ex-283 (dkriti/cgates) made changes in the metaheader (relating to

timestamp, cmd, command, source and version).

jacquard/jacquard.py

@@ -47,6 +47,7 @@
 import signal
 import sys
 import traceback
+import string
 
 from jacquard import __version__
 import jacquard.utils.command_validator as command_validator
@@ -151,14 +152,15 @@ def _get_execution_context(command):
     cwd = os.path.dirname(os.getcwd())
     now = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
 
-    return ['##jacquard=<Timestamp="{}",Command="{}",Cwd="{}">'.format(now,
+    return ['##jacquard=<timestamp="{}",command="{}",cwd="{}",source="Jacquard",version="{}">'.format(now,
                                                                        command,
-                                                                       cwd)]
+                                                                       cwd,
+                                                                       __version__)]
 
 def _dispatch(modules, arguments):
     try:
         command, args = _parse_command_line_args(modules, arguments)
-        execution_context = _get_execution_context(command)
+        execution_context = _get_execution_context(arguments)
 
         logger.initialize_logger(args)
         logger.debug("Jacquard run begins")

test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##MuTect="analysis_type=MuTect input_file=[11N_25714.sorted.bam, 11Ta_25715.sorted.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[BadCigar] intervals=[TargetRegion_buffered10bases.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=ucsc.hg19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false noop=false enable_extended_output=false artifact_detection_mode=false tumor_sample_name=25715 bam_tumor_sample_name=null normal_sample_name=25714 force_output=false force_alleles=false only_passing_calls=false initial_tumor_lod=4.0 tumor_lod=6.3 fraction_contamination=0.02 minimum_mutation_cell_fraction=0.0 normal_lod=2.2 normal_artifact_lod=1.0 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 dbsnp_normal_lod=5.5 somatic_classification_normal_power_threshold=0.95 minimum_normal_allele_fraction=0.0 tumor_f_pretest=0.0050 min_qscore=5 gap_events_threshold=3 heavily_clipped_read_fraction=0.3 clipping_bias_pvalue_threshold=0.05 fraction_mapq0_threshold=0.5 pir_median_threshold=10.0 pir_mad_threshold=3.0 required_maximum_alt_allele_mapping_quality_score=20 max_alt_alleles_in_normal_count=2 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 absolute_copy_number_data=null power_constant_af=0.30000001192092896 vcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub dbsnp=[(RodBinding name=dbsnp source=dbsnp_138.hg19.vcf)] cosmic=[(RodBinding name=cosmic source=Cosmic.v68.hg19.vcf)] normal_panel=[] coverage_20_q20_file=null power_file=null tumor_depth_file=null normal_depth_file=null filter_mismatching_base_and_quals=false"
 ##jacquard.translate.caller=MuTect
-##jacquard=<Timestamp="2015-05-15 12:12:36",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 12:12:36",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##reference=file:ucsc.hg19.fasta
 ##contig=<ID=chr1,length=249250621,assembly=hg19>
 ##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>

test/functional_tests/01_translate/benchmark/tiny.strelka.indels.translatedTags.vcf

@@ -3,7 +3,7 @@
 ##fileDate=20140709
 ##germlineIndelTheta=0.0001
 ##jacquard.translate.caller=Strelka
-##jacquard=<Timestamp="2015-05-15 14:42:14",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 14:42:14",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##priorSomaticIndelRate=1e-06
 ##reference=file:ucsc.hg19.fasta
 ##source=strelka

test/functional_tests/01_translate/benchmark/tiny.strelka.snvs.translatedTags.vcf

@@ -3,7 +3,7 @@
 ##fileDate=20140709
 ##germlineSnvTheta=0.001
 ##jacquard.translate.caller=Strelka
-##jacquard=<Timestamp="2015-05-15 14:42:14",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 14:42:14",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##priorSomaticSnvRate=1e-06
 ##reference=file:ucsc.hg19.fasta
 ##source=strelka

test/functional_tests/01_translate/benchmark/tiny.varscan.indel.translatedTags.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##jacquard.translate.caller=VarScan
-##jacquard=<Timestamp="2015-05-15 11:52:10",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 11:52:10",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##source=VarScan2
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

test/functional_tests/01_translate/benchmark/tiny.varscan.snp.translatedTags.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##jacquard.translate.caller=VarScan
-##jacquard=<Timestamp="2015-05-15 11:52:10",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 11:52:10",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##source=VarScan2
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

test/functional_tests/02_merge/benchmark/merged.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##jacquard.merge.sample=<Column=1,Name=tiny|NORMAL,Source=tiny.mutect.normalized.jacquardTags.HCsomatic.vcf|tiny.strelka.normalized.jacquardTags.HCsomatic.vcf|tiny.varscan.normalized.jacquardTags.HCsomatic.vcf>
 ##jacquard.merge.sample=<Column=2,Name=tiny|TUMOR,Source=tiny.mutect.normalized.jacquardTags.HCsomatic.vcf|tiny.strelka.normalized.jacquardTags.HCsomatic.vcf|tiny.varscan.normalized.jacquardTags.HCsomatic.vcf>
-##jacquard=<Timestamp="2015-03-30 13:37:01",Command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-03-30 13:37:01",command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",cwd="C:\Users\jebene\git">
 ##contig=<ID=chr1,length=249250621>
 ##contig=<ID=chr2,length=243199373>
 ##contig=<ID=chr3,length=198022430>

