mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-11-03 20:54:07 +01:00
[WIP] add delete_group functions and unsafe trexio_open mode
This commit is contained in:
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commit
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@ -190,6 +190,7 @@ __trexio_path__ = None
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| ~TREXIO_BACK_END_MISSING~ | 26 | 'Requested back end is disabled' |
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| ~TREXIO_INVALID_STR_LEN~ | 30 | 'Invalid max_str_len' |
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| ~TREXIO_INT_SIZE_OVERFLOW~ | 31 | 'Possible integer overflow' |
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| ~TREXIO_SAFE_MODE~ | 32 | 'Unsafe operation in safe mode' |
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# We need to force Emacs not to indent the Python code:
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# -*- org-src-preserve-indentation: t
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@ -265,6 +266,7 @@ return '\n'.join(result)
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#define TREXIO_BACK_END_MISSING ((trexio_exit_code) 26)
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#define TREXIO_INVALID_STR_LEN ((trexio_exit_code) 30)
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#define TREXIO_INT_SIZE_OVERFLOW ((trexio_exit_code) 31)
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#define TREXIO_SAFE_MODE ((trexio_exit_code) 32)
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#+end_src
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#+begin_src f90 :tangle prefix_fortran.f90 :exports none
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@ -298,6 +300,7 @@ return '\n'.join(result)
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integer(trexio_exit_code), parameter :: TREXIO_BACK_END_MISSING = 26
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integer(trexio_exit_code), parameter :: TREXIO_INVALID_STR_LEN = 30
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integer(trexio_exit_code), parameter :: TREXIO_INT_SIZE_OVERFLOW = 31
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integer(trexio_exit_code), parameter :: TREXIO_SAFE_MODE = 32
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#+end_src
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#+begin_src python :tangle prefix_python.py :exports none
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@ -332,6 +335,7 @@ return '\n'.join(result)
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TREXIO_BACK_END_MISSING = 26
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TREXIO_INVALID_STR_LEN = 30
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TREXIO_INT_SIZE_OVERFLOW = 31
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TREXIO_SAFE_MODE = 32
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#+end_src
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:END:
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@ -464,6 +468,9 @@ return '\n'.join(result)
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case TREXIO_INT_SIZE_OVERFLOW:
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return "Possible integer overflow";
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break;
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case TREXIO_SAFE_MODE:
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return "Unsafe operation in safe mode";
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break;
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#+end_example
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**** C source code
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@ -776,6 +783,7 @@ struct trexio_back_end_s {
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2) ~mode~ - character containing open mode (see below)
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- ~'w'~ - (write) creates a new file as READWRITE (overwrite existing file)
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- ~'r'~ - (read) opens existing file as READONLY
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- ~'u'~ - (unsafe) opens existing file as READWRITE with the possibility to overwrite blocks and delete full groups.
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3) ~back_end~ - integer number (or the corresponding global parameter) specifying the back end
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- ~TREXIO_HDF5~ - for HDF5 back end (integer alternative: 0)
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- ~TREXIO_TEXT~ - for TEXT back end (integer alternative: 1)
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@ -783,7 +791,7 @@ struct trexio_back_end_s {
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output:
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~trexio_t~ file handle
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Note: the ~file_name~ in TEXT back end actually corresponds to the
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**Note:** the ~file_name~ in TEXT back end actually corresponds to the
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name of the directory where ~.txt~ data files are stored. The
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actual name of each ~.txt~ file corresponds to the group name
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provided in ~trex.config~ (e.g. ~nucleus.txt~ for nuclei-related
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@ -791,6 +799,8 @@ struct trexio_back_end_s {
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are hard-coded), which is why the user should tend to avoid
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renaming the ~.txt~ data files.
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**Note:** internal consistency is not guaranteed once the file has been modified in ~'u'~ (unsafe) mode.
