern --output-file coverage.info;
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$FS_BACKEND" == "OFF" && "$DOCKERFILE" == "archlinux" && "$CXX" == "g++" ]]; then
+      echo "Submitting code coverage report";
+      docker exec nixbuilder lcov -q --capture --directory . --no-extern --output-file coverage.info;
       bash <(curl -s https://codecov.io/bash) -f coverage.info -Z;
     fi
 

.unix.ctest

@@ -39,4 +39,3 @@ ctest_build()
 ctest_test()
 ctest_memcheck()
 ctest_coverage()
-ctest_submit()

CTestConfig.cmake

@@ -1,7 +1,2 @@
 set(CTEST_PROJECT_NAME "nix")
 set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
-
-set(CTEST_DROP_METHOD "https")
-set(CTEST_DROP_SITE "cdash.0xdeadbabe.info")
-set(CTEST_DROP_LOCATION "/submit.php?project=nix")
-set(CTEST_DROP_SITE_CDASH TRUE)

backend/fs/DataArrayFS.hpp

@@ -126,6 +126,15 @@ class DataArrayFS : virtual public base::IDataArray,  public EntityWithSourcesFS
     std::shared_ptr<base::ISampledDimension> createSampledDimension(ndsize_t id, double sampling_interval);
 
 
+    std::shared_ptr<base::IDataFrameDimension> createDataFrameDimension(ndsize_t id, const nix::DataFrame &df) {
+        throw std::runtime_error("not implemented");
+    }
+
+
+    std::shared_ptr<base::IDataFrameDimension> createDataFrameDimension(ndsize_t id, const nix::DataFrame &df, unsigned col_index) {
+        throw std::runtime_error("not implemented");
+    }
+
     bool deleteDimensions();
 
     //--------------------------------------------------

backend/fs/DimensionFS.cpp

@@ -20,6 +20,8 @@ DimensionType dimensionTypeFromStr(const std::string &str) {
         return DimensionType::Range;
     } else if (str == "sample") {
         return DimensionType::Sample;
+    } else if (str == "data_frame") {
+        return DimensionType::DataFrame;
     } else {
         throw std::runtime_error("Not a valid dimension name");
     }
@@ -49,6 +51,9 @@ std::string dimensionTypeToStr(DimensionType dim) {
         case DimensionType::Sample:
             dimType = "sample";
             break;
+        case DimensionType::DataFrame:
+            dimType = "data_frame";
+            break;
     }
 
     if (dimType.empty()) {
@@ -77,6 +82,9 @@ std::shared_ptr<IDimension> openDimensionFS(const std::string &loc, FileMode mod
         case DimensionType::Sample:
             dim = std::make_shared<SampledDimensionFS>(loc, mode);
             break;
+        case DimensionType::DataFrame:
+            dim = std::make_shared<DataFrameDimensionFS>(loc, mode);
+            break;
     }
     return dim;
 }

backend/fs/DimensionFS.hpp

@@ -10,8 +10,13 @@
 #define NIX_DIMENSIONFS_HPP
 
 #include <nix/base/IDimensions.hpp>
+#include <nix/base/IBlock.hpp>
+#include <nix/base/IFile.hpp>
+#include <nix/DataFrame.hpp>
+
 #include "DirectoryWithAttributes.hpp"
 #include "DataArrayFS.hpp"
+
 #include <string>
 #include <iostream>
 #include <ctime>
@@ -142,6 +147,55 @@ class SetDimensionFS : virtual public base::ISetDimension, public DimensionFS {
 };
 
 
+class DataFrameDimensionFS : virtual public base::IDataFrameDimension, public DimensionFS {
+
+public:
+    DataFrameDimensionFS(const std::string &loc, FileMode mode)
+        :DimensionFS(loc, mode){};
+
+
+    DataFrameDimensionFS(const std::string &loc, size_t index, FileMode mode)
+        :DimensionFS(loc, index, mode){};
+
+    DimensionType dimensionType() const {
+        return DimensionType::DataFrame;
+    }
+
+    boost::optional<unsigned> columnIndex() const {
+        boost::optional<unsigned> index ={};
+        return index;
+    }
+
+    Column column(boost::optional<unsigned> col_index) const {
+        nix::Column c;
+        return c;
+    }
+
+    std::string label(boost::optional<unsigned> col_index) const {
+        std::string label = "";
+        return label;
+    }
+
+    std::string unit(boost::optional<unsigned> col_index) const {
+        std::string unit;
+        return unit;
+    };
+
+    nix::DataType columnDataType(boost::optional<unsigned> col_index) const {
+        nix::DataType dtype = nix::DataType::Nothing;
+        return dtype;
+    }
+
+    std::shared_ptr<base::IDataFrame> dataFrame() const {
+        //std::shared_ptr<base::IDataFrameFS> df; //FIXME DataFrameFS does not exist
+        return nullptr;
+    }
+
+    virtual ~DataFrameDimensionFS(){};
+
+};
+
+
 class RangeDimensionFS : virtual public base::IRangeDimension, public DimensionFS {
 
