psdi-data-conversion 0.0.35__tar.gz → 0.0.36__tar.gz

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: psdi_data_conversion
-Version: 0.0.35
+Version: 0.0.36
 Summary: Chemistry file format conversion service, provided by PSDI
 Project-URL: Homepage, https://data-conversion.psdi.ac.uk/
 Project-URL: Documentation, https://psdi-uk.github.io/psdi-data-conversion/
@@ -403,13 +403,21 @@ In addition to the dependencies listed above, this project uses the assets made
 
 ### Installation
 
-The CLA and Python library are installed together. This package is not yet available on PyPI, and so must be installed locally. This can be done most easily with:
+The CLA and Python library are installed together. This project is available on PyPI, and so can be installed via pip with:
+
+```bash
+pip install psdi-data-conversion
+```
+
+If you wish to install from source, this can be done most easily by cloning the project and then executing:
 
 ```bash
 pip install .
 ```
 
-executed from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
+from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
+
+**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
 
 Depending on your system, it may not be possible to install packages in this manner without creating a virtual environment to do so in. You can do this by first installing the `venv` module for Python3 with e.g.:
 
@@ -572,15 +580,23 @@ Enter https://data-conversion.psdi.ac.uk/ in a browser. Guidance on usage is giv
 
 ### Installation and Setup
 
-Install the package and its requirements, including the optional requirements used to run the GUI locally, by executing the following command from this project's directory:
+This project is available on PyPI, and so can be installed via pip, including the necessary dependencies for the GUI, with:
+
+```bash
+pip install psdi-data-conversion'[gui]'
+```
+
+If you wish to install the project locally from source, this can be done most easily by cloning the project and then executing:
 
 ```bash
 pip install .'[gui]'
 ```
 
-If your system does not allow installs in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
+**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
 
-If you've cloned this repository, you can use the `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
+If your system does not allow installation in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
+
+If you've installed this repository from source, you can use the provided `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
 
 ```bash
 #!/bin/bash
@@ -590,6 +606,13 @@ if [ -z $MAX_FILESIZE ]; then
   export MAX_FILESIZE=0
 fi
 
+# The envvar MAX_FILESIZE_OB can be used to set the maximum allowed filesize in MB for the Open Babel converter - 0
+# indicates no maximum. This is currently set to 1 MB by default as the converter seems to hang above this limit (not
+# even allowing the process to be cancelled). This can be changed in the future if this is patched
+if [ -z $MAX_FILESIZE_OB ]; then
+  export MAX_FILESIZE_OB=1
+fi
+
 # Logging control - "full" sets server-style logging, which is necessary to produce the output logs with the expected
 # names. This should not be changed, or else errors will occur
 export LOG_MODE=full

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/README.md

@@ -158,13 +158,21 @@ In addition to the dependencies listed above, this project uses the assets made
 
 ### Installation
 
-The CLA and Python library are installed together. This package is not yet available on PyPI, and so must be installed locally. This can be done most easily with:
+The CLA and Python library are installed together. This project is available on PyPI, and so can be installed via pip with:
+
+```bash
+pip install psdi-data-conversion
+```
+
+If you wish to install from source, this can be done most easily by cloning the project and then executing:
 
 ```bash
 pip install .
 ```
 
-executed from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
+from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
+
+**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
 
 Depending on your system, it may not be possible to install packages in this manner without creating a virtual environment to do so in. You can do this by first installing the `venv` module for Python3 with e.g.:
 
@@ -327,15 +335,23 @@ Enter https://data-conversion.psdi.ac.uk/ in a browser. Guidance on usage is giv
 
 ### Installation and Setup
 
-Install the package and its requirements, including the optional requirements used to run the GUI locally, by executing the following command from this project's directory:
+This project is available on PyPI, and so can be installed via pip, including the necessary dependencies for the GUI, with:
+
+```bash
+pip install psdi-data-conversion'[gui]'
+```
+
+If you wish to install the project locally from source, this can be done most easily by cloning the project and then executing:
 
 ```bash
 pip install .'[gui]'
 ```
 
-If your system does not allow installs in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
+**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
 
-If you've cloned this repository, you can use the `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
+If your system does not allow installation in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
+
+If you've installed this repository from source, you can use the provided `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
 
 ```bash
 #!/bin/bash
@@ -345,6 +361,13 @@ if [ -z $MAX_FILESIZE ]; then
   export MAX_FILESIZE=0
 fi
 
