Started on normalization

3 files changed, 57 insertions, 0 deletions

diff --git a/workflows/tools/normalize/README.md b/workflows/tools/normalize/README.md
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+# Normalization steps
+
+This library contains generic logic to normalize (string) data and
+transforms strings to URIs.  It should be applicable to data from
+any source (GenBank, ENA etc).
+
+Important: missing data should be missing or None! Do not fill
+in data by 'guessing'.
+
+When data is malformed a warning should be logged and added to the
+warning list. Functions should be small enough to return only 1
+warning!
+
+Pjotr Prins (c) 2021
diff --git a/workflows/tools/normalize/__init__.py b/workflows/tools/normalize/__init__.py
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+++ b/workflows/tools/normalize/__init__.py
diff --git a/workflows/tools/normalize/mapping.py b/workflows/tools/normalize/mapping.py
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+# Normalization steps
+#
+# This library contains generic logic to normalize (string) data and
+# transforms strings to URIs.  It should be applicable to data from
+# any source (GenBank, ENA etc).
+#
+#   Important: missing data should be missing or None! Do not fill
+#   in data by 'guessing'.
+#
+#   When data is malformed a warning should be logged and added to the
+#   warning list. Functions should be small enough to return only 1
+#   warning!
+#
+#   Pjotr Prins (c) 2021
+
+import types
+
+def host_species(host,mapping):
+    warning = None
+    host = types.SimpleNamespace(**host)
+    if not 'obolibrary' in host.host_species:
+        key = host.host_species
+        if key in mapping:
+            host.host_species = mapping[key]
+        else:
+            warning = f"No URI mapping for host_species <{key}>"
+    return host.__dict__,warning
+
+def specimen_source(sample,mapping):
+    warning = None
+    sample = types.SimpleNamespace(**sample)
+    try:
+        if sample.specimen_source and not 'obolibrary' in sample.specimen_source:
+            key = sample.specimen_source
+            if key in mapping:
+                sample.specimen_source = mapping[key]
+            else:
+                sample.specimen_source = None
+                warning = f"No URI mapping for specimen_source <{key}>"
+    except AttributeError:
+        pass
+    if not sample.specimen_source: del(sample.specimen_source)
+    return sample.__dict__,warning