mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-25 06:31:43 +02:00
Merge pull request #75 from TREX-CoE/add-inquire-functionality
Add inquire functionality
This commit is contained in:
commit
51c43fe1ac
@ -1,4 +1,4 @@
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#!/bin/bash
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#!/bin/bash
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set -x
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set -e
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@ -38,12 +38,12 @@ python3 -m pip install -r requirements.txt
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# Create build directory and compile extension files (*.c)
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# --no-user-cfg disables custom .cfg files of the user machine, so that only setup.cfg is used
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#python3 -s setup.py --no-user-cfg build
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#python3 -s setup.py --no-user-cfg build
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# Local inplace build of the .so module with SWIG-produced pytrexio_wrap.c (from the SWIG documentation)
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#python3 setup.py build_ext --inplace --swig-opts="-modern"
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# Create distributions:
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# Create distributions:
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# OLD WAY (DEPRECATED BY PYPA)
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# 1) sdist produces .tar.gz with all files necessary for manual compilation;
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@ -54,14 +54,7 @@ python3 -m pip install -r requirements.txt
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python3 -m build --sdist --wheel --outdir dist/
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# Install pytrexio in the current environment from the aforementioned wheel
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# OLD WAY
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# --force-reinstall is needed here because build-system pre-installs pytrexio in the environment
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# but does not install things in the corresponding site-packages directory
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#python3 -m pip install dist/trexio-*.whl --force-reinstall
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# NEW WAY
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python3 -m pip install dist/trexio-*.whl
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python3 -m pip install dist/trexio-*.whl --force-reinstall
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# Run the command below in the root directory to install the package in 'editable' (-e) mode without dependencies (--no-deps)
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#python -m pip install -e . --no-deps
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@ -83,7 +76,6 @@ rm -rf build dist trexio.egg-info
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# Additional information related to the installation of the TREXIO Python API
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#Removing MANIFEST.in leads to issues in the installation. In particular, the .c and .h source files do not get copied
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#from the src/ directory into the tar.gz which is produced by setup sdist command.
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#Removing MANIFEST.in leads to issues in the installation. In particular, the .c and .h source files do not get copied
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#from the src/ directory into the tar.gz which is produced by setup sdist command.
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#These source files are required to build the pytrexio.so extension module, which is needed for the Python API.
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@ -40,6 +40,7 @@ except:
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# create TREXIO file and open it for writing
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test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
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assert test_file.exists
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# Print docstring of the trexio.open function
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#print(trexio.open.__doc__)
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@ -153,6 +154,7 @@ del test_file
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# open previously created TREXIO file, now in 'read' mode
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test_file2 = trexio.File(output_filename, 'r', TEST_TREXIO_BACKEND)
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assert test_file2.exists
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# check for existence of some of the previously written variables
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assert trexio.has_nucleus_num
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@ -1,5 +1,4 @@
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#+TITLE: Front end API
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break;
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#+PROPERTY: comments org
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#+SETUPFILE: ../../docs/theme.setup
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# -*- mode: org -*-
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@ -696,12 +695,15 @@ class File:
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self.back_end = back_end
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self.isOpen = False
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self.exists = False
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if pytrexio_s is None:
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self.pytrexio_s = open(filename, mode, back_end)
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self.pytrexio_s = _open(filename, mode, back_end)
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self.isOpen = True
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self.exists = True
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else:
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self.pytrexio_s = pytrexio_s
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self.isOpen = None
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self.exists = None
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self.info = info
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@ -710,17 +712,23 @@ class File:
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"""Close a TREXIO File."""
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if self.isOpen:
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close(self.pytrexio_s)
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_close(self.pytrexio_s)
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self.isOpen = False
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else:
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raise Exception("TREXIO File object has not been opened.")
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def inquire(self):
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"""Inquire whether a TREXIO file exists."""
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self.exists = _inquire(self.filename)
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def __del__(self):
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"""This is a TREXIO File destructor."""
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if self.isOpen:
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close(self.pytrexio_s)
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_close(self.pytrexio_s)
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elif self.isOpen is None:
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raise Exception("[WIP]: TREXIO file handle provided but what if the file is already closed?")
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else:
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@ -972,7 +980,7 @@ end interface
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*** Python
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#+begin_src python :tangle basic_python.py
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def open(file_name: str, mode: str, back_end: int):
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def _open(file_name: str, mode: str, back_end: int):
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"""Create TREXIO file or open existing one.
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Parameters:
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@ -1149,7 +1157,7 @@ end interface
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*** Python
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#+begin_src python :tangle basic_python.py
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def close(trexio_file):
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def _close(trexio_file):
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"""Close TREXIO file.