+# The envvar MAX_FILESIZE_OB can be used to set the maximum allowed filesize in MB for the Open Babel converter - 0
+# indicates no maximum. This is currently set to 1 MB by default as the converter seems to hang above this limit (not
+# even allowing the process to be cancelled). This can be changed in the future if this is patched
+if [ -z $MAX_FILESIZE_OB ]; then
+  export MAX_FILESIZE_OB=1
+fi
+
 # Logging control - "full" sets server-style logging, which is necessary to produce the output logs with the expected
 # names. This should not be changed, or else errors will occur
 export LOG_MODE=full

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/app.py

@@ -102,8 +102,16 @@ def website():
     else:
         max_file_size = const.DEFAULT_MAX_FILE_SIZE
 
+    # And same for the Open Babel maximum file size
+    ev_max_file_size_ob = os.environ.get(const.MAX_FILESIZE_OB_EV)
+    if ev_max_file_size_ob is not None:
+        max_file_size_ob = float(ev_max_file_size_ob)*const.MEGABYTE
+    else:
+        max_file_size_ob = const.DEFAULT_MAX_FILE_SIZE_OB
+
     data = [{'token': token,
              'max_file_size': max_file_size,
+             'max_file_size_ob': max_file_size_ob,
              'service_mode': service_mode,
              'production_mode': production_mode,
              'sha': get_last_sha()}]
@@ -150,11 +158,23 @@ def convert():
                         fo.write(str(e))
                     abort(const.STATUS_CODE_GENERAL)
 
-            # Failsafe exception message
-            msg = "The following unexpected exception was raised by the converter:\n" + traceback.format_exc()+"\n"
+            # If the exception provides a status code, get it
+            status_code: int
+            if hasattr(e, "status_code"):
+                status_code = e.status_code
+            else:
+                status_code = const.STATUS_CODE_GENERAL
+
+            # If the exception provides a message, report it
+            if hasattr(e, "message"):
+                msg = f"An unexpected exception was raised by the converter, with error message:\n{e.message}\n"
+            else:
+                # Failsafe exception message
+                msg = ("The following unexpected exception was raised by the converter:\n" +
+                       traceback.format_exc()+"\n")
             with open(qualified_output_log, "w") as fo:
                 fo.write(msg)
-            abort(const.STATUS_CODE_GENERAL)
+            abort(status_code)
 
         return repr(conversion_output)
     else:

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/constants.py

@@ -40,6 +40,7 @@ CL_SCRIPT_NAME = "psdi-data-convert"
 LOG_MODE_EV = "LOG_MODE"
 LOG_LEVEL_EV = "LOG_LEVEL"
 MAX_FILESIZE_EV = "MAX_FILESIZE"
+MAX_FILESIZE_OB_EV = "MAX_FILESIZE_OB"
 
 # Files and Folders
 # -----------------
@@ -47,6 +48,7 @@ MAX_FILESIZE_EV = "MAX_FILESIZE"
 # Maximum output file size in bytes
 MEGABYTE = 1024*1024
 DEFAULT_MAX_FILE_SIZE = 0*MEGABYTE
+DEFAULT_MAX_FILE_SIZE_OB = 1*MEGABYTE
 
 DEFAULT_UPLOAD_DIR = './psdi_data_conversion/static/uploads'
 DEFAULT_DOWNLOAD_DIR = './psdi_data_conversion/static/downloads'

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/converter.py

@@ -17,6 +17,7 @@ from psdi_data_conversion.converters import base
 
 import glob
 
+from psdi_data_conversion.converters.openbabel import CONVERTER_OB
 from psdi_data_conversion.file_io import (is_archive, is_supported_archive, pack_zip_or_tar, split_archive_ext,
                                           unpack_zip_or_tar)
 
