Removed attribute for all objects. Updated tests.

Author: sbooeshaghi

seqspec/Assay.py

@@ -14,9 +14,6 @@ class SeqProtocol(BaseModel):
     name: str
     modality: str
 
-    def to_dict(self):
-        return self.model_dump()
-
     def update_from(self, patch: Union["SeqProtocol", "SeqProtocolInput"]) -> None:
         if isinstance(patch, SeqProtocolInput):
             for field in patch.model_fields_set:
@@ -68,9 +65,6 @@ class SeqKit(BaseModel):
     name: Optional[str]
     modality: str
 
-    def to_dict(self):
-        return self.model_dump()
-
     def update_from(self, patch: Union["SeqKit", "SeqKitInput"]) -> None:
         if isinstance(patch, SeqKitInput):
             for field in patch.model_fields_set:
@@ -118,9 +112,6 @@ class LibProtocol(BaseModel):
     name: str
     modality: str
 
-    def to_dict(self):
-        return self.model_dump()
-
     def update_from(self, patch: Union["LibProtocol", "LibProtocolInput"]) -> None:
         if isinstance(patch, LibProtocolInput):
             for field in patch.model_fields_set:
@@ -170,9 +161,6 @@ class LibKit(BaseModel):
     name: Optional[str]
     modality: str
 
-    def to_dict(self):
-        return self.model_dump()
-
     def update_from(self, patch: Union["LibKit", "LibKitInput"]) -> None:
         if isinstance(patch, LibKitInput):
             for field in patch.model_fields_set:
@@ -254,15 +242,8 @@ def __repr__(self) -> str:
 Regions:
 {"\n".join(rgns)}
 """
-        # return str(self.model_dump())
         return s
 
-    def to_dict(self):
-        return self.model_dump()
-
-    def to_JSON(self):
-        return self.model_dump_json(indent=4)
-
     def to_YAML(self, fname: Optional[str] = None):
         yaml_str = yaml.dump(self.model_dump(), sort_keys=False)
         if fname is None:

seqspec/File.py

@@ -17,9 +17,6 @@ def __repr__(self) -> str:
         s = f"""{self.file_id}"""
         return s
 
-    def to_dict(self):
-        return self.model_dump()
-
     def update_file_id(self, file_id: str):
         self.file_id = file_id
 

seqspec/Read.py

@@ -25,9 +25,6 @@ def __repr__(self) -> str:
         # return str(self.model_dump())
         return s
 
-    def to_dict(self):
-        return self.model_dump()
-
     def update_read_by_id(
         self,
         read_id=None,

seqspec/Region.py

@@ -208,8 +208,6 @@ def get_onlist(self) -> Optional[Onlist]:
         """Get the onlist associated with this region."""
         return self.onlist
 
-    # update_from removed per new approach
-
     def get_leaves(self, leaves: Optional[List["Region"]] = None) -> List["Region"]:
         # print(leaves)
         if leaves is None:

seqspec/seqspec_check.py

@@ -144,7 +144,7 @@ def check_schema(spec: Assay, errors=[], idx=0):
         with open(schema_fn, "r") as stream:
             schema = yaml.load(stream, Loader=yaml.Loader)
         validator = Draft4Validator(schema)
-        for idx, error in enumerate(validator.iter_errors(spec.to_dict()), 1):
+        for idx, error in enumerate(validator.iter_errors(spec.model_dump()), 1):
             err_elements = [repr(index) for index in error.path]
             err_path = f"spec[{']['.join(err_elements)}]"
             errobj = {

seqspec/seqspec_convert.py

@@ -179,7 +179,7 @@ def seqspec_to_token(spec):
     specs_regions = {}
     modalities = spec.list_modalities()
     for modality in modalities:
-        regions = [i.to_dict() for i in spec.get_libspec(modality).get_leaves()]
+        regions = [i.model_dump() for i in spec.get_libspec(modality).get_leaves()]
         specs_regions[modality] = regions
 
     # Convert to tokenized matrix

seqspec/seqspec_file.py

@@ -270,7 +270,7 @@ def format_json_files(
     for items in zip(*files.values()):
         if k == "all":
             for key, item in zip(files.keys(), items):
-                d = item.to_dict()
+                d = item.model_dump()
                 if item.urltype == "local" and fp:
                     d["url"] = str(spec_fn.parent / d["url"])
                 x.append(d)

seqspec/seqspec_info.py

@@ -152,7 +152,7 @@ def seqspec_info_meta(spec: Assay) -> Dict:
     Returns:
         Dictionary containing meta information
     """
-    sd = spec.to_dict()
+    sd = spec.model_dump()
     del sd["library_spec"]
     del sd["sequence_spec"]
     del sd["modalities"]
@@ -173,7 +173,8 @@ def seqspec_info_library_spec(spec: Assay) -> Dict:
     for m in modalities:
         libspec = spec.get_libspec(m)
         leaves = libspec.get_leaves()
-        result[m] = leaves if leaves else []
+        r = leaves if leaves else []
+        result[m] = [i.model_dump() for i in r]
     return {"library_spec": result}
 
 

tests/test_assay.py

@@ -50,15 +50,6 @@ def test_get_read(dogmaseq_dig_spec):
     with pytest.raises(IndexError):
         dogmaseq_dig_spec.get_read("non_existent_read")
 
-def test_to_json(dogmaseq_dig_spec):
-    """
-    Test to_JSON method
-    """
-    json_output = dogmaseq_dig_spec.to_JSON()
-    assert isinstance(json_output, str)
-    data = json.loads(json_output)
-    assert data["assay_id"] == "DOGMAseq-DIG"
-
 
 def test_insert_regions(temp_spec):
     """

tests/test_read.py

@@ -86,28 +86,6 @@ def test_read_set_files():
     assert len(read.files) == 1
     assert read.files[0].file_id == "file1"
 
-def test_read_to_dict():
-    """Test to_dict method"""
-    read = Read(
-        read_id="test_read",
-        name="Test Read",
-        modality="RNA",
-        primer_id="test_primer",
-        min_len=100,
-        max_len=150,
-        strand="pos"
-    )
-    
-    read_dict = read.to_dict()
-    assert read_dict["read_id"] == "test_read"
-    assert read_dict["name"] == "Test Read"
-    assert read_dict["modality"] == "RNA"
-    assert read_dict["primer_id"] == "test_primer"
-    assert read_dict["min_len"] == 100
-    assert read_dict["max_len"] == 150
-    assert read_dict["strand"] == "pos"
-    assert read_dict["files"] == []
-
 def test_read_update_read_by_id():
     """Test update_read_by_id method"""
     read = Read(
@@ -275,26 +253,6 @@ def test_file_creation():
     assert file_obj.urltype == "local"
     assert file_obj.md5 == "d41d8cd98f00b204e9800998ecf8427e"
 
-def test_file_to_dict():
-    """Test File to_dict method"""
-    file_obj = File(
-        file_id="file1",
-        filename="read1.fastq.gz",
-        filetype="fastq",
-        filesize=1000000,
-        url="file://read1.fastq.gz",
-        urltype="local",
-        md5="d41d8cd98f00b204e9800998ecf8427e"
-    )
-    
-    file_dict = file_obj.to_dict()
-    assert file_dict["file_id"] == "file1"
-    assert file_dict["filename"] == "read1.fastq.gz"
-    assert file_dict["filetype"] == "fastq"
-    assert file_dict["filesize"] == 1000000
-    assert file_dict["url"] == "file://read1.fastq.gz"
-    assert file_dict["urltype"] == "local"
-    assert file_dict["md5"] == "d41d8cd98f00b204e9800998ecf8427e"