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fix blake linting
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@paulzierep
paulzierep committed Nov 1, 2023
1 parent 4ab30c6 commit 6000063
Showing 1 changed file with 87 additions and 68 deletions.
155 changes: 87 additions & 68 deletions bin/generate_tool_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,81 +11,88 @@

def get_last_url_position(toot_id: str) -> str:
"""
Returns the last url position of the toot_id, if the value is not a
url it returns the toot_id. So works for local and toolshed installed tools.
Returns the last url position of the toot_id, if the value is not a
url it returns the toot_id. So works for local and toolshed
installed tools.
:param tool_id: galaxy tool id
"""

toot_id = toot_id.split("/")[-1]
return(toot_id)
return toot_id

def add_tool_stats_to_tools(tool_stats_path: str,
tools_path : str,
output_path: str,
column_name: str) -> pd.DataFrame:

def add_tool_stats_to_tools(tool_stats_path: str,
tools_path: str,
output_path: str,
column_name: str) -> pd.DataFrame:
"""
Adds the usage statistics to the community tool table
:param tool_stats_path: path to the table with
the tool stats (csv,
:param tool_stats_path: path to the table with
the tool stats (csv,
must include "tool_name" and "count")
:param tools_path: path to the table with
the tools (csv,
:param tools_path: path to the table with
the tools (csv,
must include "Galaxy wrapper id")
:param output_path: path to store the new table
:param column_name: column to add for the tool stats,
:param column_name: column to add for the tool stats,
different columns could be added for the main servers
"""

# parse csvs
# parse csvs
tool_stats_df = pd.read_csv(tool_stats_path)
community_tools_df = pd.read_csv(tools_path, sep = "\t")
community_tools_df = pd.read_csv(tools_path, sep="\t")

# extract tool id
tool_stats_df["Galaxy wrapper id"] = tool_stats_df["tool_name"].apply(get_last_url_position)
tool_stats_df["Galaxy wrapper id"] = \
tool_stats_df["tool_name"].apply(get_last_url_position)

# group local and toolshed tools into one entry
grouped_tool_stats_tools = tool_stats_df.groupby("Galaxy wrapper id", as_index=False)['count'].sum()
grouped_tool_stats_tools = \
tool_stats_df.groupby("Galaxy wrapper id",
as_index=False)["count"].sum()

#remove old stats entry with new stats
# remove old stats entry with new stats
if column_name in community_tools_df.columns:
community_tools_df.drop(column_name, inplace=True, axis=1)

community_tool_stats = pd.merge(grouped_tool_stats_tools, community_tools_df, on='Galaxy wrapper id')
community_tool_stats.rename(columns = {'count':column_name}, inplace=True)
community_tool_stats = pd.merge(grouped_tool_stats_tools,
community_tools_df,
on="Galaxy wrapper id")
community_tool_stats.rename(columns={"count": column_name}, inplace=True)

community_tool_stats.to_csv(output_path, sep="\t", index=False) #store the merged file
# store the merged file
community_tool_stats.to_csv(output_path, sep="\t", index=False)

return community_tool_stats

return(community_tool_stats)

def get_wordcloud(community_tool_stats: pd.DataFrame,
mask_figure: str,
wordcloud_output_path: str):

"""
Generate a wordcloud based on the counts for each Galaxy wrapper id
:param community_tool_stats: Dataframe that must
have the columns "Galaxy wrapper id" and "count"
:param mask_figure: a figure that is used to render the wordcloud
E.g. a nice shape to highlight your community
E.g. a nice shape to highlight your community
:param wordcloud_output_path: Path to store the wordcloud
"""


#create the word cloud
frec = pd.Series(community_tool_stats["count"].values,
# create the word cloud
frec = pd.Series(community_tool_stats["count"].values,
index=community_tool_stats["Galaxy wrapper id"]).to_dict()

mask = np.array(Image.open(args.wordcloud_mask))
mask[mask == 0] = 255 #set 0 in array to 255 to work with wordcloud
mask[mask == 0] = 255 # set 0 in array to 255 to work with wordcloud

wc = WordCloud(
mask = mask_figure,
background_color = "rgba(255, 255, 255, 0)",
random_state = 42,
)
mask=mask_figure,
background_color="rgba(255, 255, 255, 0)",
random_state=42,
)

wc.generate_from_frequencies(frec)

Expand All @@ -98,48 +105,60 @@ def get_wordcloud(community_tool_stats: pd.DataFrame,
plt.savefig(wordcloud_output_path)


if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Merge tools list with tool stats')
parser.add_argument('--tools',
'-t',
required=True,
help="Path to community tool list in csv format (must have column 'Galaxy wrapper id')")
parser.add_argument('--tool_stats',
'-ts',
required=True,
help="Path to tool stats list in csv format (must have column 'tool_name' and 'count')")
parser.add_argument('--wordcloud_mask',
'-wcm',
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Merge \
tools list with tool stats")
parser.add_argument(
"--tools",
"-t",
required=True,
help="Path to community tool list in csv format \
(must have column 'Galaxy wrapper id')",
)
parser.add_argument(
"--tool_stats",
"-ts",
required=True,
help="Path to tool stats list in csv format (must have \
column 'tool_name' and 'count')",
)
parser.add_argument("--wordcloud_mask",
"-wcm",
required=False,
help="Mask figure to generate the wordcloud")
parser.add_argument('--label',
'-la',
help="Label for the added column e.g. usegalaxy.eu tool usage")
parser.add_argument('--stats_output',
'-so',
required=True,
help="Output path to store the updated community list with stats")
parser.add_argument('--wc_output',
'-wco',
parser.add_argument("--label",
"-la",
help="Label for the added \
column e.g. usegalaxy.eu tool usage")
parser.add_argument(
"--stats_output",
"-so",
required=True,
help="Output path to store the updated community list with stats"
)
parser.add_argument("--wc_output",
"-wco",
required=False,
help="Output path to store the wordcloud.png")
parser.add_argument('--wordcloud',
'-wc',
action='store_true',
default=False,
help="Flag if wordcloud should be done")
parser.add_argument(
"--wordcloud",
"-wc",
action="store_true",
default=False,
help="Flag if wordcloud should be done"
)
args = parser.parse_args()

community_tool_stats = add_tool_stats_to_tools(args.tool_stats,
args.tools,
args.stats_output,
column_name=args.label,
)
community_tool_stats = add_tool_stats_to_tools(
args.tool_stats,
args.tools,
args.stats_output,
column_name=args.label,
)

if args.wordcloud:
get_wordcloud(community_tool_stats,
args.wordcloud_mask,
args.wc_output,
)


get_wordcloud(
community_tool_stats,
args.wordcloud_mask,
args.wc_output,
)

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