@@ -105,7 +106,8 @@ def get_converter(*args, name=const.CONVERTER_DEFAULT, **converter_kwargs) -> ba
     name : str
         The desired converter type, by default 'Open Babel'
     data : dict[str | Any] | None
-        A dict of any other data needed by a converter or for extra logging information, default empty dict
+        A dict of any other data needed by a converter or for extra logging information, default empty dict. See the
+        docstring of each converter for supported keys and values that can be passed to `data` here
     abort_callback : Callable[[int], None]
         Function to be called if the conversion hits an error and must be aborted, default `abort_raise`, which
         raises an appropriate exception
@@ -117,7 +119,9 @@ def get_converter(*args, name=const.CONVERTER_DEFAULT, **converter_kwargs) -> ba
     download_dir : str
         The location of output files relative to the current directory
     max_file_size : float
-        The maximum allowed file size for input/output files, in MB, default 1 MB. If 0, will be unlimited
+        The maximum allowed file size for input/output files, in MB, default 1 MB for Open Babel, unlimited for other
+        converters. If 0, will be unlimited. If an archive of files is provided, this will apply to the total of all
+        files contained in it
     no_check : bool
         If False (default), will check at setup whether or not a conversion between the desired file formats is
         supported with the specified converter
@@ -238,7 +242,7 @@ def run_converter(filename: str,
                   *args,
                   from_format: str | None = None,
                   download_dir=const.DEFAULT_DOWNLOAD_DIR,
-                  max_file_size=const.DEFAULT_MAX_FILE_SIZE,
+                  max_file_size=None,
                   log_file: str | None = None,
                   log_mode=const.LOG_SIMPLE,
                   strict=False,
@@ -261,7 +265,8 @@ def run_converter(filename: str,
     name : str
         The desired converter type, by default 'Open Babel'
     data : dict[str | Any] | None
-        A dict of any other data needed by a converter or for extra logging information, default empty dict
+        A dict of any other data needed by a converter or for extra logging information, default empty dict. See the
+        docstring of each converter for supported keys and values that can be passed to `data` here
     abort_callback : Callable[[int], None]
         Function to be called if the conversion hits an error and must be aborted, default `abort_raise`, which
         raises an appropriate exception
@@ -280,8 +285,9 @@ def run_converter(filename: str,
         into a file of the same format, their logs will be combined into a single log, and the converted files and
         individual logs will be deleted
     max_file_size : float
-        The maximum allowed file size for input/output files, in MB, default 1 MB. If 0, will be unlimited. If an
-        archive of files is provided, this will apply to the total of all files contained in it
+        The maximum allowed file size for input/output files, in MB, default 1 MB for Open Babel, unlimited for other
+        converters. If 0, will be unlimited. If an archive of files is provided, this will apply to the total of all
+        files contained in it
     no_check : bool
         If False (default), will check at setup whether or not a conversion between the desired file formats is
         supported with the specified converter
@@ -318,6 +324,10 @@ def run_converter(filename: str,
         If something goes wrong during the conversion process
     """
 
+    # Set the maximum file size based on which converter is being used if using the default
+    if max_file_size is None:
+        max_file_size = const.DEFAULT_MAX_FILE_SIZE_OB if name == CONVERTER_OB else const.DEFAULT_MAX_FILE_SIZE
+
     # Set the log file if it was unset - note that in server logging mode, this value won't be used within the
     # converter class, so it needs to be set up here to match what will be set up there
     if log_file is None:

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/converters/atomsk.py

@@ -11,7 +11,9 @@ CONVERTER_ATO = 'Atomsk'
 
 
 class AtoFileConverter(ScriptFileConverter):
-    """File Converter specialized to use Atomsk for conversions
+    """File Converter specialized to use Atomsk for conversions.
+
+    This converter does not yet support any additional configuration options provided at class init to the `data` kwarg.
     """
 
     name = CONVERTER_ATO

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/converters/base.py

@@ -34,7 +34,12 @@ except ImportError:
 class FileConverterException(RuntimeError):
     """Exception class to represent any runtime error encountered by this package.
     """
-    pass
+
+    def __init__(self,
+                 *args,
+                 logged: bool = False):
+        super().__init__(*args)
+        self.logged = logged
 
 
 class FileConverterAbortException(FileConverterException):
@@ -212,7 +217,7 @@ class FileConverter:
                  use_envvars=False,
                  upload_dir=const.DEFAULT_UPLOAD_DIR,
                  download_dir=const.DEFAULT_DOWNLOAD_DIR,
-                 max_file_size=const.DEFAULT_MAX_FILE_SIZE,
+                 max_file_size=None,
                  no_check=False,
                  log_file: str | None = None,
                  log_mode=const.LOG_FULL,
@@ -231,7 +236,8 @@ class FileConverter:
             The format to convert from, as the file extension (e.g. "pdb"). If None is provided (default), will be
             determined from the extension of `filename`
         data : dict[str | Any] | None
-            A dict of any other data needed by a converter or for extra logging information, default empty dict
+            A dict of any other data needed by a converter or for extra logging information, default empty dict. See the
+            docstring of each converter for supported keys and values that can be passed to `data` here
         abort_callback : Callable[[int], None]
             Function to be called if the conversion hits an error and must be aborted, default `abort_raise`, which
             raises an appropriate exception
@@ -275,12 +281,32 @@ class FileConverter:
 
         try:
 
