fixed dm

PyEED · Jun 11, 2024 · 3f48fd3 · 3f48fd3
1 parent b29f919
commit 3f48fd3
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Showing 19 changed files with 150 additions and 130 deletions.
diff --git a/graph-network/graph-network/populate.ipynb b/graph-network/graph-network/populate.ipynb
diff --git a/pyeed/core/abstractannotation.py b/pyeed/core/abstractannotation.py
@@ -47,11 +47,6 @@ class AbstractAnnotation(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/alignmentresult.py b/pyeed/core/alignmentresult.py
@@ -59,11 +59,6 @@ class AlignmentResult(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/blastdata.py b/pyeed/core/blastdata.py
@@ -88,11 +88,6 @@ class BlastData(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/clustalomegaresult.py b/pyeed/core/clustalomegaresult.py
@@ -1,16 +1,17 @@
 from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .alignmentresult import AlignmentResult
+
 
 class ClustalOmegaResult(
-    sdRDM.DataModel,
+    AlignmentResult,
     search_mode="unordered",
 ):
     """"""
@@ -29,11 +30,6 @@ class ClustalOmegaResult(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/dnarecord.py b/pyeed/core/dnarecord.py
@@ -1,16 +1,17 @@
-from typing import Dict, Optional, Set
+from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .sequencerecord import SequenceRecord
+
 
 class DNARecord(
-    sdRDM.DataModel,
+    SequenceRecord,
     search_mode="unordered",
 ):
     """A nucleic acid sequence and associated metadata 🧬"""
@@ -29,15 +30,6 @@ class DNARecord(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/SIO_010008"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/numberedsequence.py b/pyeed/core/numberedsequence.py
@@ -38,11 +38,6 @@ class NumberedSequence(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/organism.py b/pyeed/core/organism.py
@@ -106,11 +106,6 @@ class Organism(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/pairwisealignmentresult.py b/pyeed/core/pairwisealignmentresult.py
@@ -1,16 +1,17 @@
 from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .alignmentresult import AlignmentResult
+
 
 class PairwiseAlignmentResult(
-    sdRDM.DataModel,
+    AlignmentResult,
     search_mode="unordered",
 ):
     """"""
@@ -57,11 +58,6 @@ class PairwiseAlignmentResult(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/proteinrecord.py b/pyeed/core/proteinrecord.py
@@ -1,11 +1,10 @@
 import asyncio
 import warnings
 from concurrent.futures import ThreadPoolExecutor
-from typing import Dict, List, Optional, Set
+from typing import Dict, List, Optional
 from uuid import uuid4
 
 import nest_asyncio
-import sdRDM
 from Bio.Blast import NCBIXML
 from IPython.display import clear_output
 from lxml.etree import _Element
@@ -21,10 +20,11 @@
 
 from .dnarecord import DNARecord
 from .region import Region
+from .sequencerecord import SequenceRecord
 
 
 class ProteinRecord(
-    sdRDM.DataModel,
+    SequenceRecord,
     search_mode="unordered",
 ):
     """A protein sequence and associated metadata."""
@@ -73,15 +73,6 @@ class ProteinRecord(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/SIO_010043"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
@@ -100,6 +91,9 @@ def add_to_coding_sequence(
         self,
         start: Optional[int] = None,
         end: Optional[int] = None,
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Region:
@@ -110,11 +104,17 @@ def add_to_coding_sequence(
             id (str): Unique identifier of the 'Region' object. Defaults to 'None'.
             start (): Start position of the site.. Defaults to None
             end (): End position of the site.. Defaults to None
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "start": start,
             "end": end,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:

diff --git a/pyeed/core/region.py b/pyeed/core/region.py
@@ -1,16 +1,17 @@
-from typing import Dict, Optional, Set
+from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .abstractannotation import AbstractAnnotation
+
 
 class Region(
-    sdRDM.DataModel,
+    AbstractAnnotation,
     search_mode="unordered",
 ):
     """Regional annotation of a feature within a sequence. The direction of the region is defined by the start and end positions."""
@@ -40,15 +41,6 @@ class Region(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/SIO_000370"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/regionset.py b/pyeed/core/regionset.py
@@ -33,11 +33,6 @@ class RegionSet(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _object_terms: Set[str] = PrivateAttr(
         default={"http://semanticscience.org/resource/SIO_000370"}
     )
@@ -60,6 +55,9 @@ def add_to_regions(
         self,
         start: Optional[int] = None,
         end: Optional[int] = None,
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Region:
@@ -70,11 +68,17 @@ def add_to_regions(
             id (str): Unique identifier of the 'Region' object. Defaults to 'None'.
             start (): Start position of the site.. Defaults to None
             end (): End position of the site.. Defaults to None
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "start": start,
             "end": end,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:

diff --git a/pyeed/core/sequence.py b/pyeed/core/sequence.py
@@ -36,11 +36,6 @@ class Sequence(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/pyeed/core/sequencerecord.py b/pyeed/core/sequencerecord.py
@@ -101,11 +101,6 @@ class SequenceRecord(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
@@ -123,6 +118,9 @@ def _parse_raw_xml_data(self):
     def add_to_sites(
         self,
         positions: List[int] = ListPlus(),
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Site:
@@ -132,10 +130,16 @@ def add_to_sites(
         Args:
             id (str): Unique identifier of the 'Site' object. Defaults to 'None'.
             positions (): Position of the site(s) within the sequence.. Defaults to ListPlus()
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "positions": positions,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:
@@ -151,6 +155,9 @@ def add_to_regions(
         self,
         start: Optional[int] = None,
         end: Optional[int] = None,
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Region:
@@ -161,11 +168,17 @@ def add_to_regions(
             id (str): Unique identifier of the 'Region' object. Defaults to 'None'.
             start (): Start position of the site.. Defaults to None
             end (): End position of the site.. Defaults to None
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "start": start,
             "end": end,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None: