improved id generation

src/pyphetools/__init__.py

@@ -4,7 +4,7 @@
 from . import visualization
 from . import validation
 
-__version__ = "0.9.80"
+__version__ = "0.9.81"
 
 __all__ = [
     "creation",

src/pyphetools/creation/individual.py

@@ -219,7 +219,11 @@ def get_phenopacket_id(self, phenopacket_id=None) -> str:
                 ppkt_id = indi_id
         else:
             ppkt_id = phenopacket_id
-        ppkt_id = ppkt_id.replace(" ", "_")
+        # strip non alphanumeric characters
+        ppkt_id = ''.join(e if e.isalnum()  else "_" for e in ppkt_id)
+        ppkt_id = ppkt_id.replace("__", "_")
+        if ppkt_id.endswith("_"):
+            ppkt_id = ppkt_id[:-1]
         return ppkt_id
 
     def get_citation(self) -> Citation:

test/test_individual.py

@@ -0,0 +1,58 @@
+import hpotk
+import pytest
+
+from pyphetools.creation import Citation, Disease,Individual, HpTerm
+
+
+
+# The API requires us to pass a column name but the column name will not be used in the tests
+TEST_COLUMN = "test"
+
+
+class TestIndividual:
+
+    @pytest.fixture
+    def ind_a(self) -> Individual:
+        cite = Citation(pmid="PMID:1234", title="some title")
+        i = Individual(individual_id="Individual A (from previous publication)", citation=cite)
+        i.add_hpo_term(HpTerm(hpo_id="HP:0000490", label="Deeply set eye"))
+        i.set_disease(disease=Disease(disease_id="OMIM:123456", disease_label="label"))
+        return i
+
+    @pytest.fixture
+    def ind_b(self) -> Individual:
+        cite = Citation(pmid="PMID:36446582", title="some title")
+        i = Individual(individual_id="Alves, 2019", citation=cite)
+        i.add_hpo_term(HpTerm(hpo_id="HP:0000490", label="Deeply set eye"))
+        i.set_disease(disease=Disease(disease_id="OMIM:123456", disease_label="label"))
+        return i
+
+    @pytest.fixture
+    def ind_c(self) -> Individual:
+        cite = Citation(pmid="PMID:36446582", title="some title")
+        i = Individual(individual_id="Low, 2016_P17 (10)", citation=cite)
+        i.add_hpo_term(HpTerm(hpo_id="HP:0000490", label="Deeply set eye"))
+        i.set_disease(disease=Disease(disease_id="OMIM:123456", disease_label="label"))
+        return i
+
+
+
+
+    def test_phenopacket_identifier(
+            self,
+            ind_a: Individual,
+    ):
+        phenopacket_id = ind_a.get_phenopacket_id()
+        expected = "PMID_1234_Individual_A_from_previous_publication"
+        assert expected == phenopacket_id
+
+
+    def test_phenopacket_id_B(self, ind_b: Individual):
+        phenopacket_id = ind_b.get_phenopacket_id()
+        expected = "PMID_36446582_Alves_2019"
+        assert expected == phenopacket_id
+
+    def test_phenopacket_id_C(self, ind_c: Individual):
+        phenopacket_id = ind_c.get_phenopacket_id()
+        expected = "PMID_36446582_Low_2016_P17_10"
+        assert expected == phenopacket_id