htsworkflow/submission/submission.py

   1 """Common submission elements
   2 """
   3 import logging
   4 import os
   5 import re
   6
   7 import RDF
   8
   9 from htsworkflow.util.rdfhelp import \
  10      blankOrUri, \
  11      dafTermOntology, \
  12      dump_model, \
  13      get_model, \
  14      libraryOntology, \
  15      owlNS, \
  16      rdfNS, \
  17      submissionLog, \
  18      submissionOntology, \
  19      toTypedNode, \
  20      fromTypedNode
  21 from htsworkflow.util.hashfile import make_md5sum
  22
  23 from htsworkflow.submission.daf import \
  24      MetadataLookupException, \
  25      get_submission_uri
  26
  27 LOGGER = logging.getLogger(__name__)
  28
  29 class Submission(object):
  30     def __init__(self, name, model):
  31         self.name = name
  32         self.model = model
  33
  34         self.submissionSet = get_submission_uri(self.name)
  35         self.submissionSetNS = RDF.NS(str(self.submissionSet) + '#')
  36         self.libraryNS = RDF.NS('http://jumpgate.caltech.edu/library/')
  37
  38         self.__view_map = None
  39
  40     def scan_submission_dirs(self, result_map):
  41         """Examine files in our result directory
  42         """
  43         for lib_id, result_dir in result_map.items():
  44             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
  45             try:
  46                 self.import_analysis_dir(result_dir, lib_id)
  47             except MetadataLookupException, e:
  48                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
  49
  50     def import_analysis_dir(self, analysis_dir, library_id):
  51         """Import a submission directories and update our model as needed
  52         """
  53         #attributes = get_filename_attribute_map(paired)
  54         libNode = self.libraryNS[library_id + "/"]
  55
  56         self._add_library_details_to_model(libNode)
  57
  58         submission_files = os.listdir(analysis_dir)
  59         for filename in submission_files:
  60             self.construct_file_attributes(analysis_dir, libNode, filename)
  61
  62     def construct_file_attributes(self, analysis_dir, libNode, pathname):
  63         """Looking for the best extension
  64         The 'best' is the longest match
  65
  66         :Args:
  67         filename (str): the filename whose extention we are about to examine
  68         """
  69         path, filename = os.path.split(pathname)
  70
  71         LOGGER.debug("Searching for view")
  72         file_type = self.find_best_match(filename)
  73         if file_type is None:
  74             LOGGER.warn("Unrecognized file: {0}".format(pathname))
  75             return None
  76         if str(file_type) == str(libraryOntology['ignore']):
  77             return None
  78
  79         an_analysis_name = self.make_submission_name(analysis_dir)
  80         an_analysis = self.get_submission_node(analysis_dir)
  81         an_analysis_uri = str(an_analysis.uri)
  82         file_classification = self.model.get_target(file_type,
  83                                                     rdfNS['type'])
  84         if file_classification is None:
  85             errmsg = 'Could not find class for {0}'
  86             LOGGER.warning(errmsg.format(str(file_type)))
  87             return
  88
  89         self.model.add_statement(
  90             RDF.Statement(self.submissionSetNS[''],
  91                           submissionOntology['has_submission'],
  92                           an_analysis))
  93         self.model.add_statement(RDF.Statement(an_analysis,
  94                                                submissionOntology['name'],
  95                                                toTypedNode(an_analysis_name)))
  96         self.model.add_statement(
  97             RDF.Statement(an_analysis,
  98                           rdfNS['type'],
  99                           submissionOntology['submission']))
 100         self.model.add_statement(RDF.Statement(an_analysis,
 101                                                submissionOntology['library'],
 102                                                libNode))
 103
 104         LOGGER.debug("Adding statements to {0}".format(str(an_analysis)))
 105         # add track specific information
 106         self.model.add_statement(
 107             RDF.Statement(an_analysis,
 108                           dafTermOntology['paired'],
 109                           toTypedNode(self._is_paired(libNode))))
 110         self.model.add_statement(
 111             RDF.Statement(an_analysis,
 112                           dafTermOntology['submission'],
 113                           an_analysis))
 114
 115         # add file specific information
 116         fileNode = self.link_file_to_classes(filename,
 117                                              an_analysis,
 118                                              an_analysis_uri,
 119                                              analysis_dir)
 120         self.add_md5s(filename, fileNode, analysis_dir)
 121         self.model.add_statement(
 122             RDF.Statement(fileNode,
 123                           rdfNS['type'],
 124                           file_type))
