Mercurial > repos > iuc > ncbi_eutils_efetch
changeset 9:6c4b39080ed7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
| author | iuc |
|---|---|
| date | Mon, 23 Jan 2023 10:37:57 +0000 |
| parents | c5ff15011115 |
| children | |
| files | efetch.py eutils.py macros.xml test-data/pubmed.metadata.xml |
| diffstat | 4 files changed, 10 insertions(+), 8 deletions(-) [+] |
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--- a/efetch.py Sat Nov 27 09:54:07 2021 +0000 +++ b/efetch.py Mon Jan 23 10:37:57 2023 +0000 @@ -102,7 +102,7 @@ os.rename(relpath, 'downloads/%s' % (file)) if problem is not None: - raise(problem) + raise problem else: merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
--- a/eutils.py Sat Nov 27 09:54:07 2021 +0000 +++ b/eutils.py Mon Jan 23 10:37:57 2023 +0000 @@ -176,7 +176,7 @@ except Exception as e: print("Error parsing...") print(xml_str) - raise(e) + raise e return history @@ -221,7 +221,7 @@ except Exception as e: print("Error parsing...") print(xml_str) - raise(e) + raise e return histories
--- a/macros.xml Sat Nov 27 09:54:07 2021 +0000 +++ b/macros.xml Mon Jan 23 10:37:57 2023 +0000 @@ -2,7 +2,7 @@ <macros> <token name="@PROFILE@">18.01</token> <token name="@TOOL_VERSION@">1.70</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token> <token name="@EMAIL_ARGUMENTS@"> --user_email "$__user_email__"
--- a/test-data/pubmed.metadata.xml Sat Nov 27 09:54:07 2021 +0000 +++ b/test-data/pubmed.metadata.xml Mon Jan 23 10:37:57 2023 +0000 @@ -1,5 +1,7 @@ +<\?xml version=\"1\.0\" encoding=\"UTF-8\" \?> +<!DOCTYPE eInfoResult PUBLIC \"-//NLM//DTD einfo 20190110//EN\" \"https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20190110/einfo.dtd\"> <eInfoResult> - <DbInfo> - <DbName>pubmed</DbName> - <MenuName>PubMed</MenuName> - <Description>PubMed bibliographic record</Description> +\s*<DbInfo> +\s*<DbName>pubmed</DbName> +\s*<MenuName>PubMed</MenuName> +\s*<Description>PubMed bibliographic record</Description> \ No newline at end of file