Unverified Commit b22cbb2c authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Raise exceptions instead of returning None in internal methods 

Also clean up unneeded comments.
parent 3167b913

lib/galaxy/datatypes/isa.py

+22 −105
Original line number Diff line number Diff line
@@ -49,9 +49,6 @@ from galaxy.util.sanitize_html import sanitize_html 
if TYPE_CHECKING:

    from isatools.model import Investigation



# CONSTANTS {{{1

################################################################



# Main files regex

JSON_FILE_REGEX = re.compile(r"^.*\.json$", flags=re.IGNORECASE)

INVESTIGATION_FILE_REGEX = re.compile(r"^i_\w+\.txt$", flags=re.IGNORECASE)
@@ -62,17 +59,6 @@ ISA_ARCHIVE_NAME = "archive" 
# Set max number of lines of the history peek

_MAX_LINES_HISTORY_PEEK = 11



# Configure logger {{{1

################################################################





# Function for opening correctly a CSV file for csv.reader() for both Python 2 and 3 {{{1

################################################################





# ISA class {{{1

################################################################





class _Isa(Data):

    """Base class for implementing ISA datatypes"""
@@ -80,15 +66,9 @@ class _Isa(Data): 
    composite_type = "auto_primary_file"

    is_binary = True



    # Make investigation instance {{{2

    ################################################################



    def _make_investigation_instance(self, filename: str) -> "Investigation":

        raise NotImplementedError()



    # Constructor {{{2

    ################################################################



    def __init__(self, main_file_regex: re.Pattern, **kwd) -> None:

        super().__init__(**kwd)

        self._main_file_regex = main_file_regex
@@ -96,57 +76,34 @@ class _Isa(Data): 
        # Add the archive file as the only composite file

        self.add_composite_file(ISA_ARCHIVE_NAME, is_binary=True, optional=True)



    # Get ISA folder path {{{2

    ################################################################



    def _get_isa_folder_path(self, dataset: HasExtraFilesPath) -> str:

        isa_folder = dataset.extra_files_path

        if not isa_folder:

            raise Exception("Unvalid dataset object, or no extra files path found for this dataset.")

        return isa_folder



    # Get main file {{{2

    ################################################################



    def _get_main_file(self, dataset: HasExtraFilesPath) -> Optional[str]:

    def _get_main_file(self, dataset: HasExtraFilesPath) -> str:

        """Get the main file of the ISA archive. Either the investigation file i_*.txt for ISA-Tab, or the JSON file for ISA-JSON."""



        main_file = None

        isa_folder = self._get_isa_folder_path(dataset)

        assert os.path.exists(isa_folder)



        if os.path.exists(isa_folder):

        # Get ISA archive older

        isa_files = os.listdir(isa_folder)



            # Try to find main file

        main_file = self._find_main_file_in_archive(isa_files)



            if main_file is None:

                raise Exception("Invalid ISA archive. No main file found.")



        # Make full path

            assert main_file

            main_file = os.path.join(isa_folder, main_file)



        return main_file



    # Get investigation {{{2

    ################################################################

        return os.path.join(isa_folder, main_file)



    def _get_investigation(self, dataset: HasExtraFilesPath) -> Optional["Investigation"]:

    def _get_investigation(self, dataset: HasExtraFilesPath) -> "Investigation":

        """Create a contained instance specific to the exact ISA type (Tab or Json).

        We will use it to parse and access information from the archive."""



        investigation = None

        if (main_file := self._get_main_file(dataset)) is not None:

            investigation = self._make_investigation_instance(main_file)



        return investigation



    # Find main file in archive {{{2

    ################################################################

        main_file = self._get_main_file(dataset)

        return self._make_investigation_instance(main_file)



    def _find_main_file_in_archive(self, files_list: List) -> Optional[str]:

    def _find_main_file_in_archive(self, files_list: List) -> str:

        """Find the main file inside the ISA archive."""



        found_file = None
@@ -159,24 +116,17 @@ class _Isa(Data): 
                    found_file = matched if isinstance(matched, str) else matched[0]

                else:

                    raise Exception(

                        'More than one file match the pattern "',

                        str(self._main_file_regex),

                        '" to identify the investigation file',

                        f"More than one file match the pattern '{self._main_file_regex}' to identify the investigation file"

