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Source code for galaxy.tool_shed.util.basic_util

import logging
import os
import shutil
import sys
from string import Template

import markupsafe

from galaxy.util import nice_size, unicodify

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 evaluate_template(text, install_environment): """ Substitute variables defined in XML blocks from dependencies file. The value of the received repository_install_dir is the root installation directory of the repository that contains the tool dependency. The value of the received install_dir is the root installation directory of the tool_dependency. """ return Template(text).safe_substitute(get_env_var_values(install_environment))
[docs]def get_env_var_values(install_environment): """ Return a dictionary of values, some of which enable substitution of reserved words for the values. The received install_enviroment object has 3 important attributes for reserved word substitution: install_environment.tool_shed_repository_install_dir is the root installation directory of the repository that contains the tool dependency being installed, install_environment.install_dir is the root installation directory of the tool dependency, and install_environment.tmp_work_dir is the temporary directory where the tool dependency compilation/installation is being processed. """ env_var_dict = {} env_var_dict['REPOSITORY_INSTALL_DIR'] = install_environment.tool_shed_repository_install_dir env_var_dict['INSTALL_DIR'] = install_environment.install_dir env_var_dict['TMP_WORK_DIR'] = install_environment.tmp_work_dir env_var_dict['system_install'] = install_environment.install_dir # If the Python interpreter is 64bit then we can safely assume that the underlying system is also 64bit. env_var_dict['__is64bit__'] = sys.maxsize > 2 ** 32 return env_var_dict
[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