Upgrade curies pkg and use new passthrough option

Closes #173
nfdi4cat · Oct 30, 2023 · 0456057 · 0456057
1 parent eca38e3
commit 0456057
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Showing 2 changed files with 27 additions and 18 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -37,7 +37,7 @@ classifiers = [
 
 dependencies = [
   "base32-crockford >= 0.3.0",
-  "curies >= 0.5.6",
+  "curies >= 0.6.6",
   "networkx >= 2.8",
   "openpyxl >= 3.0.9",
   "ontospy >= 2.1.0",

diff --git a/src/voc4cat/models.py b/src/voc4cat/models.py
@@ -233,7 +233,7 @@ def to_graph(self):
 
     def to_excel(self, wb: Workbook):
         ws = wb["Concept Scheme"]
-        ws["B2"] = config.curies_converter.compress(self.uri) or self.uri
+        ws["B2"] = config.curies_converter.compress(self.uri, passthrough=True)
         ws["B3"] = self.title
         ws["B4"] = self.description
         ws["B5"] = self.created.isoformat()
@@ -365,8 +365,8 @@ def to_excel(self, wb: Workbook, row_no_features: int, row_no_concepts: int):
 
         first_row_exported = False
         for lang in chain(fully_translated, partially_translated):
-            ws[f"A{row_no_concepts}"] = (
-                config.curies_converter.compress(self.uri) or self.uri
+            ws[f"A{row_no_concepts}"] = config.curies_converter.compress(
+                self.uri, passthrough=True
             )
             ws[f"B{row_no_concepts}"] = pref_labels.get(lang, "")
             ws[f"C{row_no_concepts}"] = lang
@@ -382,45 +382,51 @@ def to_excel(self, wb: Workbook, row_no_features: int, row_no_concepts: int):
             ws[f"F{row_no_concepts}"] = ",\n".join(self.alt_labels)
             ws[f"G{row_no_concepts}"] = ",\n".join(
                 [
-                    (config.curies_converter.compress(uri) or uri)
+                    config.curies_converter.compress(uri, passthrough=True)
                     for uri in self.children
                 ]
             )
             ws[f"I{row_no_concepts}"] = (
-                (
-                    config.curies_converter.compress(self.source_vocab)
-                    or self.source_vocab
-                )
+                config.curies_converter.compress(self.source_vocab, passthrough=True)
                 if self.source_vocab
                 else None
             )
             row_no_concepts += 1
 
         ws = wb["Additional Concept Features"]
 
-        ws[f"A{row_no_features}"] = (
-            config.curies_converter.compress(self.uri) or self.uri
+        ws[f"A{row_no_features}"] = config.curies_converter.compress(
+            self.uri, passthrough=True
         )
         ws[f"B{row_no_features}"] = ",\n".join(
             [
-                (config.curies_converter.compress(uri) or uri)
+                config.curies_converter.compress(uri, passthrough=True)
                 for uri in self.related_match
             ]
         )
         ws[f"C{row_no_features}"] = ",\n".join(
-            [(config.curies_converter.compress(uri) or uri) for uri in self.close_match]
+            [
+                config.curies_converter.compress(uri, passthrough=True)
+                for uri in self.close_match
+            ]
         )
         ws[f"D{row_no_features}"] = ",\n".join(
-            [(config.curies_converter.compress(uri) or uri) for uri in self.exact_match]
+            [
+                config.curies_converter.compress(uri, passthrough=True)
+                for uri in self.exact_match
+            ]
         )
         ws[f"E{row_no_features}"] = ",\n".join(
             [
-                (config.curies_converter.compress(uri) or uri)
+                config.curies_converter.compress(uri, passthrough=True)
                 for uri in self.narrow_match
             ]
         )
         ws[f"F{row_no_features}"] = ",\n".join(
-            [(config.curies_converter.compress(uri) or uri) for uri in self.broad_match]
+            [
+                config.curies_converter.compress(uri, passthrough=True)
+                for uri in self.broad_match
+            ]
         )
 
         return row_no_concepts
@@ -461,11 +467,14 @@ def to_graph(self):
 
     def to_excel(self, wb: Workbook, row_no: int):
         ws = wb["Collections"]
-        ws[f"A{row_no}"] = config.curies_converter.compress(self.uri) or self.uri
+        ws[f"A{row_no}"] = config.curies_converter.compress(self.uri, passthrough=True)
         ws[f"B{row_no}"] = self.pref_label
         ws[f"C{row_no}"] = self.definition
         ws[f"D{row_no}"] = ",\n".join(
-            [(config.curies_converter.compress(uri) or uri) for uri in self.members]
+            [
+                config.curies_converter.compress(uri, passthrough=True)
+                for uri in self.members
+            ]
         )
         ws[f"E{row_no}"] = self.provenance