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Refactor tool_shed basic_util into Galaxy.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| import logging | ||
| import os | ||
| import shutil | ||
| import sys | ||
| from string import Template | ||
|
|
||
| import markupsafe | ||
| from six import text_type | ||
|
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| from galaxy.util import nice_size, unicodify | ||
|
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| log = logging.getLogger(__name__) | ||
|
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| CHUNK_SIZE = 2 ** 20 # 1Mb | ||
| INSTALLATION_LOG = 'INSTALLATION.log' | ||
| # Set no activity timeout to 20 minutes. | ||
| NO_OUTPUT_TIMEOUT = 3600.0 | ||
| MAXDIFFSIZE = 8000 | ||
| MAX_DISPLAY_SIZE = 32768 | ||
|
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| DOCKER_IMAGE_TEMPLATE = ''' | ||
| # Galaxy Docker image | ||
| FROM bgruening/galaxy-stable | ||
| MAINTAINER Bjoern A. Gruning, bjoern.gruening@gmail.com | ||
| WORKDIR /galaxy-central | ||
| ${selected_repositories} | ||
| # 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 :80 | ||
| EXPOSE :21 | ||
| EXPOSE :8800 | ||
| EXPOSE :9001 | ||
| # Autostart script that is invoked during container start | ||
| CMD ["/usr/bin/startup"] | ||
| ''' | ||
|
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||
| SELECTED_REPOSITORIES_TEMPLATE = ''' | ||
| RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" | ||
| ''' | ||
|
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||
|
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| 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)) | ||
|
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||
|
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| 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 | ||
|
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| def get_file_type_str(changeset_revision, file_type): | ||
| if file_type == 'zip': | ||
| file_type_str = '%s.zip' % changeset_revision | ||
| elif file_type == 'bz2': | ||
| file_type_str = '%s.tar.bz2' % changeset_revision | ||
| elif file_type == 'gz': | ||
| file_type_str = '%s.tar.gz' % changeset_revision | ||
| else: | ||
| file_type_str = '' | ||
| return file_type_str | ||
|
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| 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) | ||
|
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||
|
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| 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 | ||
|
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||
|
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||
| 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 = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % nice_size(size) | ||
| raw_text = '%s%s' % (raw_text[0:size], large_str) | ||
| return raw_text or '' | ||
|
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|
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| def stringify(list): | ||
| if list: | ||
| return ','.join(list) | ||
| return '' | ||
|
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|
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| 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 | ||
|
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| 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 "Error decoding string: %s" % str(e) | ||
| text = text_type(markupsafe.escape(text)) | ||
| text = text.replace('\n', '<br/>') | ||
| text = text.replace(' ', ' ') | ||
| text = text.replace(' ', ' ') | ||
| return text |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,150 +1 @@ | ||
| import logging | ||
| import os | ||
| import shutil | ||
| import sys | ||
| from string import Template | ||
|
|
||
| import markupsafe | ||
| from six import text_type | ||
|
|
||
| from galaxy.util import nice_size, unicodify | ||
|
|
||
| log = logging.getLogger(__name__) | ||
|
|
||
| CHUNK_SIZE = 2 ** 20 # 1Mb | ||
| INSTALLATION_LOG = 'INSTALLATION.log' | ||
| # Set no activity timeout to 20 minutes. | ||
| NO_OUTPUT_TIMEOUT = 3600.0 | ||
| MAXDIFFSIZE = 8000 | ||
| MAX_DISPLAY_SIZE = 32768 | ||
|
|
||
| DOCKER_IMAGE_TEMPLATE = ''' | ||
| # Galaxy Docker image | ||
| FROM bgruening/galaxy-stable | ||
| MAINTAINER Bjoern A. Gruning, bjoern.gruening@gmail.com | ||
| WORKDIR /galaxy-central | ||
| ${selected_repositories} | ||
| # 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 :80 | ||
| EXPOSE :21 | ||
| EXPOSE :8800 | ||
| EXPOSE :9001 | ||
| # Autostart script that is invoked during container start | ||
| CMD ["/usr/bin/startup"] | ||
| ''' | ||
|
|
||
| SELECTED_REPOSITORIES_TEMPLATE = ''' | ||
| RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" | ||
| ''' | ||
|
|
||
|
|
||
| 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)) | ||
|
|
||
|
|
||
| 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 | ||
|
|
||
|
|
||
| def get_file_type_str(changeset_revision, file_type): | ||
| if file_type == 'zip': | ||
| file_type_str = '%s.zip' % changeset_revision | ||
| elif file_type == 'bz2': | ||
| file_type_str = '%s.tar.bz2' % changeset_revision | ||
| elif file_type == 'gz': | ||
| file_type_str = '%s.tar.gz' % changeset_revision | ||
| else: | ||
| file_type_str = '' | ||
| return file_type_str | ||
|
|
||
|
|
||
| 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) | ||
|
|
||
|
|
||
| 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 | ||
|
|
||
|
|
||
| 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 = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % nice_size(size) | ||
| raw_text = '%s%s' % (raw_text[0:size], large_str) | ||
| return raw_text or '' | ||
|
|
||
|
|
||
| def stringify(list): | ||
| if list: | ||
| return ','.join(list) | ||
| return '' | ||
|
|
||
|
|
||
| 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 | ||
|
|
||
|
|
||
| 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 "Error decoding string: %s" % str(e) | ||
| text = text_type(markupsafe.escape(text)) | ||
| text = text.replace('\n', '<br/>') | ||
| text = text.replace(' ', ' ') | ||
| text = text.replace(' ', ' ') | ||
| return text | ||
| from galaxy.tool_shed.util.basic_util import * # noqa: F401,F403 |