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Merge pull request #5119 from mvdbeek/dev_toolshed_install_improvemen…
…ts_2 Improve tool validation and metadata generation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| """Provides a subset of app for verifying tools.""" | ||
| import os | ||
| import shutil | ||
| import tempfile | ||
| from contextlib import contextmanager | ||
|
|
||
| from galaxy.datatypes.registry import Registry | ||
| from galaxy.tools.data import ToolDataTableManager | ||
| from galaxy.util.bunch import Bunch | ||
| from galaxy.util.dbkeys import GenomeBuilds | ||
|
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|
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| class ValidationContext(object): | ||
| """Minimal App object for tool validation.""" | ||
|
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| def __init__(self, app_name, | ||
| security, | ||
| model, | ||
| tool_data_path, | ||
| shed_tool_data_path, | ||
| tool_data_tables=None, | ||
| registry=None, | ||
| hgweb_config_manager=None): | ||
| self.name = app_name | ||
| self.security = security | ||
| self.model = model | ||
| self.config = Bunch() | ||
| self.config.tool_data_path = tool_data_path | ||
| self.config.shed_tool_data_path = shed_tool_data_path | ||
| _, self.config.tool_data_table_config = tempfile.mkstemp() | ||
| _, self.config.shed_tool_data_table_config = tempfile.mkstemp() | ||
| self.tool_data_tables = tool_data_tables | ||
| self.datatypes_registry = registry or Registry() | ||
| self.hgweb_config_manager = hgweb_config_manager | ||
| _, self.config.len_file_path = tempfile.mkstemp() | ||
| _, self.config.builds_file_path = tempfile.mkstemp() | ||
| self.genome_builds = GenomeBuilds(self) | ||
|
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| def __enter__(self): | ||
| return self | ||
|
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| def __exit__(self, exc_type, exc_val, exc_tb): | ||
| cleanup_paths = {self.config.builds_file_path, | ||
| self.config.len_file_path, | ||
| self.config.tool_data_table_config, | ||
| self.config.shed_tool_data_table_config} | ||
| for path in cleanup_paths: | ||
| try: | ||
| os.remove(path) | ||
| except Exception: | ||
| pass | ||
|
|
||
| @staticmethod | ||
| @contextmanager | ||
| def from_app(app, work_dir=None): | ||
| cleanup = False | ||
| if not work_dir: | ||
| work_dir = tempfile.mkdtemp() | ||
| cleanup = True | ||
| tool_data_tables = ToolDataTableManager(work_dir) | ||
| with ValidationContext(app_name=app.name, | ||
| security=app.security, | ||
| model=app.model, | ||
| tool_data_path=work_dir, | ||
| shed_tool_data_path=work_dir, | ||
| tool_data_tables=tool_data_tables, | ||
| hgweb_config_manager=getattr(app, 'hgweb_config_manager', None) | ||
| ) as app: | ||
| yield app | ||
| if cleanup: | ||
| shutil.rmtree(work_dir, ignore_errors=True) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| """Safely write file to temporary file and then move file into place.""" | ||
| # Copied from https://stackoverflow.com/a/12007885. | ||
| import os | ||
| import tempfile | ||
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|
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| class RenamedTemporaryFile(object): | ||
| """ | ||
| A temporary file object which will be renamed to the specified | ||
| path on exit. | ||
| """ | ||
| def __init__(self, final_path, **kwargs): | ||
| tmpfile_dir = kwargs.pop('dir', None) | ||
|
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| # Put temporary file in the same directory as the location for the | ||
| # final file so that an atomic move into place can occur. | ||
|
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| if tmpfile_dir is None: | ||
| tmpfile_dir = os.path.dirname(final_path) | ||
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| self.tmpfile = tempfile.NamedTemporaryFile(dir=tmpfile_dir, **kwargs) | ||
| self.final_path = final_path | ||
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| def __getattr__(self, attr): | ||
| """ | ||
| Delegate attribute access to the underlying temporary file object. | ||
| """ | ||
| return getattr(self.tmpfile, attr) | ||
|
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| def __enter__(self): | ||
| self.tmpfile.__enter__() | ||
| return self | ||
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| def __exit__(self, exc_type, exc_val, exc_tb): | ||
| if exc_type is None: | ||
| self.tmpfile.delete = False | ||
| result = self.tmpfile.__exit__(exc_type, exc_val, exc_tb) | ||
| os.rename(self.tmpfile.name, self.final_path) | ||
| else: | ||
| result = self.tmpfile.__exit__(exc_type, exc_val, exc_tb) | ||
|
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||
| return result |
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