test/functional_tests/02_merge_unsorted/benchmark/merged.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##jacquard.merge.sample=<Column=1,Name=tiny|NORMAL,Source=tiny.mutect.normalized.jacquardTags.HCsomatic.vcf|tiny.strelka.normalized.jacquardTags.HCsomatic.vcf|tiny.varscan.normalized.jacquardTags.HCsomatic.vcf>
 ##jacquard.merge.sample=<Column=2,Name=tiny|TUMOR,Source=tiny.mutect.normalized.jacquardTags.HCsomatic.vcf|tiny.strelka.normalized.jacquardTags.HCsomatic.vcf|tiny.varscan.normalized.jacquardTags.HCsomatic.vcf>
-##jacquard=<Timestamp="2015-03-30 13:37:01",Command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-03-30 13:37:01",command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",cwd="C:\Users\jebene\git">
 ##contig=<ID=chr1,length=249250621>
 ##contig=<ID=chr2,length=243199373>
 ##contig=<ID=chr3,length=198022430>

test/functional_tests/03_summarize/benchmark/summarized.vcf

@@ -6,7 +6,7 @@
 ##jacquard.summarize.JQ_SUMMARY_AF_ZSCORE.JQ_SUMMARY_AF_RANGE_stdev=None
 ##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_mean=None
 ##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_stdev=None
-##jacquard=<Timestamp="2015-05-19 14:34:18",Command="<module 'jacquard.summarize' from 'C:\Users\dkriti\workspace\Jacquard\jacquard\summarize.pyc'>",Cwd="c:\Users\dkriti\workspace">
+##jacquard=<timestamp="2015-05-19 14:34:18",command="<module 'jacquard.summarize' from 'C:\Users\dkriti\workspace\Jacquard\jacquard\summarize.pyc'>",cwd="c:\Users\dkriti\workspace">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_PASSED_COUNT,Number=1,Type=Integer,Description="Count of samples where a variant caller passed the filter in any of the Jacquard tagged VCFs">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_REPORTED_COUNT,Number=1,Type=Integer,Description="Count of samples where this variant appeared in any of the Jacquard tagged VCFs (regardless of quality/filtering)">
 ##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 2 digits (based on alt_depth/total_depth. Uses TAR if available, otherwise uses uses DP2 if available, otherwise uses ACGT tier2 depth)">

test/functional_tests/jacquard_test/merge/benchmark/merged.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##jacquard.merge.sample=<Column=1,Name=tiny|NORMAL,Source=tiny.mutect.translatedTags.vcf|tiny.strelka.indels.translatedTags.vcf|tiny.strelka.snvs.translatedTags.vcf|tiny.varscan.indel.translatedTags.vcf|tiny.varscan.snp.translatedTags.vcf>
 ##jacquard.merge.sample=<Column=2,Name=tiny|TUMOR,Source=tiny.mutect.translatedTags.vcf|tiny.strelka.indels.translatedTags.vcf|tiny.strelka.snvs.translatedTags.vcf|tiny.varscan.indel.translatedTags.vcf|tiny.varscan.snp.translatedTags.vcf>
-##jacquard=<Timestamp="2015-05-15 14:47:54",Command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 14:47:54",command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",cwd="C:\Users\jebene\git">
 ##contig=<ID=chr1,length=249250621>
 ##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
 ##FORMAT=<ID=JQ_MT_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 2 digits (based on FA)">

test/functional_tests/jacquard_test/summarize/benchmark/summarized.vcf

@@ -5,8 +5,8 @@
 ##jacquard.summarize.JQ_SUMMARY_AF_ZSCORE.JQ_SUMMARY_AF_RANGE_stdev=0.01
 ##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_mean=2.0
 ##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_stdev=1.0
-##jacquard=<Timestamp="2015-05-19 14:38:10",Command="<module 'jacquard.summarize' from 'C:\Users\dkriti\workspace\Jacquard\jacquard\summarize.pyc'>",Cwd="c:\Users\dkriti\workspace">
-##jacquard=<Timestamp="2015-05-15 14:47:54",Command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-19 14:38:10",command="<module 'jacquard.summarize' from 'C:\Users\dkriti\workspace\Jacquard\jacquard\summarize.pyc'>",cwd="c:\Users\dkriti\workspace">
+##jacquard=<timestamp="2015-05-15 14:47:54",command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",cwd="C:\Users\jebene\git">
 ##contig=<ID=chr1,length=249250621>
 ##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_PASSED_COUNT,Number=1,Type=Integer,Description="Count of samples where a variant caller passed the filter in any of the Jacquard tagged VCFs">