 125         LOGGER.debug("Done.")
 126
 127     def link_file_to_classes(self, filename, submissionNode, submission_uri, analysis_dir):
 128         # add file specific information
 129         fileNode = RDF.Node(RDF.Uri('file://'+ os.path.abspath(filename)))
 130         self.model.add_statement(
 131             RDF.Statement(submissionNode,
 132                           dafTermOntology['has_file'],
 133                           fileNode))
 134         self.model.add_statement(
 135             RDF.Statement(fileNode,
 136                           dafTermOntology['filename'],
 137                           filename))
 138         return fileNode
 139
 140     def add_md5s(self, filename, fileNode, analysis_dir):
 141         LOGGER.debug("Updating file md5sum")
 142         submission_pathname = os.path.join(analysis_dir, filename)
 143         md5 = make_md5sum(submission_pathname)
 144         if md5 is None:
 145             errmsg = "Unable to produce md5sum for {0}"
 146             LOGGER.warning(errmsg.format(submission_pathname))
 147         else:
 148             self.model.add_statement(
 149                 RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
 150
 151     def _add_library_details_to_model(self, libNode):
 152         # attributes that can have multiple values
 153         set_attributes = set((libraryOntology['has_lane'],
 154                               libraryOntology['has_mappings'],
 155                               dafTermOntology['has_file']))
 156         parser = RDF.Parser(name='rdfa')
 157         new_statements = parser.parse_as_stream(libNode.uri)
 158         toadd = []
 159         for s in new_statements:
 160             # always add "collections"
 161             if s.predicate in set_attributes:
 162                 toadd.append(s)
 163                 continue
 164             # don't override things we already have in the model
 165             targets = list(self.model.get_targets(s.subject, s.predicate))
 166             if len(targets) == 0:
 167                 toadd.append(s)
 168
 169         for s in toadd:
 170             self.model.append(s)
 171
 172         self._add_lane_details(libNode)
 173
 174     def _add_lane_details(self, libNode):
 175         """Import lane details
 176         """
 177         query = RDF.Statement(libNode, libraryOntology['has_lane'], None)
 178         lanes = []
 179         for lane_stmt in self.model.find_statements(query):
 180             lanes.append(lane_stmt.object)
 181
 182         parser = RDF.Parser(name='rdfa')
 183         for lane in lanes:
 184             LOGGER.debug("Importing %s" % (lane.uri,))
 185             try:
 186                 parser.parse_into_model(self.model, lane.uri)
 187             except RDF.RedlandError, e:
 188                 LOGGER.error("Error accessing %s" % (lane.uri,))
 189                 raise e
 190
 191
 192     def find_best_match(self, filename):
 193         """Search through potential filename matching patterns
 194         """
 195         if self.__view_map is None:
 196             self.__view_map = self._get_filename_view_map()
 197
 198         results = []
 199         for pattern, view in self.__view_map.items():
 200             if re.match(pattern, filename):
 201                 results.append(view)
 202
 203         if len(results) > 1:
 204             msg = "%s matched multiple views %s" % (
 205                 filename,
 206                 [str(x) for x in results])
 207             raise ModelException(msg)
 208         elif len(results) == 1:
 209             return results[0]
 210         else:
 211             return None
 212
 213     def _get_filename_view_map(self):
 214         """Query our model for filename patterns
 215
 216         return a dictionary of compiled regular expressions to view names
 217         """
 218         filename_query = RDF.Statement(
 219             None, dafTermOntology['filename_re'], None)
 220
 221         patterns = {}
 222         for s in self.model.find_statements(filename_query):
 223             view_name = s.subject
 224             literal_re = s.object.literal_value['string']
 225             LOGGER.debug("Found: %s" % (literal_re,))
 226             try:
 227                 filename_re = re.compile(literal_re)
 228             except re.error, e:
 229                 LOGGER.error("Unable to compile: %s" % (literal_re,))
 230             patterns[literal_re] = view_name
 231         return patterns
 232
 233     def make_submission_name(self, analysis_dir):
 234         analysis_dir = os.path.normpath(analysis_dir)
 235         analysis_dir_name = os.path.split(analysis_dir)[1]
 236         if len(analysis_dir_name) == 0:
 237             raise RuntimeError(
 238                 "Submission dir name too short: {0}".format(analysis_dir))
 239         return analysis_dir_name
 240
 241     def get_submission_node(self, analysis_dir):
 242         """Convert a submission directory name to a submission node
 243         """
 244         submission_name = self.make_submission_name(analysis_dir)
 245         return self.submissionSetNS[submission_name]
 246
 247     def _get_library_attribute(self, libNode, attribute):
 248         if not isinstance(attribute, RDF.Node):
 249             attribute = libraryOntology[attribute]
 250
 251         targets = list(self.model.get_targets(libNode, attribute))
 252         if len(targets) > 0:
 253             return self._format_library_attribute(targets)
 254         else:
 255             return None
 256
 257         #targets = self._search_same_as(libNode, attribute)
 258         #if targets is not None:
 259         #    return self._format_library_attribute(targets)
 260
 261         # we don't know anything about this attribute
 262         self._add_library_details_to_model(libNode)
 263
 264         targets = list(self.model.get_targets(libNode, attribute))
 265         if len(targets) > 0:
 266             return self._format_library_attribute(targets)
 267
 268         return None
 269
 270     def _format_library_attribute(self, targets):
 271         if len(targets) == 0:
 272             return None
 273         elif len(targets) == 1:
 274             return fromTypedNode(targets[0])
 275         elif len(targets) > 1:
 276             return [fromTypedNode(t) for t in targets]
 277
 278     def _is_paired(self, libNode):
 279         """Determine if a library is paired end"""
 280         library_type = self._get_library_attribute(libNode, 'library_type')
 281         if library_type is None:
 282             errmsg = "%s doesn't have a library type"
 283             raise ModelException(errmsg % (str(libNode),))
 284
 285         single = ['CSHL (lacking last nt)',
 286                   'Single End (non-multiplexed)',
 287                   'Small RNA (non-multiplexed)',]
 288         paired = ['Barcoded Illumina',
 289                   'Multiplexing',
 290                   'Nextera',
 291                   'Paired End (non-multiplexed)',]
 292         if library_type in single:
 293             return False
 294         elif library_type in paired:
 295             return True
 296         else:
 297             raise MetadataLookupException(
 298                 "Unrecognized library type %s for %s" % \
 299                 (library_type, str(libNode)))
 300
 301     def execute_query(self, template, context):
 302         """Execute the query, returning the results
 303         """
 304         formatted_query = template.render(context)
 305         LOGGER.debug(formatted_query)
 306         query = RDF.SPARQLQuery(str(formatted_query))
 307         rdfstream = query.execute(self.model)
 308         results = []
 309         for r in rdfstream:
 310             results.append(r)
 311         return results