From 4617afc4cb405d2d81301b31e0e3ce6a31c6ae97 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 10 Jan 2024 15:58:33 +0100 Subject: [PATCH] only use usegalaxy atm --- bin/extract_galaxy_tools.py | 52 + .../tool_usage_per_user_2022_23_EU.csv | 3016 +++++++++++++++++ 2 files changed, 3068 insertions(+) create mode 100644 data/usage_stats/tool_usage_per_user_2022_23_EU.csv diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py index c17676cc..61fb42a4 100644 --- a/bin/extract_galaxy_tools.py +++ b/bin/extract_galaxy_tools.py @@ -31,6 +31,56 @@ "https://usegalaxy.eu", ] +GALAXY_TOOL_STATS = {"https://usegalaxy.eu usage": "../data/usage_stats/tool_usage_per_user_2022_23_EU.csv"} + +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. + + :param tool_id: galaxy tool id + """ + + toot_id = toot_id.split("/")[-1] + return toot_id + + +def add_tool_stats_to_tools(tools_df: pd.DataFrame, tool_stats_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, + must include "tool_name" and "count") + :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, + different columns could be added for the main servers + """ + + # parse csvs + tool_stats_df = pd.read_csv(tool_stats_path) + + # extract tool id + 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() + + community_tool_stats = pd.merge(grouped_tool_stats_tools, tools_df, on="Galaxy wrapper id") + community_tool_stats.rename(columns={"count": column_name}, inplace=True) + + return community_tool_stats + + +def add_usage_stats_for_all_server(tools_df): + for column, path in GALAXY_TOOL_STATS.items(): + tools_df = add_tool_stats_to_tools(tools_df, path, column) + return tools_df + def read_file(filepath: Optional[str]) -> List[str]: """ @@ -453,6 +503,8 @@ def export_tools(tools: List[Dict], output_fp: str, format_list_col: bool = Fals df["Galaxy tool ids"] = format_list_column(df["Galaxy tool ids"]) df = add_instances_to_table(df) + df = add_usage_stats_for_all_server(df) + df.to_csv(output_fp, sep="\t", index=False) diff --git a/data/usage_stats/tool_usage_per_user_2022_23_EU.csv b/data/usage_stats/tool_usage_per_user_2022_23_EU.csv new file mode 100644 index 00000000..ab8d209a --- /dev/null +++ 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