                    )



        if found_file is None:

            raise Exception("Invalid ISA archive. No main file found.")

        return found_file



    # Set peek {{{2

    ################################################################



    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:

        """Set the peek and blurb text. Get first lines of the main file and set it as the peek."""



        main_file = self._get_main_file(dataset)



        if main_file is None:

            raise RuntimeError("Unable to find the main file within the 'files_path' folder")



        # Read first lines of main file

        with open(main_file, encoding="utf-8") as f:

            data: List = []
@@ -192,9 +142,6 @@ class _Isa(Data): 
                dataset.peek = "file does not exist"

                dataset.blurb = "file purged from disk"



    # Display peek {{{2

    ################################################################



    def display_peek(self, dataset: DatasetProtocol) -> str:

        """Create the HTML table used for displaying peek, from the peek text found by set_peek() method."""
@@ -213,9 +160,6 @@ class _Isa(Data): 
        except Exception as exc:

            return f"Can't create peek: {util.unicodify(exc)}"



    # Generate primary file {{{2

    ################################################################



    def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:

        """Generate the primary file. It is an HTML file containing description of the composite dataset

        as well as a list of the composite files that it contains."""
@@ -232,16 +176,10 @@ class _Isa(Data): 
            return "\n".join(rval)

        return "<div>No dataset available</div>"



    # Dataset content needs grooming {{{2

    ################################################################



    def dataset_content_needs_grooming(self, file_name: str) -> bool:

        """This function is called on an output dataset file after the content is initially generated."""

        return os.path.basename(file_name) == ISA_ARCHIVE_NAME



    # Groom dataset content {{{2

    ################################################################



    def groom_dataset_content(self, file_name: str) -> None:

        """This method is called by Galaxy to extract files contained in a composite data type."""

        # XXX Is the right place to extract files? Should this step not be a cleaning step instead?
@@ -269,9 +207,6 @@ class _Isa(Data): 
            else:

                shutil.move(temp_folder, output_path)



    # Display data {{{2

    ################################################################



    def display_data(

        self,

        trans,
@@ -293,8 +228,10 @@ class _Isa(Data): 
            return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)



        # prepare the preview of the ISA dataset

        try:

            investigation = self._get_investigation(dataset)

        if investigation is None:

        except Exception:

            logger.exception(f"Failed to display dataset {dataset.id}")

            html = """<html><header><title>Error while reading ISA archive.</title></header>

                   <body>

                        <h1>An error occurred while reading content of ISA archive.</h1>
@@ -338,25 +275,15 @@ class _Isa(Data): 
        return sanitize_html(html).encode("utf-8"), headers





# ISA-Tab class {{{1

################################################################





class IsaTab(_Isa):

    file_ext = "isa-tab"



    # Constructor {{{2

    ################################################################



    def __init__(self, **kwd):

        super().__init__(main_file_regex=INVESTIGATION_FILE_REGEX, **kwd)



    # Make investigation instance {{{2

    ################################################################



    def _make_investigation_instance(self, filename: str) -> "Investigation":

    def _make_investigation_instance(self, filename: str):

        if not isatab_meta:

            return

            raise Exception(ISA_MISSING_MODULE_MESSAGE)

        # Parse ISA-Tab investigation file

        parser = isatab_meta.InvestigationParser()

        isa_dir = os.path.dirname(filename)
@@ -373,25 +300,15 @@ class IsaTab(_Isa): 
        return isa





# ISA-JSON class {{{1

################################################################





class IsaJson(_Isa):

    file_ext = "isa-json"



    # Constructor {{{2

    ################################################################



    def __init__(self, **kwd):

        super().__init__(main_file_regex=JSON_FILE_REGEX, **kwd)



    # Make investigation instance {{{2

    ################################################################



    def _make_investigation_instance(self, filename: str) -> "Investigation":

    def _make_investigation_instance(self, filename: str):

        if not isajson:

            return

            raise Exception(ISA_MISSING_MODULE_MESSAGE)

        # Parse JSON file

        with open(filename, newline="", encoding="utf8") as fp:

            isa = isajson.load(fp)