def classifications(ctx, classifications, results, readlevel, readlevel_path):
"""Retrieve performed metagenomic classifications"""
# basic operation -- just print
if not readlevel and not results:
cli_resource_fetcher(ctx, "classifications", classifications)
# fetch the results
elif not readlevel and results:
if len(classifications) != 1:
log.error(
"Can only request results data on one Classification at a time"
)
else:
classification = ctx.obj['API'].Classifications.get(
classifications[0])
if not classification:
log.error('Could not find classification {} (404 status code)'.
format(classifications[0]))
return
results = classification.results(json=True)
pprint(results, ctx.obj['NOPPRINT'])
# fetch the readlevel
elif readlevel is not None and not results:
if len(classifications) != 1:
log.error(
"Can only request read-level data on one Classification at a time"
)
else:
classification = ctx.obj['API'].Classifications.get(
classifications[0])
if not classification:
log.error('Could not find classification {} (404 status code)'.
format(classifications[0]))
return
tsv_url = classification.readlevel()['url']
log.info("Downloading tsv data from: {}".format(tsv_url))
download_file_helper(tsv_url, readlevel_path)
# both given -- complain
else:
log.error(
"Can only request one of read-level data or results data at a time"
)
def documents_list(ctx, json):
docs_list = cli_resource_fetcher(ctx, "documents", [], print_results=json)
if json:
return
if not docs_list:
click.echo("You haven't uploaded any files yet, and no files have been shared with you.")
else:
def _size_formatter(size):
suffix = "B"
if size > 1e9:
suffix = "GB"
size /= 1e9
elif size >= 1e6:
suffix = "MB"
size /= 1e6
elif size >= 1e3:
suffix = "KB"
size /= 1e3
return "%g %s" % (round(size, 2), suffix)
formatters = ["%-18s", "%-34s", "%-25s", "%-11s", "%-12s"]
table = [
["ID", "Name", "Owner", "Size", "Created On"],
["-" * 16, "-" * 32, "-" * 23, "-" * 9, "-" * 10],
]
docs_list = sorted(
docs_list,
reverse=True,
key=lambda x: time.mktime(dateutil.parser.parse(x["created_at"]).timetuple()),
)
for doc in docs_list:
fname = doc["filename"]
owner = doc["uploader"].email
table.append(
[
doc["$uri"].split("/")[-1],
fname if len(fname) <= 32 else fname[:29] + "...",
owner if len(owner) <= 23 else owner[:20] + "...",
_size_formatter(doc["size"]) if doc["size"] else "N/A",
dateutil.parser.parse(doc["created_at"]).strftime("%Y-%m-%d"),
]
)
for row in table:
formatted_row = []
for formatter, content in zip(formatters, row):
formatted_row.append(formatter % content)
click.echo("".join(formatted_row))
def documents_list(ctx, json):
docs_list = cli_resource_fetcher(ctx, "documents", [], print_results=json)
if json:
return
if not docs_list:
click.echo("You haven't uploaded any files yet, and no files have been shared with you.")
else:
def _size_formatter(size):
suffix = "B"
if size > 1e9:
suffix = "GB"
size /= 1e9
elif size >= 1e6:
suffix = "MB"
size /= 1e6
elif size >= 1e3:
suffix = "KB"
size /= 1e3
return "%g %s" % (round(size, 2), suffix)
formatters = ["%-18s", "%-34s", "%-25s", "%-11s", "%-12s"]
table = [
["ID", "Name", "Owner", "Size", "Created On"],
["-" * 16, "-" * 32, "-" * 23, "-" * 9, "-" * 10],
]
docs_list = sorted(
docs_list,
reverse=True,
key=lambda x: time.mktime(dateutil.parser.parse(x["created_at"]).timetuple()),
)
for doc in docs_list:
fname = doc["filename"]
owner = doc["uploader"].email
table.append(
[
doc["$uri"].split("/")[-1],
fname if len(fname) <= 32 else fname[:29] + "...",
owner if len(owner) <= 23 else owner[:20] + "...",
_size_formatter(doc["size"]) if doc["size"] else "N/A",
dateutil.parser.parse(doc["created_at"]).strftime("%Y-%m-%d"),
]
)
for row in table:
formatted_row = []
for formatter, content in zip(formatters, row):
formatted_row.append(formatter % content)
click.echo("".join(formatted_row))
def classifications(ctx, classifications, results, readlevel, readlevel_path):
"""Retrieve performed metagenomic classifications"""
# basic operation -- just print
if not readlevel and not results:
cli_resource_fetcher(ctx, "classifications", classifications)
# fetch the results
elif not readlevel and results:
if len(classifications) != 1:
log.error("Can only request results data on one Classification at a time")
else:
classification = ctx.obj["API"].Classifications.get(classifications[0])
if not classification:
log.error(
"Could not find classification {} (404 status code)".format(classifications[0])
)
return
results = classification.results(json=True)
pprint(results, ctx.obj["NOPPRINT"])
# fetch the readlevel
elif readlevel is not None and not results:
if len(classifications) != 1:
log.error("Can only request read-level data on one Classification at a time")
else:
classification = ctx.obj["API"].Classifications.get(classifications[0])
if not classification:
log.error(
"Could not find classification {} (404 status code)".format(classifications[0])
)
return
tsv_url = classification._readlevel()["url"]
log.info("Downloading tsv data from: {}".format(tsv_url))
download_file_helper(tsv_url, readlevel_path)
# both given -- complain
else:
log.error("Can only request one of read-level data or results data at a time")
def samples(ctx, samples):
"""Retrieve uploaded samples"""
cli_resource_fetcher(ctx, "samples", samples)
def panels(ctx, panels):
"""Retrieve performed in silico panel results"""
cli_resource_fetcher(ctx, "panels", panels)
def analyses(ctx, analyses):
"""Retrieve performed analyses"""
cli_resource_fetcher(ctx, "analyses", analyses)
def samples(ctx, samples):
"""Retrieve uploaded samples"""
cli_resource_fetcher(ctx, "samples", samples)
def panels(ctx, panels):
"""Retrieve performed in silico panel results"""
cli_resource_fetcher(ctx, "panels", panels)
def analyses(ctx, analyses):
"""Retrieve performed analyses"""
cli_resource_fetcher(ctx, "analyses", analyses)