6 from htsworkflow.submission.submission import Submission
8 from htsworkflow.util.rdfhelp import \
14 from django.conf import settings
15 from django.template import Context, loader
17 LOGGER = logging.getLogger(__name__)
19 class GEOSubmission(Submission):
20 def __init__(self, name, model, host):
21 super(GEOSubmission, self).__init__(name, model, host)
23 def make_soft(self, result_map):
25 platform = self.get_platform_metadata()
26 platform_attribs = dict(platform)
27 platform_id = platform_attribs['^platform']
28 series = self.get_series_metadata()
29 series_attribs = dict(series)
30 series_id = series_attribs['^series']
31 for lib_id, result_dir in result_map.items():
32 an_analysis = self.get_submission_node(result_dir)
33 metadata = self.get_sample_metadata(an_analysis)
34 if len(metadata) == 0:
35 errmsg = 'No metadata found for {0}'
36 LOGGER.error(errmsg.format(str(an_analysis),))
38 elif len(metadata) > 1:
39 errmsg = 'Confused there are more than one sample for %s'
40 LOGGER.debug(errmsg % (str(an_analysis),))
41 metadata = metadata[0]
42 metadata['raw'] = self.get_raw_files(an_analysis)
43 metadata['supplimental'] = self.get_sample_files(an_analysis)
44 metadata['run'] = self.get_run_details(an_analysis)
45 samples.append(metadata)
47 soft_template = loader.get_template('geo_submission.soft')
52 'platform_id': platform_id,
53 'series_id': series_id,
55 print str(soft_template.render(context))
57 def check_for_name(self, analysis_node):
59 self.model.get_target(analysis_node,
60 submissionOntology['name']))
62 logger.error("Need name for %s" % (str(analysis_node)))
67 def get_platform_metadata(self):
68 """Gather information for filling out sample section of a SOFT file
70 query_template = loader.get_template('geo_platform.sparql')
71 submission = str(self.submissionSetNS[''].uri)
73 'submission': submission,
76 results = self.execute_query(query_template, context)
77 return self.query_to_soft_dictionary(results, 'platform')
79 def get_series_metadata(self):
80 """Gather information for filling out sample section of a SOFT file
82 query_template = loader.get_template('geo_series.sparql')
83 submission = str(self.submissionSetNS[''].uri)
85 'submission': submission,
88 results = self.execute_query(query_template, context)
89 return self.query_to_soft_dictionary(results, 'series')
91 def get_sample_metadata(self, analysis_node):
92 """Gather information for filling out sample section of a SOFT file
94 query_template = loader.get_template('geo_samples.sparql')
97 'submission': str(analysis_node.uri),
98 'submissionSet': str(self.submissionSetNS[''].uri),
101 results = self.execute_query(query_template, context)
103 r['dataProtocol'] = str(r['dataProtocol']).replace('\n', ' ')
107 def get_sample_files(self, analysis_node):
108 """Gather derived files
110 query_template = loader.get_template('geo_files.sparql')
113 'submission': str(analysis_node.uri),
114 'file_class': str(geoSoftNS['supplemental'].uri)
117 return self.execute_query(query_template, context)
119 def get_raw_files(self, analysis_node):
120 """Gather raw data e.g. fastq files.
122 query_template = loader.get_template('geo_fastqs.sparql')
125 'submission': str(analysis_node.uri),
126 'file_class': str(geoSoftNS['raw'].uri),
130 for row in self.execute_query(query_template, context):
132 for k, v in row.items():
134 library = str(data['library'])
135 lanes.setdefault(library, []).append(data)
137 for library, files in lanes.items():
139 errmsg = "Don't know what to do with more than 2 raw files"
140 raise ValueError(errmsg)
141 elif len(files) == 2:
143 elif len(files) == 1:
145 elif len(files) == 0:
146 raise RuntimeError("Empty library list discovered")
147 files = self._format_filename(files, is_paired)
148 files = self._format_flowcell_type(files, is_paired)
149 files = self._format_read_length(files, is_paired)
150 result.append(files[0])
153 def _format_flowcell_type(self, files, is_paired):
154 """Used by get_raw_files to format value for single_or_paired-end
157 if 'flowcell_type' in f:
158 flowcell_type = fromTypedNode(f['flowcell_type'])
159 if flowcell_type is None:
161 elif flowcell_type.lower() == "paired":
162 f['flowcell_type'] = 'paired-end'
164 f['flowcell_type'] = 'single'
168 def _format_read_length(self, files, is_paired):
171 read_count = 2 if is_paired else 1
173 if 'read_length' in f:
174 read_length = str(fromTypedNode(f['read_length']))
175 f['read_length'] = ",".join([read_length] * read_count)
178 def _format_filename(self, files, is_paired):
179 """Format file name for get_raw_files, also report if paired
185 f0['filename'] = "%s, %s" % (str(f0['filename']),
187 f0['md5sum'] = "%s, %s" % (str(f0['md5sum']),
191 files[0]['filename'] = str(files[0]['filename'])
192 files[0]['md5sum'] = str(files[0]['md5sum'])
196 def get_run_details(self, analysis_node):
197 """Get information about runs
199 query_template = loader.get_template('geo_run_details.sparql')
202 'submission': str(analysis_node.uri),
205 return self.execute_query(query_template, context)
207 def query_to_soft_dictionary(self, results, heading):
210 name = strip_namespace(geoSoftNS, r['name'])
212 if name.lower() == heading.lower():
216 for v in fromTypedNode(r['value']).split(os.linesep):
219 attributes.append((name, v))