test/functional_tests/jacquard_test/translate/benchmark/tiny.mutect.translatedTags.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##MuTect="analysis_type=MuTect input_file=[11N_25714.sorted.bam, 11Ta_25715.sorted.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[BadCigar] intervals=[TargetRegion_buffered10bases.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=ucsc.hg19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false noop=false enable_extended_output=false artifact_detection_mode=false tumor_sample_name=25715 bam_tumor_sample_name=null normal_sample_name=25714 force_output=false force_alleles=false only_passing_calls=false initial_tumor_lod=4.0 tumor_lod=6.3 fraction_contamination=0.02 minimum_mutation_cell_fraction=0.0 normal_lod=2.2 normal_artifact_lod=1.0 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 dbsnp_normal_lod=5.5 somatic_classification_normal_power_threshold=0.95 minimum_normal_allele_fraction=0.0 tumor_f_pretest=0.0050 min_qscore=5 gap_events_threshold=3 heavily_clipped_read_fraction=0.3 clipping_bias_pvalue_threshold=0.05 fraction_mapq0_threshold=0.5 pir_median_threshold=10.0 pir_mad_threshold=3.0 required_maximum_alt_allele_mapping_quality_score=20 max_alt_alleles_in_normal_count=2 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 absolute_copy_number_data=null power_constant_af=0.30000001192092896 vcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub dbsnp=[(RodBinding name=dbsnp source=dbsnp_138.hg19.vcf)] cosmic=[(RodBinding name=cosmic source=Cosmic.v68.hg19.vcf)] normal_panel=[] coverage_20_q20_file=null power_file=null tumor_depth_file=null normal_depth_file=null filter_mismatching_base_and_quals=false"
 ##jacquard.translate.caller=MuTect
-##jacquard=<Timestamp="2015-05-15 12:16:12",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 12:16:12",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##reference=file:ucsc.hg19.fasta
 ##contig=<ID=chr1,length=249250621,assembly=hg19>
 ##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>

test/functional_tests/jacquard_test/translate/benchmark/tiny.strelka.indels.translatedTags.vcf

@@ -3,7 +3,7 @@
 ##fileDate=20140709
 ##germlineIndelTheta=0.0001
 ##jacquard.translate.caller=Strelka
-##jacquard=<Timestamp="2015-05-15 14:45:25",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 14:45:25",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##priorSomaticIndelRate=1e-06
 ##reference=file:ucsc.hg19.fasta
 ##source=strelka

test/functional_tests/jacquard_test/translate/benchmark/tiny.strelka.snvs.translatedTags.vcf

@@ -3,7 +3,7 @@
 ##fileDate=20140709
 ##germlineSnvTheta=0.001
 ##jacquard.translate.caller=Strelka
-##jacquard=<Timestamp="2015-05-15 14:45:25",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 14:45:25",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##priorSomaticSnvRate=1e-06
 ##reference=file:ucsc.hg19.fasta
 ##source=strelka

test/functional_tests/jacquard_test/translate/benchmark/tiny.varscan.indel.translatedTags.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##jacquard.translate.caller=VarScan
-##jacquard=<Timestamp="2015-05-15 11:46:25",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 11:46:25",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##source=VarScan2
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

test/functional_tests/jacquard_test/translate/benchmark/tiny.varscan.snp.translatedTags.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##jacquard.translate.caller=VarScan
-##jacquard=<Timestamp="2015-05-15 11:46:25",Command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",Cwd="C:\Users\jebene\git">
+##jacquard=<timestamp="2015-05-15 11:46:25",command="<module 'jacquard.translate' from 'C:\Users\jebene\git\Jacquard\jacquard\translate.pyc'>",cwd="C:\Users\jebene\git">
 ##source=VarScan2
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

test/jacquard_test.py

@@ -60,7 +60,7 @@ def test_version(self):
     def test_get_execution_context(self):
         command = "foo input_dir output_dir"
         actual = jacquard._get_execution_context(command)
-        expected = r'##jacquard=<Timestamp=".*",Command="foo input_dir output_dir",Cwd=".*">'
+        expected = r'##jacquard=<timestamp=".*",command="foo input_dir output_dir",cwd=".*",source="Jacquard",version=".*">'
         self.assertRegexpMatches(actual[0], expected)
 
     def test_set_interrupt_handler(self):

test/utils/test_case.py

@@ -63,8 +63,8 @@ def _compare_files(self, output, output_file, expected_dir):
                           len(actual))
 
         for i in range(len(expected)):
-            if expected[i].startswith("##jacquard=<Timestamp="):
-                self.assertStartsWith(actual[i], "##jacquard=<Timestamp=")
+            if expected[i].startswith("##jacquard=<timestamp="):
+                self.assertStartsWith(actual[i], "##jacquard=<timestamp=")
             else:
                 self.assertEquals(expected[i].rstrip(),
                                   actual[i].rstrip())