From 5923185345449f89281f6d5208e6f09dc29b41b9 Mon Sep 17 00:00:00 2001
From: Martin Czygan <martin.czygan@gmail.com>
Date: Wed, 12 May 2021 00:14:00 +0200
Subject: tasks: move id extraction to skate-map

---
 python/refcat/tasks.py | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/python/refcat/tasks.py b/python/refcat/tasks.py
index 868a755..4f7c138 100644
--- a/python/refcat/tasks.py
+++ b/python/refcat/tasks.py
@@ -342,3 +342,72 @@ class RefsDOI(Refcat):
 
     def output(self):
         return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd)
+
+
+class RefsPMID(Refcat):
+    """
+    Sorted (pmid, doc) tuples from refs; PMID is an integer.
+    """
+    def requires(self):
+        return RefsWithUnstructured()
+
+    def run(self):
+        output = shellout("""
+                          zstdcat -T0 {input} |
+                          skate-map -m ff -x biblio.pmid -skip-on-empty 1 |
+                          LC_ALL=C sort -T {tmpdir} -k1,1 -S25% --parallel 4 |
+                          zstd -T0 -c > {output}
+                          """,
+                          n=self.n,
+                          tmpdir=self.tmpdir,
+                          input=self.input().path)
+        luigi.LocalTarget(output).move(self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd)
+
+
+class RefsPMCID(Refcat):
+    """
+    Sorted (pmcid, doc) tuples from refs, e.g. PMC2860560, ...
+    """
+    def requires(self):
+        return RefsWithUnstructured()
+
+    def run(self):
+        output = shellout("""
+                          zstdcat -T0 {input} |
+                          skate-map -m ff -x biblio.pmcid -skip-on-empty 1 |
+                          LC_ALL=C sort -T {tmpdir} -k1,1 -S25% --parallel 4 |
+                          zstd -T0 -c > {output}
+                          """,
+                          n=self.n,
+                          tmpdir=self.tmpdir,
+                          input=self.input().path)
+        luigi.LocalTarget(output).move(self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd)
+
+
+class RefsArxiv(Refcat):
+    """
+    Sorted (arxiv, doc) tuples from refs, e.g. 1802.3912, ...
+    """
+    def requires(self):
+        return RefsWithUnstructured()
+
+    def run(self):
+        output = shellout("""
+                          zstdcat -T0 {input} |
+                          skate-map -m ff -x biblio.arxiv_id -skip-on-empty 1 |
+                          LC_ALL=C sort -T {tmpdir} -k1,1 -S25% --parallel 4 |
+                          zstd -T0 -c > {output}
+                          """,
+                          n=self.n,
+                          tmpdir=self.tmpdir,
+                          input=self.input().path)
+        luigi.LocalTarget(output).move(self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd)
-- 
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