compare tool_ids

bin/extract_galaxy_tools.py

@@ -47,15 +47,15 @@
 
 def get_last_url_position(toot_id: str) -> str:
     """
-    Returns the second last url position of the toot_id, if the value is not a
+    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
     """
 
     if "/" in toot_id:
-        toot_id = toot_id.split("/")[-2]
+        toot_id = toot_id.split("/")[-1]
     return toot_id
 
 
@@ -69,7 +69,6 @@ def add_tool_stats_to_tools(tools_df: pd.DataFrame, tool_stats_path: Path, colum
     :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
     """
@@ -81,13 +80,31 @@ def add_tool_stats_to_tools(tools_df: pd.DataFrame, tool_stats_path: Path, colum
     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()
+    # also group tools with different versions
+    grouped_tool_stats_tools = tool_stats_df.groupby("Galaxy wrapper id")["count"].sum()
+
+    # new column to store the stats
+    tools_df[column_name] = np.NaN
+
+    # check for each tool_id if a count exists in the stats file
+    # and sum the stats for each suite
+    for row_index, row in tools_df.iterrows():
+        counts = []
+        if isinstance(row["Galaxy tool ids"], str):
+            for tool_id in row["Galaxy tool ids"].split(","):
+                tool_id = tool_id.strip()
+                if tool_id in grouped_tool_stats_tools:
+                    count = grouped_tool_stats_tools[tool_id]
+                    counts.append(count)
+
+            if len(counts) == 0:
+                summed_count = np.NaN
+            else:
+                summed_count = sum(counts)
 
-    # keep all rows of the tools table (how='right'), also for those where no stats are available
-    community_tool_stats = pd.merge(grouped_tool_stats_tools, tools_df, how="right", on="Galaxy wrapper id")
-    community_tool_stats.rename(columns={"count": column_name}, inplace=True)
+            tools_df.loc[row_index, column_name] = summed_count
 
-    return community_tool_stats
+    return tools_df
 
 
 def add_usage_stats_for_all_server(tools_df: pd.DataFrame) -> pd.DataFrame:
@@ -206,7 +223,7 @@ def get_xref(el: et.Element, attrib_type: str) -> Optional[str]:
         for xref in xref_items:
             if xref is not None and xref.attrib["type"] == attrib_type:
                 # should not contain any space of linebreak
-                xref_sanitized = str(xref.text).strip()
+                xref_sanitized = str(xref.text).replace("\n", "").replace(" ", "")
                 return xref_sanitized
     return None