fix(docs): remove efo code references (#636)

close #630

Author: korikuzma

docs/hgvs_dup_del_mode.md

@@ -9,7 +9,7 @@ The mode can be set to `default`, `copy_number_count`, `copy_number_change`, or
 - if baseline_copies is not set and endpoints are ambiguous:
     - copy_number_change
     - if copy_change not provided:
-        - copy_change = `efo:0030067` (loss) if del, `efo:0030070` (gain) if dup
+        - copy_change = "loss" if del, "gain" if dup
 - elif baseline_copies is provided:
     - copy_number_count
     - copies are baseline_copies + 1 for dup, baseline_copies - 1 for del

src/variation/hgvs_dup_del_mode.py

@@ -57,7 +57,7 @@ def default_mode(
         """Use default characteristics to return a variation.
         If baseline_copies not provided and endpoints are ambiguous - copy_number_change
             if copy_change not provided:
-                copy_change - `efo:0030067` (loss) if del, `efo:0030070` (gain) if dup
+                copy_change - "loss" if del, "gain" if dup
         elif baseline_copies provided: copy_number_count
             copies are baseline + 1 for dup, baseline - 1 for del
         else

src/variation/schemas/copy_number_schema.py

@@ -307,7 +307,7 @@ def validate_fields(cls, v: dict) -> dict:
                 "accession": None,
                 "start0": 10001,
                 "end0": 1223133,
-                "copy_change": "efo:0030069",
+                "copy_change": "complete genomic loss",
                 "start_pos_type": "number",
                 "end_pos_type": "number",
                 "start1": None,

tests/to_copy_number_variation/test_hgvs_to_copy_number.py

@@ -1213,8 +1213,6 @@ async def test_invalid_cnv(test_cnv_handler):
         "NC_000018.9:g.(48556994_48573289)_48573471dup",
         "NC_000018.9:g.48556994_(48573289_48573471)dup",
     ]:
-        resp = await test_cnv_handler.hgvs_to_copy_number_change(
-            q, copy_change="efo:0030070"
-        )
+        resp = await test_cnv_handler.hgvs_to_copy_number_change(q, copy_change="gain")
         assert resp.warnings == [f"Unable to find classification for: {q}"], q
         assert resp.copy_number_change is None, q