Merge pull request #75 from TREX-CoE/add-inquire-functionality

Add inquire functionality

python/install_pytrexio.sh

@@ -1,4 +1,4 @@
-#!/bin/bash                                                    
+#!/bin/bash
 
 set -x
 set -e
@@ -38,12 +38,12 @@ python3 -m pip install -r requirements.txt
 
 # Create build directory and compile extension files (*.c)
 # --no-user-cfg disables custom .cfg files of the user machine, so that only setup.cfg is used
-#python3 -s setup.py --no-user-cfg build 
+#python3 -s setup.py --no-user-cfg build
 
 # Local inplace build of the .so module with SWIG-produced pytrexio_wrap.c (from the SWIG documentation)
 #python3 setup.py build_ext --inplace --swig-opts="-modern"
 
-# Create distributions: 
+# Create distributions:
 
 # OLD WAY (DEPRECATED BY PYPA)
 #   1) sdist produces .tar.gz with all files necessary for manual compilation;
@@ -54,14 +54,7 @@ python3 -m pip install -r requirements.txt
 python3 -m build --sdist --wheel --outdir dist/
 
 # Install pytrexio in the current environment from the aforementioned wheel
-
-# OLD WAY
-# --force-reinstall is needed here because build-system pre-installs pytrexio in the environment 
-#                   but does not install things in the corresponding site-packages directory
-#python3 -m pip install dist/trexio-*.whl --force-reinstall
-
-# NEW WAY
-python3 -m pip install dist/trexio-*.whl
+python3 -m pip install dist/trexio-*.whl --force-reinstall
 
 # Run the command below in the root directory to install the package in 'editable' (-e) mode without dependencies (--no-deps)
 #python -m pip install -e . --no-deps
@@ -83,7 +76,6 @@ rm -rf build dist trexio.egg-info
 
 # Additional information related to the installation of the TREXIO Python API
 
-#Removing MANIFEST.in leads to issues in the installation. In particular, the .c and .h source files do not get copied 
-#from the src/ directory into the tar.gz which is produced by setup sdist command. 
+#Removing MANIFEST.in leads to issues in the installation. In particular, the .c and .h source files do not get copied
+#from the src/ directory into the tar.gz which is produced by setup sdist command.
 #These source files are required to build the pytrexio.so extension module, which is needed for the Python API.
-

python/test/test_api.py

@@ -40,6 +40,7 @@ except:
 
 # create TREXIO file and open it for writing
 test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
+assert test_file.exists
 
 # Print docstring of the trexio.open function
 #print(trexio.open.__doc__)
@@ -153,6 +154,7 @@ del test_file
 
 # open previously created TREXIO file, now in 'read' mode
 test_file2 = trexio.File(output_filename, 'r', TEST_TREXIO_BACKEND)
+assert test_file2.exists
 
 # check for existence of some of the previously written variables
 assert trexio.has_nucleus_num

src/templates_front/templator_front.org

@@ -1,5 +1,4 @@
 #+TITLE: Front end API
-break;
 #+PROPERTY: comments org
 #+SETUPFILE: ../../docs/theme.setup
 # -*- mode: org -*-
@@ -696,12 +695,15 @@ class File:
         self.back_end = back_end
 
         self.isOpen = False
+        self.exists = False
         if pytrexio_s is None:
-            self.pytrexio_s = open(filename, mode, back_end)
+            self.pytrexio_s = _open(filename, mode, back_end)
             self.isOpen = True
+            self.exists = True
         else:
             self.pytrexio_s = pytrexio_s
             self.isOpen = None
+            self.exists = None
 
         self.info = info
 
@@ -710,17 +712,23 @@ class File:
         """Close a TREXIO File."""
 
         if self.isOpen:
-            close(self.pytrexio_s)
+            _close(self.pytrexio_s)
             self.isOpen = False
         else:
             raise Exception("TREXIO File object has not been opened.")
 
 
+    def inquire(self):
+        """Inquire whether a TREXIO file exists."""
+
+        self.exists = _inquire(self.filename)
+
+
     def __del__(self):
         """This is a TREXIO File destructor."""
 
         if self.isOpen:
-            close(self.pytrexio_s)
+            _close(self.pytrexio_s)
         elif self.isOpen is None:
             raise Exception("[WIP]: TREXIO file handle provided but what if the file is already closed?")
         else:
@@ -972,7 +980,7 @@ end interface
 *** Python
 
    #+begin_src python :tangle basic_python.py
-def open(file_name: str, mode: str, back_end: int):
+def _open(file_name: str, mode: str, back_end: int):
     """Create TREXIO file or open existing one.
 
     Parameters:
@@ -1149,7 +1157,7 @@ end interface
 *** Python
 
    #+begin_src python :tangle basic_python.py
-def close(trexio_file):
+def _close(trexio_file):
     """Close TREXIO file.
 
     Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
@@ -1163,6 +1171,77 @@ def close(trexio_file):
         raise
    #+end_src
 
+** File existence
+
+ ~trexio_inquire~ check whether TREXIO file exists.
+
+    input parameters:
+ ~file_name~     - string containing file name
+
+    output:
+ ~trexio_exit_code~ exit code.
+
+*** C
+
+    #+begin_src c :tangle prefix_front.h :exports none
+trexio_exit_code trexio_inquire(const char* file_name);
+    #+end_src
+
+    #+begin_src c :tangle prefix_front.c
+trexio_exit_code
+trexio_inquire (const char* file_name)
+{
+
+  if (file_name == NULL || file_name[0] == '\0') return TREXIO_INVALID_ARG_1;
+
+ /* First check if the TREXIO file exists and if it is a directory */
+  trexio_exit_code rc_text = trexio_text_inquire(file_name);
+
+#ifdef HAVE_HDF5
+ /* FILE_ERROR here means that the file exists but it is not a directory -> check with HDF5 */
+  if (rc_text == TREXIO_FILE_ERROR) {
+    trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(file_name);
+    return rc_hdf5;
+  /* If rc_text is TREXIO_SUCCESS -> file is a TREXIO directory; TREXIO_FAILURE -> file/directory does not exist */
+  } else {
+    return rc_text;
+  }
+#else
+  return rc_text;
+#endif
+}
+    #+end_src
+
+*** Fortran
+
+  The function below is a C binding.
+  The front end Fortran function for ~trexio_inquire~ can be found in the ~Fortran helper/wrapper functions~.
+
+   #+begin_src f90 :tangle prefix_fortran.f90
+interface
+   integer function trexio_inquire_c (filename) bind(C, name="trexio_inquire")
+     use, intrinsic :: iso_c_binding
+     import
+     character(kind=c_char), dimension(*)       :: filename
+   end function trexio_inquire_c
+end interface
+   #+end_src
+
+*** Python
+
+   #+begin_src python :tangle basic_python.py
+def _inquire(file_name: str) -> bool:
+    """Check whether ~file_name~ TREXIO file exists.
+    """
+    rc = pytr.trexio_inquire(trexio_file_name)
+    if rc == TREXIO_SUCCESS:
+        return True
+    elif rc == TREXIO_FAILURE:
+        return False
+    else:
+        raise Error(rc)
+   #+end_src
+
 * Templates for front end
 ** Description
 
@@ -1769,7 +1848,7 @@ trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_doub
 
     case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-      rc = trexio_hdf5_write_$group_dset$(file, 
+      rc = trexio_hdf5_write_$group_dset$(file,
                                           (const $group_dset_dtype_double$*) $group_dset$_p,
                                           rank, dims);
       break;
@@ -2629,7 +2708,7 @@ trexio_write_$group_dset$(trexio_t* const file,
   if (file->one_based) {
 
     uint64_t index_size = rank * buffer_size;
-    
+
     int32_t* index_sparse_p = CALLOC(index_size, int32_t);
     if (index_sparse_p == NULL) return TREXIO_ALLOCATION_FAILED;
 
@@ -3801,6 +3880,23 @@ contains
    end function trexio_open
   #+end_src
 
+  The function below adapts the original C-based ~trexio_inquire~ for Fortran.
+  This is needed due to the same reasons as for ~trexio_open~ function.
+  Note, that Fortran interface calls the main ~TREXIO~ API, which is written in C.
+
+  #+begin_src f90 :tangle helper_fortran.f90
+   integer function trexio_inquire (filename)
+     use, intrinsic :: iso_c_binding
+     implicit none
+     character(len=*), intent(in)        :: filename
+     character(len=len_trim(filename)+1) :: filename_c
+
+     filename_c = trim(filename) // c_null_char
+     trexio_inquire = trexio_inquire_c(filename_c)
+   end function trexio_inquire
+
+  #+end_src
+
   The subroutine below transforms an array of Fortran strings into one big string using ~TREXIO_DELIM~ symbol
   as a delimeter and adds ~NULL~ character in the end in order to properly pass the desired string to
   C API. This is needed due to the fact that strings in C are terminated by ~NULL~ character ~\0~.

src/templates_hdf5/templator_hdf5.org

@@ -69,13 +69,29 @@ typedef struct trexio_hdf5_s {
 } trexio_hdf5_t;
   #+end_src
 
+** Template for HDF5 init/deinit
 
   #+begin_src c :tangle struct_hdf5.h :exports none
 trexio_exit_code trexio_hdf5_init(trexio_t* const file);
 trexio_exit_code trexio_hdf5_deinit(trexio_t* const file);
+trexio_exit_code trexio_hdf5_inquire(const char* file_name);
   #+end_src
 
-** Template for HDF5 init/deinit
+  #+begin_src c :tangle basic_hdf5.c
+trexio_exit_code
+trexio_hdf5_inquire(const char* file_name)
+{
+ /* H5Fis_hdf5 determines whether file is in HDF5 format */
+  htri_t rc = H5Fis_hdf5(file_name);
+  if (rc > 0 ) {
+    return TREXIO_SUCCESS;    //exists and HDF5
+  } else if (rc == 0) {
+    return TREXIO_FILE_ERROR; //exists but not HDF5
+  } else {
+    return TREXIO_FAILURE;    //does not exist or function fails
+  }
+}
+  #+end_src
 
