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Source code for galaxy.tool_shed.util.basic_util

import logging
import os
import shutil

import markupsafe

from galaxy.util import (

log = logging.getLogger(__name__)

CHUNK_SIZE = 2**20  # 1Mb
# Set no activity timeout to 20 minutes.

# Galaxy Docker image

FROM bgruening/galaxy-stable

MAINTAINER Bjoern A. Gruning, bjoern.gruening@gmail.com

WORKDIR /galaxy-central


# Mark folders as imported from the host.
VOLUME ["/export/", "/data/", "/var/lib/docker"]

# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app)
EXPOSE :8800
EXPOSE :9001

# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]

RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}"

[docs]def get_file_type_str(changeset_revision, file_type): if file_type == "zip": file_type_str = f"{changeset_revision}.zip" elif file_type == "bz2": file_type_str = f"{changeset_revision}.tar.bz2" elif file_type == "gz": file_type_str = f"{changeset_revision}.tar.gz" else: file_type_str = "" return file_type_str
[docs]def move_file(current_dir, source, destination, rename_to=None): source_path = os.path.abspath(os.path.join(current_dir, source)) destination_directory = os.path.join(destination) if rename_to is not None: destination_path = os.path.join(destination_directory, rename_to) else: source_file = os.path.basename(source_path) destination_path = os.path.join(destination_directory, source_file) if not os.path.exists(destination_directory): os.makedirs(destination_directory) shutil.move(source_path, destination_path)
[docs]def remove_dir(dir): """Attempt to remove a directory from disk.""" if dir: if os.path.exists(dir): try: shutil.rmtree(dir) except Exception: pass
[docs]def size_string(raw_text, size=MAX_DISPLAY_SIZE): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len(raw_text) >= size: large_str = ( f"\nFile contents truncated because file size is larger than maximum viewing size of {nice_size(size)}\n" ) raw_text = f"{raw_text[0:size]}{large_str}" return raw_text or ""
[docs]def stringify(list): if list: return ",".join(list) return ""
[docs]def strip_path(fpath): """Attempt to strip the path from a file name.""" if not fpath: return fpath try: file_path, file_name = os.path.split(fpath) except Exception: file_name = fpath return file_name
[docs]def to_html_string(text): """Translates the characters in text to an html string""" if text: try: text = unicodify(text) except UnicodeDecodeError as e: return f"Error decoding string: {str(e)}" text = str(markupsafe.escape(text)) text = text.replace("\n", "<br/>") text = text.replace(" ", "&nbsp;&nbsp;&nbsp;&nbsp;") text = text.replace(" ", "&nbsp;") return text
__all__ = ( "CHUNK_SIZE", "DOCKER_IMAGE_TEMPLATE", "get_file_type_str", "INSTALLATION_LOG", "MAX_DISPLAY_SIZE", "MAXDIFFSIZE", "NO_OUTPUT_TIMEOUT", "move_file", "remove_dir", "SELECTED_REPOSITORIES_TEMPLATE", "size_string", "stringify", "strip_path", "to_html_string", )