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Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
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@ -1163,6 +1171,77 @@ def close(trexio_file):
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raise
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#+end_src
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** File existence
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~trexio_inquire~ check whether TREXIO file exists.
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input parameters:
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~file_name~ - string containing file name
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output:
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~trexio_exit_code~ exit code.
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*** C
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#+begin_src c :tangle prefix_front.h :exports none
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trexio_exit_code trexio_inquire(const char* file_name);
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_inquire (const char* file_name)
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{
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if (file_name == NULL || file_name[0] == '\0') return TREXIO_INVALID_ARG_1;
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/* First check if the TREXIO file exists and if it is a directory */
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trexio_exit_code rc_text = trexio_text_inquire(file_name);
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#ifdef HAVE_HDF5
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/* FILE_ERROR here means that the file exists but it is not a directory -> check with HDF5 */
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if (rc_text == TREXIO_FILE_ERROR) {
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trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(file_name);
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return rc_hdf5;
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/* If rc_text is TREXIO_SUCCESS -> file is a TREXIO directory; TREXIO_FAILURE -> file/directory does not exist */
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} else {
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return rc_text;
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}
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#else
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return rc_text;
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#endif
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}
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#+end_src
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*** Fortran
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The function below is a C binding.
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The front end Fortran function for ~trexio_inquire~ can be found in the ~Fortran helper/wrapper functions~.
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#+begin_src f90 :tangle prefix_fortran.f90
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interface
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integer function trexio_inquire_c (filename) bind(C, name="trexio_inquire")
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use, intrinsic :: iso_c_binding
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import
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character(kind=c_char), dimension(*) :: filename
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end function trexio_inquire_c
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end interface
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#+end_src
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*** Python
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#+begin_src python :tangle basic_python.py
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def _inquire(file_name: str) -> bool:
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"""Check whether ~file_name~ TREXIO file exists.
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"""
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rc = pytr.trexio_inquire(trexio_file_name)
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if rc == TREXIO_SUCCESS:
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return True
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elif rc == TREXIO_FAILURE:
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return False
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else:
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raise Error(rc)
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#+end_src
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* Templates for front end
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** Description
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@ -1769,7 +1848,7 @@ trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_doub
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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rc = trexio_hdf5_write_$group_dset$(file,
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rc = trexio_hdf5_write_$group_dset$(file,
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(const $group_dset_dtype_double$*) $group_dset$_p,
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rank, dims);
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break;
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@ -2629,7 +2708,7 @@ trexio_write_$group_dset$(trexio_t* const file,
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if (file->one_based) {
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uint64_t index_size = rank * buffer_size;
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int32_t* index_sparse_p = CALLOC(index_size, int32_t);
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if (index_sparse_p == NULL) return TREXIO_ALLOCATION_FAILED;
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@ -3801,6 +3880,23 @@ contains
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end function trexio_open
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#+end_src
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The function below adapts the original C-based ~trexio_inquire~ for Fortran.
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This is needed due to the same reasons as for ~trexio_open~ function.
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Note, that Fortran interface calls the main ~TREXIO~ API, which is written in C.
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#+begin_src f90 :tangle helper_fortran.f90
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integer function trexio_inquire (filename)
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use, intrinsic :: iso_c_binding
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implicit none
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character(len=*), intent(in) :: filename
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character(len=len_trim(filename)+1) :: filename_c
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filename_c = trim(filename) // c_null_char
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trexio_inquire = trexio_inquire_c(filename_c)
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end function trexio_inquire
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#+end_src
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The subroutine below transforms an array of Fortran strings into one big string using ~TREXIO_DELIM~ symbol
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as a delimeter and adds ~NULL~ character in the end in order to properly pass the desired string to
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C API. This is needed due to the fact that strings in C are terminated by ~NULL~ character ~\0~.