   #+begin_src c :tangle basic_hdf5.c
 trexio_exit_code
@@ -134,7 +150,9 @@ trexio_hdf5_init (trexio_t* const file)
 
   return TREXIO_SUCCESS;
 }
+  #+end_src
 
+  #+begin_src c :tangle basic_hdf5.c
 trexio_exit_code
 trexio_hdf5_deinit (trexio_t* const file)
 {

src/templates_text/templator_text.org

@@ -105,6 +105,33 @@ typedef struct trexio_text_s {
 
     #+begin_src c :tangle basic_text.h :exports none
 trexio_exit_code trexio_text_init(trexio_t* const file);
+trexio_exit_code trexio_text_inquire(const char* file_name);
+trexio_exit_code trexio_text_deinit(trexio_t* const file);
+trexio_exit_code trexio_text_lock(trexio_t* const file);
+trexio_exit_code trexio_text_unlock(trexio_t* const file);
+    #+end_src
+
+    #+begin_src c :tangle basic_text.c
+trexio_exit_code
+trexio_text_inquire (const char* file_name)
+{
+ /* Check if the file with "file_name" exists and that it is a directory */
+  struct stat st;
+
+  int rc = stat(file_name, &st);
+
+  bool file_exists = rc == 0;
+
+  if (file_exists) {
+
+    bool is_a_directory = st.st_mode & S_IFDIR;
+    if (!is_a_directory) return TREXIO_FILE_ERROR;
+
+    return TREXIO_SUCCESS;
+  } else {
+    return TREXIO_FAILURE;
+  }
+}
     #+end_src
 
     #+begin_src c :tangle basic_text.c
@@ -119,30 +146,19 @@ trexio_text_init (trexio_t* const file)
  /* Put all pointers to NULL but leave parent untouched */
   memset(&(f->parent)+1,0,sizeof(trexio_text_t)-sizeof(trexio_t));
 
- /* If directory doesn't exist, create it in write mode */
-  struct stat st;
+ /* Check if directory exists */
+  trexio_exit_code rc;
+  rc = trexio_text_inquire(file->file_name);
+ /* TREXIO file exists but is not  a directory */
+  if (rc == TREXIO_FILE_ERROR) return rc;
+ /* If directory does not exist - create it in write mode */
+  if (rc == TREXIO_FAILURE) {
 
-  int rc = stat(file->file_name, &st);
+    if (file->mode == 'r') return TREXIO_READONLY;
 
-  bool file_exists = rc == 0;
+    int rc_dir = mkdir(file->file_name, 0777);
+    if (rc_dir != 0) return TREXIO_ERRNO;
 
-  if (file_exists) {
-
-    bool is_a_directory = st.st_mode & S_IFDIR;
-    if (!is_a_directory) {
-      return TREXIO_FILE_ERROR;
-    }
-
-  } else {
-
-    if (file->mode == 'r') {
-      return TREXIO_READONLY;
-    }
-
-    rc = mkdir(file->file_name, 0777);
-    if (rc != 0) {
-      return TREXIO_ERRNO;
-    }
   }
 
  /* Create the lock file in the directory */
@@ -166,7 +182,7 @@ trexio_text_init (trexio_t* const file)
       if (errno == EACCES) {
         /* The directory is read-only and the lock file can't be written.
           Create a dummy temporary file for dummy locking.
-        */
+        ,*/
         char dirname[TREXIO_MAX_FILENAME_LENGTH] = "/tmp/trexio.XXXXXX";
         if (mkdtemp(dirname) == NULL) return TREXIO_ERRNO;
         strncpy (file_name, dirname, TREXIO_MAX_FILENAME_LENGTH);
@@ -184,10 +200,6 @@ trexio_text_init (trexio_t* const file)
 }
     #+end_src
 
-    #+begin_src c :tangle basic_text.h :exports none
-trexio_exit_code trexio_text_lock(trexio_t* const file);
-    #+end_src
-
     #+begin_src c :tangle basic_text.c
 trexio_exit_code trexio_text_lock(trexio_t* const file) {
   if (file == NULL) return TREXIO_INVALID_ARG_1;
@@ -210,15 +222,6 @@ trexio_exit_code trexio_text_lock(trexio_t* const file) {
 }
     #+end_src
 
-
-    #+begin_src c :tangle basic_text.h :exports none
-trexio_exit_code trexio_text_deinit(trexio_t* const file);
-    #+end_src
-
-    #+begin_src c :tangle basic_text.h :exports none
-trexio_exit_code trexio_text_unlock(trexio_t* const file);
-    #+end_src
-
     #+begin_src c :tangle basic_text.c
 trexio_exit_code
 trexio_text_unlock (trexio_t* const file)

tests/open_hdf5.c

@@ -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;
 }
-
-

tests/open_text.c

@@ -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;
 }
-
-

tests/test_f.f90

@@ -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)