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Source code for galaxy.tool_util.provided_metadata

import json
import logging
import os
import re

from galaxy.util import stringify_dictionary_keys

log = logging.getLogger(__name__)

[docs]def parse_tool_provided_metadata(meta_file, provided_metadata_style=None, job_wrapper=None): """Return a ToolProvidedMetadata object for specified file path. If meta_file is absent, return a NullToolProvidedMetadata. If provided_metadata_style is None attempt to guess tool provided metadata type. """ if not os.path.exists(meta_file): return NullToolProvidedMetadata() if provided_metadata_style is None: provided_metadata_style = _guess_tool_provided_metadata_style(meta_file) assert provided_metadata_style in ["legacy", "default"] if provided_metadata_style == "legacy": return LegacyToolProvidedMetadata(meta_file, job_wrapper=job_wrapper) elif provided_metadata_style == "default": return ToolProvidedMetadata(meta_file)
def _guess_tool_provided_metadata_style(path): try: with open(path, "r") as f: metadata = json.load(f) metadata_type = metadata.get("type", None) return "legacy" if metadata_type in ["dataset", "new_primary_dataset"] else "default" except ValueError: # Either empty or multiple JSON lines, either way we can safely treat # it as legacy style. return "legacy"
[docs]class BaseToolProvidedMetadata(object):
[docs] def get_new_datasets(self, output_name): """Find new datasets for dataset discovery for specified output. Return a list of such datasets. Called only in the context of discovering datasets when discover_via="tool_provided_metadata" is defined in the tool. """ return []
[docs] def has_failed_outputs(self): """Determine if generation of any of the outputs failed. """ return False
[docs] def get_new_dataset_meta_by_basename(self, output_name, basename): """For a discovered dataset, get the corresponding metadata entry. The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry. """ return {}
[docs] def get_unnamed_outputs(self): """Return unnamed outputs dataset introduced for upload 2.0. Needs more formal specification but see output_collect for how destinations, types, elements, etc... are consumed. """ return []
[docs] def get_dataset_meta(self, output_name, dataset_id): """Return primary dataset metadata for specified output. """ return {}
[docs] def rewrite(self): """Write metadata back to the file system. If metadata has not changed via outputs specified as mutable, the implementation class may opt to not re-write the file. """ return None
[docs] def get_new_datasets_for_metadata_collection(self): """Return all datasets tracked that are not explicit primary outputs. """ return []
[docs]class NullToolProvidedMetadata(BaseToolProvidedMetadata): pass
[docs]class LegacyToolProvidedMetadata(BaseToolProvidedMetadata):
[docs] def __init__(self, meta_file, job_wrapper=None): self.meta_file = meta_file self.tool_provided_job_metadata = [] with open(meta_file, 'r') as f: for line in f: try: line = stringify_dictionary_keys(json.loads(line)) assert 'type' in line except Exception: log.exception('(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % job_wrapper.job_id) log.debug('Offending data was: %s' % line) continue # Set the dataset id if it's a dataset entry and isn't set. # This isn't insecure. We loop the job's output datasets in # the finish method, so if a tool writes out metadata for a # dataset id that it doesn't own, it'll just be ignored. dataset_id_not_specified = line['type'] == 'dataset' and 'dataset_id' not in line if dataset_id_not_specified: dataset_basename = line['dataset'] if job_wrapper: try: line['dataset_id'] = job_wrapper.get_output_file_id(dataset_basename) except KeyError: log.warning('(%s) Tool provided job dataset-specific metadata without specifying a dataset' % job_wrapper.job_id) continue else: match = re.match(r'dataset_(\d+)\.dat', dataset_basename) line['dataset_id'] = int(match.group(1)) self.tool_provided_job_metadata.append(line)
[docs] def get_dataset_meta(self, output_name, dataset_id): for meta in self.tool_provided_job_metadata: if meta['type'] == 'dataset' and int(meta['dataset_id']) == dataset_id: return meta return {}
[docs] def get_new_dataset_meta_by_basename(self, output_name, basename): for meta in self.tool_provided_job_metadata: if meta['type'] == 'new_primary_dataset' and meta['filename'] == basename: return meta
[docs] def get_new_datasets(self, output_name): log.warning("Called get_new_datasets with legacy tool metadata provider - that is unimplemented.") return []
[docs] def has_failed_outputs(self): found_failed = False for meta in self.tool_provided_job_metadata: if meta.get("failed", False): found_failed = True return found_failed
[docs] def get_unnamed_outputs(self): return []
[docs] def rewrite(self): with open(self.meta_file, 'wt') as job_metadata_fh: for meta in self.tool_provided_job_metadata: job_metadata_fh.write("%s\n" % (json.dumps(meta)))
[docs] def get_new_datasets_for_metadata_collection(self): for meta in self.tool_provided_job_metadata: if meta['type'] == 'new_primary_dataset': yield meta
[docs]class ToolProvidedMetadata(BaseToolProvidedMetadata):
[docs] def __init__(self, meta_file): self.meta_file = meta_file with open(meta_file, 'r') as f: self.tool_provided_job_metadata = json.load(f)
[docs] def get_dataset_meta(self, output_name, dataset_id): return self.tool_provided_job_metadata.get(output_name, {})
[docs] def get_new_dataset_meta_by_basename(self, output_name, basename): datasets = self.tool_provided_job_metadata.get(output_name, {}).get("datasets", []) for meta in datasets: if meta['filename'] == basename: return meta
[docs] def get_new_datasets(self, output_name): datasets = self.tool_provided_job_metadata.get(output_name, {}).get("datasets", []) if not datasets: elements = self.tool_provided_job_metadata.get(output_name, {}).get("elements", []) if elements: datasets = self._elements_to_datasets(elements) return datasets
def _elements_to_datasets(self, elements, level=0): for element in elements: extra_kwds = {"identifier_%d" % level: element["name"]} if "elements" in element: for inner_element in self._elements_to_datasets(element["elements"], level=level + 1): dataset = extra_kwds.copy() dataset.update(inner_element) yield dataset else: dataset = extra_kwds extra_kwds.update(element) yield extra_kwds
[docs] def has_failed_outputs(self): found_failed = False for output_name, meta in self.tool_provided_job_metadata.items(): if output_name == "__unnamed_outputs": continue if meta.get("failed", False): found_failed = True return found_failed
[docs] def get_unnamed_outputs(self): log.debug("unnamed outputs [%s]" % self.tool_provided_job_metadata) return self.tool_provided_job_metadata.get("__unnamed_outputs", [])
[docs] def rewrite(self): with open(self.meta_file, 'wt') as job_metadata_fh: json.dump(self.tool_provided_job_metadata, job_metadata_fh)