Include externals

src/spyglass/common/common_usage.py

@@ -144,6 +144,22 @@ def stop_export(self, **kwargs) -> None:
     #       before actually exporting anything, which is more associated with
     #       Selection
 
+    def _list_raw_files(self, key: dict) -> list[str]:
+        """Return a list of unique nwb file names for a given restriction/key."""
+        file_table = self * self.File & key
+        return list(
+            {
+                *AnalysisNwbfile.join(file_table, log_export=False).fetch(
+                    "nwb_file_name"
+                )
+            }
+        )
+
+    def _list_analysis_files(self, key: dict) -> list[str]:
+        """Return a list of unique analysis file names for a given restriction/key."""
+        file_table = self * self.File & key
+        return list(file_table.fetch("analysis_file_name"))
+
     def list_file_paths(self, key: dict, as_dict=True) -> list[str]:
         """Return a list of unique file paths for a given restriction/key.
 
@@ -159,18 +175,60 @@ def list_file_paths(self, key: dict, as_dict=True) -> list[str]:
             If False, returns a list of strings without key.
         """
         file_table = self * self.File & key
-        analysis_fp = [
-            AnalysisNwbfile().get_abs_path(fname)
-            for fname in file_table.fetch("analysis_file_name")
-        ]
-        nwbfile_fp = [
-            Nwbfile().get_abs_path(fname)
-            for fname in AnalysisNwbfile.join(
-                file_table, log_export=False
-            ).fetch("nwb_file_name")
-        ]
-        unique_ft = list({*analysis_fp, *nwbfile_fp})
-        return [{"file_path": p} for p in unique_ft] if as_dict else unique_ft
+        unique_fp = {
+            *[
+                AnalysisNwbfile().get_abs_path(p)
+                for p in self._list_analysis_files(key)
+            ],
+            *[Nwbfile().get_abs_path(p) for p in self._list_raw_files(key)],
+        }
+
+        return [{"file_path": p} for p in unique_fp] if as_dict else unique_fp
+
+    @property
+    def _externals(self) -> dj.external.ExternalMapping:
+        """Return the external mapping for the common_n schema."""
+        return dj.external.ExternalMapping(schema=AnalysisNwbfile)
+
+    def _add_externals_to_restr_graph(
+        self, restr_graph: RestrGraph, key: dict
+    ) -> RestrGraph:
+        """Add external tables to a RestrGraph for a given restriction/key.
+
+        Tables added as nodes with restrictions based on file paths. Names
+        added to visited set to appear in restr_ft obj bassed to SQLDumpHelper.
+
+        Parameters
+        ----------
+        restr_graph : RestrGraph
+            A RestrGraph object to add external tables to.
+        key : dict
+            Any valid restriction key for ExportSelection.Table
+
+        Returns
+        -------
+        restr_graph : RestrGraph
+            The updated RestrGraph
+        """
+        raw_tbl = self._externals["raw"]
+        raw_name = raw_tbl.full_table_name
+        raw_restr = (
+            "filepath in ('" + "','".join(self._list_raw_files(key)) + "')"
+        )
+        restr_graph.graph.add_node(raw_name, ft=raw_tbl, restr=raw_restr)
+
+        analysis_tbl = self._externals["analysis"]
+        analysis_name = analysis_tbl.full_table_name
+        analysis_restr = (  # filepaths have analysis subdir. regexp substrings
+            "filepath REGEXP '" + "|".join(self._list_analysis_files(key)) + "'"
+        )  # regexp is slow, but we're only doing this once, and future-proof
+        restr_graph.graph.add_node(
+            analysis_name, ft=analysis_tbl, restr=analysis_restr
+        )
+
+        restr_graph.visited.update({raw_name, analysis_name})
+
+        return restr_graph
 
     def get_restr_graph(
         self, key: dict, verbose=False, cascade=True
@@ -193,9 +251,11 @@ def get_restr_graph(
                 "table_name", "restriction", as_dict=True
             )
         )
-        return RestrGraph(
+
+        restr_graph = RestrGraph(
             seed_table=self, leaves=leaves, verbose=verbose, cascade=cascade
         )
+        return self._add_externals_to_restr_graph(restr_graph, key)
 
     def preview_tables(self, **kwargs) -> list[dj.FreeTable]:
         """Return a list of restricted FreeTables for a given restriction/key.

src/spyglass/utils/dj_graph.py

@@ -808,13 +808,14 @@ def file_paths(self) -> List[str]:
         directly by the user.
         """
         self.cascade()
-        return [
-            self.analysis_file_tbl.get_abs_path(file)
-            for file in set(
-                [f for files in self.file_dict.values() for f in files]
-            )
-            if file is not None
-        ]
+
+        files = {
+            file
+            for table in self.visited
+            for file in self._get_node(table).get("files", [])
+        }
+
+        return [self.analysis_file_tbl.get_abs_path(file) for file in files]
 
 
 class TableChain(RestrGraph):

src/spyglass/utils/mixins/export.py

@@ -319,7 +319,9 @@ def restrict(self, restriction):
             return super().restrict(restriction)
         log_export = "fetch_nwb" not in self._called_funcs()
         return self._run_with_log(
-            super().restrict, restriction=dj.AndList([restriction, self.restriction]), log_export=log_export
+            super().restrict,
+            restriction=dj.AndList([restriction, self.restriction]),
+            log_export=log_export,
         )
 
     def join(self, other, log_export=True, *args, **kwargs):