tasks: add BrefWithDOI

1 files changed, 27 insertions, 1 deletions

diff --git a/python/refcat/tasks.py b/python/refcat/tasks.py
index f4aacb1..8dcc676 100644
--- a/python/refcat/tasks.py
+++ b/python/refcat/tasks.py
@@ -398,7 +398,7 @@ class ReleaseIdentDOIList(Refcat):
 
 class ReleaseIdentDOIMapping(Refcat):
     """
-    Create a mapping database from release ident to DOI.
+    Create a mapping database from release ident to DOI. 21min.
     """
     def requires(self):
         return ReleaseIdentDOIList()
@@ -411,6 +411,32 @@ class ReleaseIdentDOIMapping(Refcat):
         return luigi.LocalTarget(path=self.path(ext="db"))
 
 
+class BrefWithDOI(Refcat):
+    """
+    Take the paper matches and add source and target DOI.
+    """
+    def requires(self):
+        return {
+            "bref": Bref(),
+            "mapping": ReleaseIdentDOIMapping(),
+        }
+
+    def run(self):
+        output = shellout("""
+                          zstdcat {bref} |
+                          tabby -A -db {mapping}
+                              -m source_release_ident:source_doi
+                              -m target_release_ident:target_doi
+                          | zstd -c -T0 > {output}
+                          """,
+                          bref=self.input().get("bref"),
+                          mapping=self.input().get("mapping"))
+        luigi.LocalTarget(output).move(self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd)
+
+
 class UnmatchedRefs(Refcat):
     """
     File with not yet considered refs (e.g. no title, doi, ...); around