Source code for galaxy.datatypes.ngsindex

"""
NGS indexes
"""
import logging
import os

from galaxy.datatypes.protocols import (
    DatasetProtocol,
    HasExtraFilesAndMetadata,
)
from galaxy.util import UNKNOWN
from .metadata import MetadataElement
from .text import Html

log = logging.getLogger(__name__)


[docs]class BowtieIndex(Html):
    """
    base class for BowtieIndex
    is subclassed by BowtieColorIndex and BowtieBaseIndex
    """

    MetadataElement(
        name="base_name",
        desc="base name for this index set",
        default="galaxy_generated_bowtie_index",
        set_in_upload=True,
        readonly=True,
    )
    MetadataElement(
        name="sequence_space",
        desc="sequence_space for this index set",
        default=UNKNOWN,
        set_in_upload=True,
        readonly=True,
    )

    composite_type = "auto_primary_file"

[docs]    def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
        """
        This is called only at upload to write the html file
        cannot rename the datasets here - they come with the default unfortunately
        """
        return "<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>"

[docs]    def regenerate_primary_file(self, dataset: DatasetProtocol) -> None:
        """
        cannot do this until we are setting metadata
        """
        bn = dataset.metadata.base_name
        flist = os.listdir(dataset.extra_files_path)
        rval = [
            f"<html><head><title>Files for Composite Dataset {bn}</title></head><p/>Comprises the following files:<p/><ul>"
        ]
        for fname in flist:
            sfname = os.path.split(fname)[-1]
            rval.append(f'<li><a href="{sfname}">{sfname}</a>')
        rval.append("</ul></html>")
        with open(dataset.get_file_name(), "w") as f:
            f.write("\n".join(rval))
            f.write("\n")

[docs]    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
        if not dataset.dataset.purged:
            dataset.peek = f"Bowtie index file ({dataset.metadata.sequence_space})"
            dataset.blurb = f"{dataset.metadata.sequence_space} space"
        else:
            dataset.peek = "file does not exist"
            dataset.blurb = "file purged from disk"

[docs]    def display_peek(self, dataset: DatasetProtocol) -> str:
        try:
            return dataset.peek
        except Exception:
            return "Bowtie index file"


[docs]class BowtieColorIndex(BowtieIndex):
    """
    Bowtie color space index
    """

    MetadataElement(
        name="sequence_space",
        desc="sequence_space for this index set",
        default="color",
        set_in_upload=True,
        readonly=True,
    )

    file_ext = "bowtie_color_index"


[docs]class BowtieBaseIndex(BowtieIndex):
    """
    Bowtie base space index
    """

    MetadataElement(
        name="sequence_space",
        desc="sequence_space for this index set",
        default="base",
        set_in_upload=True,
        readonly=True,
    )

    file_ext = "bowtie_base_index"