Branch:
rosetta:main
「revision: №62133」
Test:
linux.clang.integration.release_debug_no_symbols
SubTest:
code_template_tests_citations
SubTest files:
「file-system-view」
Daemon:
hojo-3
State:
code_template_tests_citations
Brief Diff:
Files /home/benchmark/working_dir/main:62132/code_template_tests_citations/database/citations/rosetta_citations.txt and /home/benchmark/working_dir/main:62133/code_template_tests_citations/database/citations/rosetta_citations.txt differ
Files /home/benchmark/working_dir/main:62132/code_template_tests_citations/err1.log and /home/benchmark/working_dir/main:62133/code_template_tests_citations/err1.log differ
Only in /home/benchmark/working_dir/main:62133/code_template_tests_citations: err2.log
Files /home/benchmark/working_dir/main:62132/code_template_tests_citations/out.log and /home/benchmark/working_dir/main:62133/code_template_tests_citations/out.log differ
Files /home/benchmark/working_dir/main:62132/code_template_tests_citations/.test_did_not_run.log and /home/benchmark/working_dir/main:62133/code_template_tests_citations/.test_did_not_run.log differ
Full Diff:
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62132/code_template_tests_citations/database/citations/rosetta_citations.txt /home/benchmark/working_dir/main:62133/code_template_tests_citations/database/citations/rosetta_citations.txt
18a19,39
> "" "Williamson" "DI"
> [END_PRIMARY_AUTHORS]
> [BEGIN_YEAR]
> 2009
> [END_YEAR]
> [BEGIN_TITLE]
> Caterpillars evolved from onychophorans by hybridogenesis
> [END_TITLE]
> [BEGIN_JOURNAL]
> Proc Natl Acad Sci U S A
> [END_JOURNAL]
> [BEGIN_VOLUME_ISSUE_PAGES]
> 106(47):19901-5
> [END_VOLUME_ISSUE_PAGES]
> [BEGIN_DOI]
> 10.1073/pnas.0908357106
> [END_DOI]
> [END_CITATION]
>
> [BEGIN_CITATION]
> [BEGIN_PRIMARY_AUTHORS]
541a563
>
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62132/code_template_tests_citations/err1.log /home/benchmark/working_dir/main:62133/code_template_tests_citations/err1.log
1,12d0
< Traceback (most recent call last):
< File "ROSETTA/source/code_templates/add_citation_by_pubmed_id.py", line 245, in <module>
< main(sys.argv)
< File "ROSETTA/source/code_templates/add_citation_by_pubmed_id.py", line 232, in main
< new_citation.init_from_pmid( new_pmid )
< File "ROSETTA/source/code_templates/add_citation_by_pubmed_id.py", line 91, in init_from_pmid
< publication = Publication( PubMedLookup( pmid, '' ), resolve_doi=False )
< File "/home/benchmark/prefix/hojo-3/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/lib/python3.9/site-packages/pubmed_lookup/pubmed_lookup.py", line 51, in __init__
< self.set_pub_year_month_day(xml_dict)
< File "/home/benchmark/prefix/hojo-3/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/lib/python3.9/site-packages/pubmed_lookup/pubmed_lookup.py", line 208, in set_pub_year_month_day
< pubdate_xml = reduce(dict.get, key_path, xml_dict)
< TypeError: descriptor 'get' for 'dict' objects doesn't apply to a 'str' object
Only in /home/benchmark/working_dir/main:62133/code_template_tests_citations: err2.log
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62132/code_template_tests_citations/out.log /home/benchmark/working_dir/main:62133/code_template_tests_citations/out.log
2a3,6
> Successfully found article titled "Caterpillars evolved from onychophorans by hybridogenesis.".
> Adding PubMed ID 19717430 (DOI 10.1073/pnas.0908357106). to citations file.
> Wrote sorted citations list to "database//citations/rosetta_citations.txt". Please be sure to commit your changes with "git add database//citations/rosetta_citations.txt && git commit".
> Successfully imported pubmed-lookup package.
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62132/code_template_tests_citations/.test_did_not_run.log /home/benchmark/working_dir/main:62133/code_template_tests_citations/.test_did_not_run.log
1c1
< *** Test code_template_tests_citations did not run! Check your --mode flag and paths. [2024-10-11 01:38:55.649585]
---
> *** Test code_template_tests_citations did not run! Check your --mode flag and paths. [2024-10-11 01:59:24.127823]
Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!