| Previous changeset 5:e1b3b37aa69f (2021-10-27) Next changeset 7:6f6537780379 (2022-02-24) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 7eafac9d91b39e43fd3820ab1431cab1c930bb01" |
|
modified:
check_remote.py ena_upload.xml process_xlsx.py |
| b |
| diff -r e1b3b37aa69f -r 4aab5ae907b6 check_remote.py --- a/check_remote.py Wed Oct 27 16:38:10 2021 +0000 +++ b/check_remote.py Mon Nov 15 11:47:13 2021 +0000 |
| [ |
| @@ -12,7 +12,7 @@ ''' assert entry_type in ['study', 'sample', 'experiment', 'run'] params_dict = {} - query_str = ' AND '.join(['%s=%s' % (key, value) for (key, value) in query_dict.items()]) + query_str = ' AND '.join(['%s="%s"' % (key, value) for (key, value) in query_dict.items()]) params_dict['query'] = query_str params_dict['result'] = 'read_' + entry_type params_dict['fields'] = entry_type + '_alias' |
| b |
| diff -r e1b3b37aa69f -r 4aab5ae907b6 ena_upload.xml --- a/ena_upload.xml Wed Oct 27 16:38:10 2021 +0000 +++ b/ena_upload.xml Mon Nov 15 11:47:13 2021 +0000 |
| b |
| @@ -374,7 +374,7 @@ <has_n_lines n="2"/> <has_n_columns n="8"/> <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> - <has_line_matching expression="SARS-CoV-2_genomes_01\tmodify\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> + <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> </assert_contents> </output> <output name="samples_table_out"> @@ -425,7 +425,7 @@ <has_n_lines n="2"/> <has_n_columns n="8"/> <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> - <has_line_matching expression="SARS-CoV-2_genomes_01\tmodify\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> + <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> </assert_contents> </output> <output name="samples_table_out"> |
| b |
| diff -r e1b3b37aa69f -r 4aab5ae907b6 process_xlsx.py --- a/process_xlsx.py Wed Oct 27 16:38:10 2021 +0000 +++ b/process_xlsx.py Mon Nov 15 11:47:13 2021 +0000 |
| [ |
| @@ -14,7 +14,7 @@ ''' define action ['add' | 'modify'] that needs to be perfomed for this entry ''' query = {entry_type + '_alias': alias} remote_accessions = check_remote_entry(entry_type, query) - if len(remote_accessions) > 0: + if isinstance(remote_accessions, list) and len(remote_accessions) > 0: print(f'Found: {entry_type} entry with alias {alias}') return 'modify' else: |