 public:

backend/fs/Directory.cpp

@@ -136,7 +136,8 @@ bool Directory::removeObjectByNameOrAttribute(const std::string &attribute, cons
 
 
 void Directory::createDirectoryLink(const std::string &target, const std::string &name) {
-    if (boost::filesystem::exists({target})) {
+    bfs::path p(target);
+    if (boost::filesystem::exists(p)) {
         boost::filesystem::create_directory_symlink(boost::filesystem::path(target), loc / boost::filesystem::path(name));
     } else {
         throw std::runtime_error("Directory::createLink: target does not exist");

backend/fs/SectionFS.cpp

@@ -104,7 +104,6 @@ void SectionFS::repository(const none_t t) {
 
 void SectionFS::link(const std::string &id) {
     bfs::path p(location()), l("link");
-
     if (bfs::exists(p / l)) {
         link(none);
     }
@@ -122,8 +121,9 @@ void SectionFS::link(const std::string &id) {
 
 std::shared_ptr<base::ISection> SectionFS::link() const {
     std::shared_ptr<base::ISection> sec;
-
-    if (bfs::exists({location() + "/link"})) {
+    bfs::path p(location());
+    p /= "link";
+    if (bfs::exists(p)) {
         auto sec_tmp = std::make_shared<SectionFS>(file(), location() + "/link");
         // re-get above section "sec_tmp": parent missing, findSections will set it!
         auto found = File(file()).findSections(util::IdFilter<Section>(sec_tmp->id()));
@@ -136,8 +136,10 @@ std::shared_ptr<base::ISection> SectionFS::link() const {
 
 
 void SectionFS::link(const none_t t) {
-    if (bfs::exists({location() + "/link"})) {
-        bfs::remove_all({location() + "/link"});
+    bfs::path p(location());
+    p /= "link";
+    if (bfs::exists(p)) {
+        bfs::remove_all(p);
     }
     forceUpdatedAt();
 }

backend/hdf5/DataArrayHDF5.cpp

@@ -206,6 +206,18 @@ std::shared_ptr<base::ISampledDimension> DataArrayHDF5::createSampledDimension(n
 }
 
 
+std::shared_ptr<base::IDataFrameDimension> DataArrayHDF5::createDataFrameDimension(ndsize_t index, const nix::DataFrame &df, unsigned col_index) {
+    H5Group g = createDimensionGroup(index);
+    return make_shared<DataFrameDimensionHDF5>(g, index, file(), block(), df, col_index);
+}
+
+
+std::shared_ptr<base::IDataFrameDimension> DataArrayHDF5::createDataFrameDimension(ndsize_t index, const nix::DataFrame &df) {
+    H5Group g = createDimensionGroup(index);
+    return make_shared<DataFrameDimensionHDF5>(g, index, file(), block(), df);
+}
+
+
 H5Group DataArrayHDF5::createDimensionGroup(ndsize_t index) {
     boost::optional<H5Group> g = dimension_group(true);
 

backend/hdf5/DataArrayHDF5.hpp

@@ -15,6 +15,7 @@
 #define NIX_DATA_ARRAY_HDF5_H
 
 #include <nix/base/IDataArray.hpp>
+#include <nix/DataFrame.hpp>
 #include "EntityWithSourcesHDF5.hpp"
 
 #include <boost/multi_array.hpp>
@@ -114,6 +115,12 @@ class DataArrayHDF5 : virtual public base::IDataArray,  public EntityWithSources
     std::shared_ptr<base::ISampledDimension> createSampledDimension(ndsize_t id, double sampling_interval);
 
 
+    std::shared_ptr<base::IDataFrameDimension> createDataFrameDimension(ndsize_t id, const nix::DataFrame &df);
+
+
+    std::shared_ptr<base::IDataFrameDimension> createDataFrameDimension(ndsize_t id, const nix::DataFrame &df, unsigned col_index);
+
+
     bool deleteDimensions();
 
     //--------------------------------------------------