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Fix issue#347 #352

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merged 1 commit into from
May 30, 2024
Merged

Fix issue#347 #352

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11 changes: 8 additions & 3 deletions autometa/config/databases.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,9 +200,10 @@ def get_remote_checksum(self, section: str, option: str) -> str:
raise ValueError(
f"'section' must be 'ncbi' or 'markers'. Provided: {section}"
)
if not ncbi_is_connected():
raise ConnectionError("Cannot connect to the NCBI rsync server")
print(f"The section is : {section}")
if section == "ncbi":
if not ncbi_is_connected():
raise ConnectionError("Cannot connect to the NCBI rsync server")
host = self.config.get(section, "host")
ftp_fullpath = self.config.get("checksums", option)
chksum_fpath = ftp_fullpath.split(host)[-1]
Expand Down Expand Up @@ -604,7 +605,11 @@ def compare_checksums(self, section: str = None) -> Dict[str, Dict]:
# Skip user added options not required by Autometa
continue
# nodes.dmp, names.dmp and merged.dmp are all in taxdump.tar.gz
option = "taxdump" if option in {"nodes", "names", "merged", "delnodes"} else option
option = (
"taxdump"
if option in {"nodes", "names", "merged", "delnodes"}
else option
)
fpath = self.config.get(section, option)
fpath_md5 = f"{fpath}.md5"
# We can not checksum a file that does not exist.
Expand Down
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