+            if max_file_size is None:
+                from psdi_data_conversion.converters.openbabel import CONVERTER_OB
+                if self.name == CONVERTER_OB:
+                    self.max_file_size = const.DEFAULT_MAX_FILE_SIZE_OB*const.MEGABYTE
+                else:
+                    self.max_file_size = const.DEFAULT_MAX_FILE_SIZE*const.MEGABYTE
+            else:
+                self.max_file_size = max_file_size*const.MEGABYTE
+
+            # Set values from envvars if desired
+            if use_envvars:
+                # Get the maximum allowed size from the envvar for it
+                from psdi_data_conversion.converters.openbabel import CONVERTER_OB
+                if self.name == CONVERTER_OB:
+                    ev_max_file_size = os.environ.get(const.MAX_FILESIZE_OB_EV)
+                else:
+                    ev_max_file_size = os.environ.get(const.MAX_FILESIZE_EV)
+
+                if ev_max_file_size is not None:
+                    self.max_file_size = float(ev_max_file_size)*const.MEGABYTE
+
             # Set member variables directly from input
             self.in_filename = filename
             self.to_format = to_format
             self.upload_dir = upload_dir
             self.download_dir = download_dir
-            self.max_file_size = max_file_size*const.MEGABYTE
             self.log_file = log_file
             self.log_mode = log_mode
             self.log_level = log_level
@@ -312,13 +338,6 @@ class FileConverter:
             self.err: str | None = None
             self.quality: str | None = None
 
-            # Set values from envvars if desired
-            if use_envvars:
-                # Get the maximum allowed size from the envvar for it
-                ev_max_file_size = os.environ.get(const.MAX_FILESIZE_EV)
-                if ev_max_file_size is not None:
-                    self.max_file_size = float(ev_max_file_size)*const.MEGABYTE
-
             # Create directory 'uploads' if not extant.
             if not os.path.exists(self.upload_dir):
                 os.makedirs(self.upload_dir, exist_ok=True)
@@ -351,10 +370,13 @@ class FileConverter:
             self.logger.debug("Finished FileConverter initialisation")
 
         except Exception as e:
+            # Don't catch a deliberate abort; let it pass through
             if isinstance(e, l_abort_exceptions):
-                # Don't catch a deliberate abort; let it pass through
-                self.logger.error(f"Unexpected exception raised while initializing the converter, of type '{type(e)}' "
-                                  f"with message: {str(e)}")
+                if not hasattr(e, "logged") or e.logged is False:
+                    self.logger.error(f"Unexpected exception raised while running the converter, of type '{type(e)}' "
+                                      f"with message: {str(e)}")
+                    if e:
+                        e.logged = True
                 raise
             # Try to run the standard abort method. There's a good chance this will fail though depending on what went
             # wrong when during init, so we fallback to printing the exception to stderr
@@ -362,6 +384,8 @@ class FileConverter:
                 if not isinstance(e, FileConverterHelpException):
                     self.logger.error(f"Exception triggering an abort was raised while initializing the converter. "
                                       f"Exception was type '{type(e)}', with message: {str(e)}")
+                    if e:
+                        e.logged = True
                 self._abort(message="The application encountered an error while initializing the converter:\n" +
                             traceback.format_exc(), e=e)
             except Exception as ee:
@@ -445,20 +469,28 @@ class FileConverter:
         """
 
         try:
+            self.logger.debug("Checking input file size")
+            self._check_input_file_size_and_status()
+
             self.logger.debug("Starting file conversion")
             self._convert()
 
             self.logger.debug("Finished file conversion; performing cleanup tasks")
             self._finish_convert()
         except Exception as e:
+            # Don't catch a deliberate abort; let it pass through
             if isinstance(e, l_abort_exceptions):
-                # Don't catch a deliberate abort; let it pass through
-                self.logger.error(f"Unexpected exception raised while running the converter, of type '{type(e)}' with "
-                                  f"message: {str(e)}")
+                # Log the error if it hasn't yet been logged
+                if not hasattr(e, "logged") or e.logged is False:
+                    self.logger.error(f"Unexpected exception raised while running the converter, of type '{type(e)}' "
+                                      f"with message: {str(e)}")
+                    e.logged = True
                 raise
             if not isinstance(e, FileConverterHelpException):
                 self.logger.error(f"Exception triggering an abort was raised while running the converter. Exception "
                                   f"was type '{type(e)}', with message: {str(e)}")
+                if e:
+                    e.logged = True
             self._abort(message="The application encountered an error while running the converter:\n" +
                         traceback.format_exc(), e=e)
 