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*** C
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#+begin_src c :tangle prefix_front.h :exports none
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@ -815,7 +825,7 @@ trexio_open(const char* file_name, const char mode,
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return NULL;
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}
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if (mode != 'r' && mode != 'w') {
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if (mode != 'r' && mode != 'w' && mode != 'u') {
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if (rc_open != NULL) *rc_open = TREXIO_INVALID_ARG_2;
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return NULL;
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}
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@ -3894,6 +3904,88 @@ def has_$group_str$(trexio_file) -> bool:
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return False
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#+end_src
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** Templates for front end delete an entire group (UNSAFE MODE)
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*** Introduction
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This section concerns API calls related to string attributes.
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| Function name | Description |
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|-------------------------+-------------------------------------------|
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| ~trexio_delete_$group$~ | Delete a given group from the TREXIO file |
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*** C templates for front end
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#+begin_src c :tangle delete_group_front.h :exports none
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trexio_exit_code trexio_delete_$group$(trexio_t* const file);
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#+end_src
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#+begin_src c :tangle delete_group_front.c
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trexio_exit_code
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trexio_delete_$group$ (trexio_t* const file)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (file->mode != 'u') return TREXIO_SAFE_MODE;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_delete_$group$(file);
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_delete_$group$(file);
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_delete_$group$(file);
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break;
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,*/
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}
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return TREXIO_FAILURE;
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}
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#+end_src
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*** Fortran templates for front end
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The ~Fortran~ templates that provide an access to the ~C~ API calls from Fortran.
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These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
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#+begin_src f90 :tangle delete_group_front_fortran.f90
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interface
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integer(trexio_exit_code) function trexio_delete_$group$ (trex_file) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(trexio_t), intent(in), value :: trex_file
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end function trexio_delete_$group$
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end interface
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#+end_src
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*** Python templates for front end
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#+begin_src python :tangle delete_group_front.py
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def delete_$group$(trexio_file) -> None:
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"""Delete the entire $group$ group from the TREXIO file.
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Parameters:
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trexio_file:
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TREXIO File object.
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Raises:
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- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
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- Exception from some other error (e.g. RuntimeError).
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"""
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rc = pytr.trexio_delete_$group$(trexio_file.pytrexio_s)
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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#+end_src
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* Fortran helper/wrapper functions
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The function below adapts the original C-based ~trexio_open~ for Fortran.
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@ -10,7 +10,9 @@ cat populated/pop_basic_hdf5.c >> trexio_hdf5.c
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cat populated/pop_has_*.c >> trexio_hdf5.c
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cat populated/pop_read_*.c >> trexio_hdf5.c
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cat populated/pop_write_*.c >> trexio_hdf5.c
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cat populated/pop_delete_group_hdf5.c >> trexio_hdf5.c
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cat populated/pop_hrw_*.h >> trexio_hdf5.h
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cat populated/pop_delete_group_hdf5.h >> trexio_hdf5.h
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cat helpers_hdf5.c >> trexio_hdf5.c
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cat suffix_hdf5.h >> trexio_hdf5.h
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@ -49,8 +49,7 @@
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#+end_src
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* HDF5 back end
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** Template for HDF5 definitions
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* Template for HDF5 definitions
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#+begin_src c :tangle def_hdf5.c
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#define $GROUP$_GROUP_NAME "$group$"
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@ -59,7 +58,7 @@
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#define $GROUP_STR$_NAME "$group_str$"
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#+end_src
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** Template for HDF5 structures
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* Template for HDF5 structures
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#+begin_src c :tangle struct_hdf5.h
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typedef struct trexio_hdf5_s {
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@ -69,7 +68,7 @@ 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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* 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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@ -113,6 +112,7 @@ trexio_hdf5_init (trexio_t* const file)
