Mercurial > repos > bebatut > data_manager_qiime_database_downloader
changeset 11:8ff075db547a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 9a8e5333c047c6a5c18ca8f139a979704644ad87-dirty
| author | bebatut |
|---|---|
| date | Fri, 05 May 2017 03:13:55 -0400 |
| parents | 5c3bf1589fcf |
| children | c068e97553b0 |
| files | data_manager/data_manager_qiime_download.py |
| diffstat | 1 files changed, 7 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager/data_manager_qiime_download.py Thu May 04 14:31:25 2017 -0400 +++ b/data_manager/data_manager_qiime_download.py Fri May 05 03:13:55 2017 -0400 @@ -132,13 +132,13 @@ print("Error") -def download_archive(db, version): +def download_archive(db, version, ext): """ """ filepath = "archive" if protocol[db] == "http": - url = "%s%s.%s" % (baseUrl[db], version, extension[db]) + url = "%s%s.%s" % (baseUrl[db], version, ext) r = requests.get(url, stream=True) r.raise_for_status() with open(filepath, "wb") as fd: @@ -147,7 +147,10 @@ elif protocol[db] == "ftp": ftp = ftplib.FTP(baseUrl[db]) ftp.login("anonymous", "ftplib-example-1") - ftp.cwd("%s%s" % (ftp_dir[db], version)) + if db == "greengenes" and version == "13_8": + ftp.cwd("%s%s" % (ftp_dir[db], "13_5")) + else: + ftp.cwd("%s%s" % (ftp_dir[db], version)) filepath = "%s%s%s.%s" % ( ftp_file_prefix[db], version, @@ -297,7 +300,7 @@ ext = ext[version] print("Download archive") - filepath = download_archive(db, version) + filepath = download_archive(db, version, ext) print("Extract archive %s" % filepath) archive_content_path = extract_archive(filepath, ext)