tasks: add BrefDOITable

1 files changed, 21 insertions, 0 deletions

diff --git a/python/refcat/tasks.py b/python/refcat/tasks.py
index 75a3daa..39d4486 100644
--- a/python/refcat/tasks.py
+++ b/python/refcat/tasks.py
@@ -438,6 +438,27 @@ class BrefWithDOI(Refcat):
         return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd)
 
 
+class BrefDOITable(Refcat):
+    """
+    Extract a table with source ident, target ident, source doi, target doi.
+    """
+    def requires(self):
+        return BrefWithDOI()
+
+    def run(self):
+        output = shellout("""
+                          zstdcat -T0 {input} |
+                          parallel --block 10M -j 20 --pipe
+                              "jq -rc '[.source_release_ident, .target_release_ident, .source_doi, .target_doi] | @tsv'
+                          | zstd -c -T0 > {output}
+                          """,
+                          input=self.input().path)
+        luigi.LocalTarget(output).move(self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(path=self.path(ext="tsv.zst"))
+
+
 class UnmatchedRefs(Refcat):
     """
     File with not yet considered refs (e.g. no title, doi, ...); around