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// reading the existing file -> open as RDONLY
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f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
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break;
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case 'u':
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case 'w':
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// writing the existing file -> open as RDWRITE
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f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
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@ -125,6 +125,7 @@ trexio_hdf5_init (trexio_t* const file)
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case 'r':
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// reading non-existing file -> error
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return TREXIO_FAILURE;
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case 'u':
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case 'w':
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// writing non-existing file -> create it
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f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
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@ -138,6 +139,7 @@ trexio_hdf5_init (trexio_t* const file)
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case 'r':
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f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
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break;
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case 'u':
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case 'w':
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if (f_exists == 1) {
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f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
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@ -170,7 +172,7 @@ trexio_hdf5_deinit (trexio_t* const file)
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}
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#+end_src
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** Template for HDF5 has/read/write the numerical attribute
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* Template for HDF5 has/read/write a numerical attribute
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#+begin_src c :tangle hrw_attr_num_hdf5.h :exports none
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trexio_exit_code trexio_hdf5_has_$group_num$ (trexio_t* const file);
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@ -266,7 +268,7 @@ trexio_hdf5_has_$group_num$ (trexio_t* const file)
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}
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#+end_src
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** Template for HDF5 has/read/write the dataset of numerical data
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* Template for HDF5 has/read/write a dataset of numerical data
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#+begin_src c :tangle hrw_dset_data_hdf5.h :exports none
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trexio_exit_code trexio_hdf5_has_$group_dset$(trexio_t* const file);
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@ -389,7 +391,7 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
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}
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#+end_src
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** Template for HDF5 has/read/write the dataset of sparse data
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* Template for HDF5 has/read/write a dataset of sparse data
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Sparse data is stored using extensible datasets of HDF5. Extensibility is required
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due to the fact that the sparse data will be written in chunks of user-defined size.
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@ -590,7 +592,7 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
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}
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#+end_src
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** Template for HDF5 has/read/write the dataset of strings
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* Template for HDF5 has/read/write a dataset of strings
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#+begin_src c :tangle hrw_dset_str_hdf5.h :exports none
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trexio_exit_code trexio_hdf5_has_$group_dset$(trexio_t* const file);
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@ -795,7 +797,7 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
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}
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#+end_src
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** Template for HDF5 has/read/write the string attribute
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* Template for HDF5 has/read/write a string attribute
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#+begin_src c :tangle hrw_attr_str_hdf5.h :exports none
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trexio_exit_code trexio_hdf5_has_$group_str$ (trexio_t* const file);
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@ -919,7 +921,38 @@ trexio_hdf5_has_$group_str$ (trexio_t* const file)
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}
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#+end_src
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** Helper functions
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* Template for HDF5 delete a group (UNSAFE mode)
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**Note:** in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
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and the associated memory was not necessarily freed (see [[https://stackoverflow.com/questions/1124994/removing-data-from-a-hdf5-file][this StackOverflow discussion]] for example).
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Nevertheless, we highly recommend to reopen the file in SAFE mode (e.g. ~'r'~ or ~'w'~) after deleting the data.
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#+begin_src c :tangle delete_group_hdf5.h :exports none
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trexio_exit_code trexio_hdf5_delete_$group$ (trexio_t* const file);
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#+end_src
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#+begin_src c :tangle delete_group_hdf5.c
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trexio_exit_code
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trexio_hdf5_delete_$group$ (trexio_t* const file)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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trexio_hdf5_t* f = (trexio_hdf5_t*) file;
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// delete the link to the existing group: this should free the associated space
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H5Gclose(f->$group$_group);
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herr_t status = H5Ldelete(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
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if (status < 0) return TREXIO_FAILURE;
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// re-create the group (with the new link ?)