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@ -69,13 +69,29 @@ typedef struct trexio_hdf5_s {
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} trexio_hdf5_t;
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#+end_src
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** Template for HDF5 init/deinit
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#+begin_src c :tangle struct_hdf5.h :exports none
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trexio_exit_code trexio_hdf5_init(trexio_t* const file);
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trexio_exit_code trexio_hdf5_deinit(trexio_t* const file);
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trexio_exit_code trexio_hdf5_inquire(const char* file_name);
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#+end_src
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** Template for HDF5 init/deinit
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#+begin_src c :tangle basic_hdf5.c
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trexio_exit_code
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trexio_hdf5_inquire(const char* file_name)
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{
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/* H5Fis_hdf5 determines whether file is in HDF5 format */
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htri_t rc = H5Fis_hdf5(file_name);
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if (rc > 0 ) {
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return TREXIO_SUCCESS; //exists and HDF5
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} else if (rc == 0) {
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return TREXIO_FILE_ERROR; //exists but not HDF5
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} else {
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return TREXIO_FAILURE; //does not exist or function fails
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}
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}
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#+end_src
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#+begin_src c :tangle basic_hdf5.c
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trexio_exit_code
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@ -134,7 +150,9 @@ trexio_hdf5_init (trexio_t* const file)
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle basic_hdf5.c
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trexio_exit_code
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trexio_hdf5_deinit (trexio_t* const file)
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{
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@ -105,6 +105,33 @@ typedef struct trexio_text_s {
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#+begin_src c :tangle basic_text.h :exports none
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trexio_exit_code trexio_text_init(trexio_t* const file);
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trexio_exit_code trexio_text_inquire(const char* file_name);
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trexio_exit_code trexio_text_deinit(trexio_t* const file);
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trexio_exit_code trexio_text_lock(trexio_t* const file);
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trexio_exit_code trexio_text_unlock(trexio_t* const file);
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#+end_src
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#+begin_src c :tangle basic_text.c
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trexio_exit_code
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trexio_text_inquire (const char* file_name)
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{
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/* Check if the file with "file_name" exists and that it is a directory */
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struct stat st;
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int rc = stat(file_name, &st);
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bool file_exists = rc == 0;
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if (file_exists) {
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bool is_a_directory = st.st_mode & S_IFDIR;
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if (!is_a_directory) return TREXIO_FILE_ERROR;
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return TREXIO_SUCCESS;
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} else {
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return TREXIO_FAILURE;
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}
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}
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#+end_src
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#+begin_src c :tangle basic_text.c
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@ -119,30 +146,19 @@ trexio_text_init (trexio_t* const file)
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/* Put all pointers to NULL but leave parent untouched */
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memset(&(f->parent)+1,0,sizeof(trexio_text_t)-sizeof(trexio_t));
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/* If directory doesn't exist, create it in write mode */
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struct stat st;
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/* Check if directory exists */
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trexio_exit_code rc;
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rc = trexio_text_inquire(file->file_name);
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/* TREXIO file exists but is not a directory */
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if (rc == TREXIO_FILE_ERROR) return rc;
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/* If directory does not exist - create it in write mode */
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if (rc == TREXIO_FAILURE) {
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int rc = stat(file->file_name, &st);
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if (file->mode == 'r') return TREXIO_READONLY;
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bool file_exists = rc == 0;
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int rc_dir = mkdir(file->file_name, 0777);
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if (rc_dir != 0) return TREXIO_ERRNO;
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if (file_exists) {
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bool is_a_directory = st.st_mode & S_IFDIR;
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if (!is_a_directory) {
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return TREXIO_FILE_ERROR;
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}
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} else {
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if (file->mode == 'r') {
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return TREXIO_READONLY;
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}
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rc = mkdir(file->file_name, 0777);
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if (rc != 0) {
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return TREXIO_ERRNO;
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}
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}
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/* Create the lock file in the directory */
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@ -166,7 +182,7 @@ trexio_text_init (trexio_t* const file)
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if (errno == EACCES) {
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/* The directory is read-only and the lock file can't be written.
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Create a dummy temporary file for dummy locking.
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*/
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,*/
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char dirname[TREXIO_MAX_FILENAME_LENGTH] = "/tmp/trexio.XXXXXX";
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if (mkdtemp(dirname) == NULL) return TREXIO_ERRNO;
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strncpy (file_name, dirname, TREXIO_MAX_FILENAME_LENGTH);
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@ -184,10 +200,6 @@ trexio_text_init (trexio_t* const file)
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}
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#+end_src
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#+begin_src c :tangle basic_text.h :exports none
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trexio_exit_code trexio_text_lock(trexio_t* const file);
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#+end_src
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#+begin_src c :tangle basic_text.c
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trexio_exit_code trexio_text_lock(trexio_t* const file) {
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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@ -210,15 +222,6 @@ trexio_exit_code trexio_text_lock(trexio_t* const file) {
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}
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||||
#+end_src
|
||||
|
||||
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#+begin_src c :tangle basic_text.h :exports none
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||||
trexio_exit_code trexio_text_deinit(trexio_t* const file);
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#+end_src
|
||||
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#+begin_src c :tangle basic_text.h :exports none
|
||||
trexio_exit_code trexio_text_unlock(trexio_t* const file);
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#+end_src
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||||
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||||
#+begin_src c :tangle basic_text.c
|
||||
trexio_exit_code
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trexio_text_unlock (trexio_t* const file)
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|
@ -85,7 +85,7 @@ static int test_open_errors (const back_end_t backend) {
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fprintf(stderr, "%s \n", trexio_string_of_error(rc));
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||||
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// open existing file with non-supported back end, should return TREXIO_INVALID_ARG_3
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file = trexio_open(TREXIO_VOID, 'w', 666, &rc);
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file = trexio_open(TREXIO_FILE, 'w', 666, &rc);
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assert (file == NULL);
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assert (rc == TREXIO_INVALID_ARG_3);
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fprintf(stderr, "%s \n", trexio_string_of_error(rc));
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@ -96,6 +96,28 @@ static int test_open_errors (const back_end_t backend) {
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}
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||||
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||||
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||||
static int test_inquire (const back_end_t backend) {
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||||
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||||
/* Try to call trexio_inquire function */
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||||
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||||
trexio_exit_code rc;
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||||
|
||||
/*================= START OF TEST ==================*/
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||||
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||||
// inquire non-existing file
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||||
rc = trexio_inquire(TREXIO_VOID);
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||||
assert (rc == TREXIO_FAILURE);
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||||
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||||
// inquire existing file
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||||
rc = trexio_inquire(TREXIO_FILE);
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||||
assert (rc == TREXIO_SUCCESS);
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||||
|
||||
/*================= END OF TEST ==================*/
|
||||
|
||||
return 0;
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||||
}
|
||||
|
||||
|
||||
int main(void) {
|
||||
|
||||
/*============== Test launcher ================*/
|
||||
@ -107,11 +129,10 @@ int main(void) {
|
||||
test_open_w (TREXIO_FILE, TEST_BACKEND);
|
||||
test_open_r (TREXIO_FILE, TEST_BACKEND);
|
||||
test_open_errors(TEST_BACKEND);
|
||||
test_inquire (TEST_BACKEND);
|
||||
|
||||
rc = system(RM_COMMAND);
|
||||
assert (rc == 0);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
@ -85,7 +85,7 @@ static int test_open_errors (const back_end_t backend) {
|
||||
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
|
||||
|
||||
// open existing file with non-supported back end, should return TREXIO_INVALID_ARG_3
|
||||
file = trexio_open(TREXIO_VOID, 'w', 666, &rc);
|
||||
file = trexio_open(TREXIO_FILE, 'w', 666, &rc);
|
||||
assert (file == NULL);
|
||||
assert (rc == TREXIO_INVALID_ARG_3);
|
||||
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
|
||||
@ -96,6 +96,28 @@ static int test_open_errors (const back_end_t backend) {
|
||||
}
|
||||
|
||||
|
||||
static int test_inquire (const back_end_t backend) {
|
||||
|
||||
/* Try to call trexio_inquire function */
|
||||
|
||||
trexio_exit_code rc;
|
||||
|
||||
/*================= START OF TEST ==================*/
|
||||
|
||||
// inquire non-existing file
|
||||
rc = trexio_inquire(TREXIO_VOID);
|
||||
assert (rc == TREXIO_FAILURE);
|
||||
|
||||
// inquire existing file
|
||||
rc = trexio_inquire(TREXIO_FILE);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
/*================= END OF TEST ==================*/
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int main(void) {
|
||||
|
||||
/*============== Test launcher ================*/
|
||||
@ -107,11 +129,10 @@ int main(void) {
|
||||
test_open_w (TREXIO_FILE, TEST_BACKEND);
|
||||
test_open_r (TREXIO_FILE, TEST_BACKEND);
|
||||
test_open_errors(TEST_BACKEND);
|
||||
test_inquire (TEST_BACKEND);
|
||||
|
||||
rc = system(RM_COMMAND);
|
||||
assert (rc == 0);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
@ -103,6 +103,9 @@ subroutine test_write(file_name, back_end)
|
||||
|
||||
! ================= START OF TEST ===================== !
|
||||
|
||||
rc = trexio_inquire(file_name)
|
||||
call trexio_assert(rc, TREXIO_FAILURE)
|
||||
|
||||
trex_file = trexio_open(file_name, 'w', back_end, rc)
|
||||
call trexio_assert(rc, TREXIO_SUCCESS)
|
||||
|
||||
@ -217,6 +220,9 @@ subroutine test_read(file_name, back_end)
|
||||
|
||||
! ================= START OF TEST ===================== !
|
||||
|
||||
rc = trexio_inquire(file_name)
|
||||
call trexio_assert(rc, TREXIO_SUCCESS)
|
||||
|
||||
trex_file = trexio_open(file_name, 'r', back_end, rc)
|
||||
call trexio_assert(rc, TREXIO_SUCCESS)
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user