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28 changes: 15 additions & 13 deletions progenomes/cli/view.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,3 @@
import polars as pl
import pandas as pd

INITIAL_URL = "https://progenomes.embl.de/data"

URL_MAPPING = [
Expand Down Expand Up @@ -63,21 +60,26 @@
]


def process_url(item: str):
mapping = next(iter(i for i in URL_MAPPING if i["name"] == item))
def get_url(item: str):
for mapping in URL_MAPPING:
if mapping["name"] == item:
break
else:
raise ValueError(f"Item '{item}' not found in URL mapping.")
mapping = next(iter(i for i in URL_MAPPING if i["name"] == item), None)
if mapping["file-prefix"] is None:
return f"{INITIAL_URL}/{mapping['filename']}.{mapping['filetype']}", mapping[
"filetype"
]
path = f"{mapping['filename']}.{mapping['filetype']}"
else:
return (
f"{INITIAL_URL}/{mapping['file-prefix']}_{mapping['filename']}.{mapping['filetype']}",
mapping["filetype"],
)
path = f"{mapping['file-prefix']}_{mapping['filename']}.{mapping['filetype']}"
return (
f"{INITIAL_URL}/{path}", mapping["filetype"],
)


def view(target):
url, filetype = process_url(target)
import polars as pl
import pandas as pd
url, filetype = get_url(target)
if "tab.bz2" in filetype:
return pl.from_pandas(pd.read_table(url))
elif "tsv.bz2" in filetype:
Expand Down
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