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f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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if (f->$group$_group <= 0L) return TREXIO_INVALID_ID;
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return TREXIO_SUCCESS;
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}
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#+end_src
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* Helper functions
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#+begin_src c :tangle helpers_hdf5.c
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trexio_exit_code
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@ -13,9 +13,11 @@ cat basic_text.h >> trexio_text.h
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cat populated/pop_free_group_text.c >> trexio_text.c
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cat populated/pop_read_group_text.c >> trexio_text.c
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cat populated/pop_flush_group_text.c >> trexio_text.c
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cat populated/pop_delete_group_text.c >> trexio_text.c
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cat populated/pop_free_group_text.h >> trexio_text.h
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cat populated/pop_read_group_text.h >> trexio_text.h
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cat populated/pop_flush_group_text.h >> trexio_text.h
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cat populated/pop_delete_group_text.h >> trexio_text.h
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cat populated/pop_has_dset_data_text.c >> trexio_text.c
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cat populated/pop_has_dset_str_text.c >> trexio_text.c
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@ -265,7 +265,7 @@ trexio_text_deinit (trexio_t* const file)
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}
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#+end_src
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** Template for text read struct
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** Template for text read a group
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#+begin_src c :tangle read_group_text.h :exports none
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$group$_t* trexio_text_read_$group$(trexio_text_t* const file);
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@ -558,7 +558,7 @@ trexio_text_read_$group$ (trexio_text_t* const file)
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}
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#+end_src
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** Template for text flush struct
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** Template for text flush a group
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#+begin_src c :tangle flush_group_text.h :exports none
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trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file);
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@ -574,7 +574,6 @@ trexio_text_flush_$group$ (trexio_text_t* const file)
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if (file->parent.mode == 'r') return TREXIO_READONLY;
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$group$_t* $group$ = file->$group$;
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if ($group$ == NULL) return TREXIO_SUCCESS;
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if ($group$->to_flush == 0) return TREXIO_SUCCESS;
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@ -663,12 +662,14 @@ trexio_text_free_$group$ (trexio_text_t* const file)
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// END REPEAT GROUP_ATTR_STR
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FREE ($group$);
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file->$group$ = NULL;
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return TREXIO_SUCCESS;
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}
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#+end_src
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** Template for has/read/write the numerical attribute
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** Template for has/read/write a numerical attribute
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#+begin_src c :tangle hrw_attr_num_text.h :exports none
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trexio_exit_code trexio_text_has_$group_num$ (trexio_t* const file);
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@ -732,7 +733,7 @@ trexio_text_has_$group_num$ (trexio_t* const file)
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}
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#+end_src
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** Template for has/read/write the dataset of numerical data
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** Template for has/read/write a dataset of numerical data
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The ~group_dset~ array is assumed allocated with the appropriate size.
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@ -827,7 +828,7 @@ trexio_text_has_$group_dset$ (trexio_t* const file)
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}
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#+end_src
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** Template for has/read/write the dataset of strings
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** Template for has/read/write a dataset of strings
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The ~group_dset~ array is assumed allocated with the appropriate size.
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@ -927,7 +928,7 @@ trexio_text_has_$group_dset$ (trexio_t* const file)
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}
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#+end_src
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** Template for has/read/write the string attribute
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** Template for has/read/write a string attribute
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#+begin_src c :tangle hrw_attr_str_text.h :exports none
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trexio_exit_code trexio_text_has_$group_str$ (trexio_t* const file);
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@ -1274,6 +1275,35 @@ trexio_exit_code trexio_text_has_$group_dset$(trexio_t* const file)
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}
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#+end_src
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|
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** Template for text delete a group (UNSAFE mode)
|
||||
|
||||
#+begin_src c :tangle delete_group_text.h :exports none
|
||||
trexio_exit_code trexio_text_delete_$group$ (trexio_t* const file);
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle delete_group_text.c
|
||||
trexio_exit_code
|
||||
trexio_text_delete_$group$ (trexio_t* const file)
|
||||
{
|
||||
if (file == NULL) return TREXIO_INVALID_ARG_1;
|
||||
|
||||
trexio_text_t* f = (trexio_text_t*) file;
|
||||
|
||||
$group$_t* $group$ = trexio_text_read_$group$(f);
|
||||
if ($group$ == NULL) return TREXIO_FAILURE;
|
||||
|
||||
int rc = remove($group$->file_name);
|
||||
if (rc == -1) return TREXIO_FAILURE;
|
||||
|
||||
$group$->to_flush = 0;
|
||||
|
||||
trexio_exit_code rc_free = trexio_text_free_$group$(f);
|
||||
if (rc_free != TREXIO_SUCCESS) return rc_free;
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
* Constant file suffixes (not used by the generator) :noexport:
|
||||
|
||||
#+begin_src c :tangle suffix_text.h
|
||||
|
||||
Loading…
Reference in New Issue
Block a user