@@ -522,13 +554,23 @@ class FileConverter:
             # Note this message in the dev logger as well
             if not isinstance(e, FileConverterHelpException):
                 self.logger.error(message)
+                if e:
+                    e.logged = True
 
-        # Call the abort callback function now. We first try to add information to it, but in case that isn't supported,
-        # we fall back to just calling it with the status code
+        # Call the abort callback function now. We first try passing information to the callback function
         try:
             self.abort_callback(status_code, message, e=e, **kwargs)
         except TypeError:
-            self.abort_callback(status_code)
+            # The callback function doesn't support arguments, so we instead call the callback, catch any exception it
+            # raises, monkey-patch on the extra info, and reraise it
+            try:
+                self.abort_callback(status_code)
+            except Exception as ee:
+                ee.status_code = status_code
+                ee.message = message
+                ee.e = e
+                ee.abort_kwargs = kwargs
+                raise ee
 
     def _abort_from_err(self):
         """Call an abort after a call to the converter has completed, but it's returned an error. Create a message for
@@ -538,7 +580,7 @@ class FileConverter:
                           self._create_message() +
                           self.out + '\n' +
                           self.err)
-        self._abort(message=self.err)
+        self._abort(message=self.err, logged=True)
 
     def _create_message(self) -> str:
         """Create a log of options passed to the converter - this method should be overloaded to log any information
@@ -578,19 +620,38 @@ class FileConverter:
 
         self.logger.info(message)
 
-    def _check_file_size_and_status(self):
-        """Get file sizes, checking that output file isn't too large
+    def _check_input_file_size_and_status(self):
+        """Get input file size and status, checking that the file isn't too large
+        """
 
-        Returns
-        -------
-        in_size : int
-            Size of input file in bytes
-        out_size : int
-            Size of output file in bytes
+        try:
+            self.in_size = os.path.getsize(os.path.realpath(self.in_filename))
+        except FileNotFoundError:
+            # Something went wrong and the output file doesn't exist
+            err_message = f"Expected output file {self.in_filename} does not exist."
+            self.logger.error(err_message)
+            self.err += f"ERROR: {err_message}\n"
+            self._abort_from_err()
+
+        # Check that the input file doesn't exceed the maximum allowed size
+        if self.max_file_size > 0 and self.in_size > self.max_file_size:
+
+            self._abort(const.STATUS_CODE_SIZE,
+                        f"ERROR converting {os.path.basename(self.in_filename)} to " +
+                        os.path.basename(self.out_filename) + ": "
+                        f"Input file exceeds maximum size.\nInput file size is "
+                        f"{self.in_size/const.MEGABYTE:.2f} MB; maximum input file size is "
+                        f"{self.max_file_size/const.MEGABYTE:.2f} MB.\n",
+                        max_file_size=self.max_file_size,
+                        in_size=self.in_size,
+                        out_size=None)
+
+    def _check_output_file_size_and_status(self):
+        """Get output file size and status, checking that the file isn't too large
         """
-        in_size = os.path.getsize(os.path.realpath(self.in_filename))
+
         try:
-            out_size = os.path.getsize(os.path.realpath(self.out_filename))
+            self.out_size = os.path.getsize(os.path.realpath(self.out_filename))
         except FileNotFoundError:
             # Something went wrong and the output file doesn't exist
             err_message = f"Expected output file {self.out_filename} does not exist."
@@ -599,20 +660,19 @@ class FileConverter:
             self._abort_from_err()
 
         # Check that the output file doesn't exceed the maximum allowed size
-        if self.max_file_size > 0 and out_size > self.max_file_size:
+        if self.max_file_size > 0 and self.out_size > self.max_file_size:
 
             self._abort(const.STATUS_CODE_SIZE,
                         f"ERROR converting {os.path.basename(self.in_filename)} to " +
                         os.path.basename(self.out_filename) + ": "
                         f"Output file exceeds maximum size.\nInput file size is "
-                        f"{in_size/const.MEGABYTE:.2f} MB; Output file size is {out_size/const.MEGABYTE:.2f} "
+                        f"{self.in_size/const.MEGABYTE:.2f} MB; Output file size is {self.out_size/const.MEGABYTE:.2f} "
                         f"MB; maximum output file size is {self.max_file_size/const.MEGABYTE:.2f} MB.\n",
-                        in_size=in_size,
-                        out_size=out_size,
-                        max_file_size=self.max_file_size)
-        self.logger.debug(f"Output file found to have size {out_size/const.MEGABYTE:.2f} MB")
+                        max_file_size=self.max_file_size,
+                        in_size=self.in_size,
+                        out_size=self.out_size)
 
-        return in_size, out_size
+        self.logger.debug(f"Output file found to have size {self.out_size/const.MEGABYTE:.2f} MB")
 
     def get_quality(self) -> str:
         """Query the JSON file to obtain conversion quality
@@ -630,7 +690,7 @@ class FileConverter:
         """Run final common steps to clean up a conversion and log success or abort due to an error
         """
 
-        self.in_size, self.out_size = self._check_file_size_and_status()
+        self._check_output_file_size_and_status()
 
         if self.delete_input:
             os.remove(self.in_filename)

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/converters/c2x.py

@@ -11,7 +11,9 @@ CONVERTER_C2X = 'c2x'
 
 
 class C2xFileConverter(ScriptFileConverter):
-    """File Converter specialized to use c2x for conversions
+    """File Converter specialized to use c2x for conversions.
+
+    This converter does not yet support any additional configuration options provided at class init to the `data` kwarg.
     """
 
     name = CONVERTER_C2X

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/converters/openbabel.py

@@ -76,7 +76,46 @@ def get_coord_gen(l_opts: list[str] | None) -> dict[str, str]:
 
 
 class OBFileConverter(FileConverter):
-    """File Converter specialized to use Open Babel for conversions
+    """File Converter specialized to use Open Babel for conversions.
+
+    This converter supports some additional configuration options which can be provided at class init or call to
+    `run_converter()` through providing a dict to the `data` kwarg. The supported keys and values are:
+
+    "from_flags": str
+        String of concatenated one-letter flags for how to read the input file. To list the flags supported for a given
+        input format, call ``psdi-data-convert -l -f <format> -w Open Babel`` at the command-line and look for the
+        "Allowed input flags" section, if one exists, or alternatively call the library function
+        ``psdi_data_conversion.database.get_in_format_args("Open Babel", <format>)`` from within Python code.
+
+    "to_flags": str
+        String of concatenated one-letter flags for how to write the output file. To list the flags supported for a
+        given output format, call ``psdi-data-convert -l -f <format> -w Open Babel`` at the command-line and look for
+        the "Allowed output flags" section, if one exists, or alternatively call the library function
+        ``psdi_data_conversion.database.get_out_format_args("Open Babel", <format>)`` from within Python code.
+
+    "from_options": str
+        String of space-separated options for how to read the input file. Each option "word" in this string should start
+        with the letter indicating which option is being used, followed by the value for that option. To list the
+        options supported for a given input format, call ``psdi-data-convert -l -f <format> -w Open Babel`` at the
+        command-line and look for the "Allowed input options" section, if one exists, or alternatively call the library
+        function ``psdi_data_conversion.database.get_in_format_args("Open Babel", <format>)`` from within Python code.
+
+    "to_options": str
+        String of space-separated options for how to write the output file. Each option "word" in this string should
+        start with the letter indicating which option is being used, followed by the value for that option. To list the
+        options supported for a given output format, call ``psdi-data-convert -l -t <format> -w Open Babel`` at the
+        command-line and look for the "Allowed output options" section, if one exists, or alternatively call the library
+        function ``psdi_data_conversion.database.get_out_format_args("Open Babel", <format>)`` from within Python code.
+
+    "coordinates": str
+        One of "Gen2D", "Gen3D", or "neither", specifying how positional coordinates should be generated in the output
+        file. Default "neither"
+
+    "coordOption": str
+        One of "fastest", "fast", "medium", "better", or "best", specifying the quality of the calculation of
+        coordinates. Default "medium"
+
+    Note that some other keys are supported for compatibility purposes, but these may be deprecated in the future.
     """
 
     name = CONVERTER_OB

{psdi_data_conversion-0.0.35 → psdi_data_conversion-0.0.36}/psdi_data_conversion/database.py

@@ -284,6 +284,11 @@ class ConverterInfo:
         d_format_args: dict[str | int, set[ArgInfo]] = {}
         l_parent_format_info = self.parent.l_format_info
 
+        # If the converter doesn't provide argument info, set l_arg_info to an empty list so it can be iterated in
+        # the next step, rather than None
+        if not l_arg_info:
+            l_arg_info = []
+
         for arg_info in l_arg_info:
 
             if arg_info is None: