Minor bug fix

NMRPy · Sep 25, 2023 · 1fcefb7 · 1fcefb7
1 parent e168661
commit 1fcefb7
Show file tree

Hide file tree

Showing 9 changed files with 33 additions and 166 deletions.
diff --git a/nmrpy/datamodel/core/__init__.py b/nmrpy/datamodel/core/__init__.py
@@ -10,16 +10,10 @@
 from .publication import Publication
 from .cv import CV
 from .term import Term
-from .vessel import Vessel
-from .abstractspecies import AbstractSpecies
-from .protein import Protein
-from .reactant import Reactant
 from .fileformats import FileFormats
 from .subjects import Subjects
 from .publicationtypes import PublicationTypes
 from .identifiertypes import IdentifierTypes
-from .sboterm import SBOTerm
-from .datatypes import DataTypes
 
 __doc__ = ""
 
@@ -36,14 +30,8 @@
     "Publication",
     "CV",
     "Term",
-    "Vessel",
-    "AbstractSpecies",
-    "Protein",
-    "Reactant",
     "FileFormats",
     "Subjects",
     "PublicationTypes",
     "IdentifierTypes",
-    "SBOTerm",
-    "DataTypes",
 ]
diff --git a/nmrpy/datamodel/core/citation.py b/nmrpy/datamodel/core/citation.py
@@ -5,15 +5,15 @@
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature, IDGenerator
 
-from typing import Any
 from pydantic import AnyUrl
+from typing import Any
 
-from .publication import Publication
 from .term import Term
-from .publicationtypes import PublicationTypes
+from .identifiertypes import IdentifierTypes
+from .publication import Publication
 from .subjects import Subjects
+from .publicationtypes import PublicationTypes
 from .person import Person
-from .identifiertypes import IdentifierTypes
 
 
 @forge_signature

diff --git a/nmrpy/datamodel/core/experiment.py b/nmrpy/datamodel/core/experiment.py
@@ -6,17 +6,18 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
+from .fidarray import FIDArray
+from .fid import FID
+from .parameters import Parameters
 from .processingsteps import ProcessingSteps
 from .identity import Identity
-from .parameters import Parameters
-from .fid import FID
-from .fidarray import FIDArray
 
 
 @forge_signature
 class Experiment(sdRDM.DataModel):
     """Rohdaten -> Zwischenschritte nur nennen + interessante Parameter -> Endergebnis; Peaklist + Rangelist; rapidly pulsed (if then +calibration factor) vs fully relaxed
-    Also preparation of EnzymeML doc"""
+    Also preparation of EnzymeML doc https://github.com/EnzymeML/enzymeml-specifications/@AbstractSpecies, https://github.com/EnzymeML/enzymeml-specifications/@Protein, https://github.com/EnzymeML/enzymeml-specifications/@Reactant
+    """
 
     id: Optional[str] = Field(
         description="Unique identifier of the given object.",
@@ -29,6 +30,12 @@ class Experiment(sdRDM.DataModel):
         description="A descriptive name for the overarching experiment.",
     )
 
+    enzymeml_species: List[str] = Field(
+        description="A species object from an EnzymeML document.",
+        default_factory=ListPlus,
+        multiple=True,
+    )
+
     fid: List[FID] = Field(
         description="A single NMR spectrum.",
         default_factory=ListPlus,

diff --git a/nmrpy/datamodel/core/fid.py b/nmrpy/datamodel/core/fid.py
@@ -7,12 +7,9 @@
 
 from pydantic.types import FrozenSet
 
+from .parameters import Parameters
 from .processingsteps import ProcessingSteps
-from .abstractspecies import AbstractSpecies
-from .protein import Protein
 from .identity import Identity
-from .parameters import Parameters
-from .reactant import Reactant
 
 
 @forge_signature
@@ -64,8 +61,8 @@ class FID(sdRDM.DataModel):
 
     def add_to_peak_identities(
         self,
-        name: str,
-        enzymeml_species: Union[AbstractSpecies, Protein, Reactant, None] = None,
+        name: Optional[str] = None,
+        species_id: Optional[str] = None,
         associated_peaks: List[float] = ListPlus(),
         associated_ranges: List[FrozenSet] = ListPlus(),
         associated_integrals: List[float] = ListPlus(),
@@ -76,16 +73,16 @@ def add_to_peak_identities(
 
         Args:
             id (str): Unique identifier of the 'Identity' object. Defaults to 'None'.
-            name (): Descriptive name for the species.
-            enzymeml_species (): A species object from an EnzymeML document.. Defaults to None
+            name (): Descriptive name for the species. Defaults to None
+            species_id (): ID of an EnzymeML species. Defaults to None
             associated_peaks (): Peaks belonging to the given species. Defaults to ListPlus()
             associated_ranges (): Sets of ranges belonging to the given peaks. Defaults to ListPlus()
             associated_integrals (): Integrals resulting from the given peaks and ranges of a species. Defaults to ListPlus()
         """
 
         params = {
             "name": name,
-            "enzymeml_species": enzymeml_species,
+            "species_id": species_id,
             "associated_peaks": associated_peaks,
             "associated_ranges": associated_ranges,
             "associated_integrals": associated_integrals,

diff --git a/nmrpy/datamodel/core/identity.py b/nmrpy/datamodel/core/identity.py
@@ -1,16 +1,12 @@
 import sdRDM
 
-from typing import Optional, Union, List
+from typing import List, Optional
 from pydantic import Field
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 from pydantic.types import FrozenSet
 
-from .abstractspecies import AbstractSpecies
-from .protein import Protein
-from .reactant import Reactant
-
 
 @forge_signature
 class Identity(sdRDM.DataModel):
@@ -22,14 +18,14 @@ class Identity(sdRDM.DataModel):
         xml="@id",
     )
 
-    name: str = Field(
-        ...,
+    name: Optional[str] = Field(
+        default=None,
         description="Descriptive name for the species",
     )
 
-    enzymeml_species: Union[AbstractSpecies, Protein, Reactant, None] = Field(
+    species_id: Optional[str] = Field(
         default=None,
-        description="A species object from an EnzymeML document.",
+        description="ID of an EnzymeML species",
     )
 
     associated_peaks: List[float] = Field(

diff --git a/nmrpy/datamodel/core/nmrpy.py b/nmrpy/datamodel/core/nmrpy.py
@@ -6,8 +6,8 @@
 
 from datetime import datetime as Datetime
 
-from .citation import Citation
 from .experiment import Experiment
+from .citation import Citation
 
 
 @forge_signature

diff --git a/nmrpy/datamodel/core/publication.py b/nmrpy/datamodel/core/publication.py
@@ -7,9 +7,9 @@
 
 from pydantic import AnyUrl
 
+from .identifiertypes import IdentifierTypes
 from .publicationtypes import PublicationTypes
 from .person import Person
-from .identifiertypes import IdentifierTypes
 
 
 @forge_signature

diff --git a/nmrpy/datamodel/schemes/datamodel_schema.md b/nmrpy/datamodel/schemes/datamodel_schema.md
@@ -1,56 +1,19 @@
 ```mermaid
 classDiagram
-    AbstractSpecies <-- Protein
-    AbstractSpecies <-- Complex
-    AbstractSpecies <-- Reactant
-    AbstractSpecies <-- Protein
-    AbstractSpecies <-- Reactant
-    EnzymeMLDocument *-- Creator
-    EnzymeMLDocument *-- Vessel
-    EnzymeMLDocument *-- Protein
-    EnzymeMLDocument *-- Complex
-    EnzymeMLDocument *-- Reactant
-    EnzymeMLDocument *-- Reaction
-    EnzymeMLDocument *-- KineticParameter
-    EnzymeMLDocument *-- Measurement
-    EnzymeMLDocument *-- File
-    AbstractSpecies *-- Vessel
-    Protein *-- SBOTerm
-    Complex *-- SBOTerm
-    Reactant *-- SBOTerm
-    Reaction *-- SBOTerm
-    Reaction *-- ReactionElement
-    Reaction *-- KineticModel
-    ReactionElement *-- SBOTerm
-    ReactionElement *-- AbstractSpecies
-    KineticModel *-- SBOTerm
-    KineticModel *-- KineticParameter
-    KineticParameter *-- SBOTerm
-    Measurement *-- MeasurementData
-    MeasurementData *-- AbstractSpecies
-    MeasurementData *-- Replicate
-    Replicate *-- DataTypes
-    Replicate *-- AbstractSpecies
     NMRpy *-- Experiment
     NMRpy *-- Citation
     Experiment *-- FID
     Experiment *-- FIDArray
     FID *-- Parameters
     FID *-- ProcessingSteps
     FID *-- Identity
-    Identity *-- AbstractSpecies
-    Identity *-- Protein
-    Identity *-- Reactant
     Citation *-- Subjects
     Citation *-- Person
     Citation *-- Publication
     Citation *-- Term
     Person *-- IdentifierTypes
     Publication *-- PublicationTypes
     Publication *-- Person
-    AbstractSpecies *-- Vessel
-    Protein *-- SBOTerm
-    Reactant *-- SBOTerm
     
     class NMRpy {
         +datetime datetime_created*
@@ -61,6 +24,7 @@ classDiagram
     
     class Experiment {
         +string name*
+        +string[0..*] enzymeml_species
         +FID[0..*] fid
         +FIDArray fid_array
     }
@@ -103,8 +67,8 @@ classDiagram
     }
     
     class Identity {
-        +string name*
-        +AbstractSpecies, Protein, Reactant enzymeml_species
+        +string name
+        +string species_id
         +float[0..*] associated_peaks
         +frozenset[0..*] associated_ranges
         +float[0..*] associated_integrals
@@ -159,41 +123,6 @@ classDiagram
         +any value
     }
     
-    class Vessel {
-        +string name*
-        +posfloat volume*
-        +string unit*
-        +StrictBool constant*
-        +string uri
-        +string creator_id
-    }
-    
-    class AbstractSpecies {
-        +string name*
-        +Vessel vessel_id*
-        +float init_conc
-        +StrictBool constant*
-        +string unit
-        +string uri
-        +string creator_id
-    }
-    
-    class Protein {
-        +string sequence*
-        +string ecnumber
-        +string organism
-        +string organism_tax_id
-        +string uniprotid
-        +SBOTerm ontology*
-    }
-    
-    class Reactant {
-        +string smiles
-        +string inchi
-        +string chebi_id
-        +SBOTerm ontology*
-    }
-    
     class FileFormats {
         << Enumeration >>
         +VARIAN
@@ -219,54 +148,4 @@ classDiagram
         +ORCID
     }
     
-    class SBOTerm {
-        << Enumeration >>
-        +BIOCHEMICAL_REACTION
-        +ACID_BASE_REACTION
-        +CONFORMATIONAL_TRANSITION
-        +CONVERSION
-        +DEGRADATION
-        +DISSOCIATION
-        +IONISATION
-        +ISOMERISATION
-        +NON_COVALENT_BINDING
-        +REDOX_REACTION
-        +SPONTANEOUS_REACTION
-        +PROTEIN
-        +GENE
-        +SMALL_MOLECULE
-        +ION
-        +RADICAL
-        +INTERACTOR
-        +SUBSTRATE
-        +PRODUCT
-        +CATALYST
-        +INHIBITOR
-        +ESSENTIAL_ACTIVATOR
-        +NON_ESSENTIAL_ACTIVATOR
-        +POTENTIATOR
-        +MACROMOLECULAR_COMPLEX
-        +PROTEIN_COMPLEX
-        +DIMER
-        +MICHAELIS_MENTEN
-        +K_CAT
-        +K_M
-        +V_MAX
-    }
-    
-    class DataTypes {
-        << Enumeration >>
-        +CONCENTRATION
-        +ABSORPTION
-        +FEED
-        +BIOMASS
-        +CONVERSION
-        +PEAK_AREA
-    }
-    
-    class https://github.com/EnzymeML/enzymeml-specifications/ {
-        << External Object >>
-        +Repository <sdRDM.markdown.markdownparser.MarkdownParser object at 0x13ede0cd0>
-    }
-    
 ```
diff --git a/specifications/nmrpy.md b/specifications/nmrpy.md
@@ -27,13 +27,13 @@ Root element of the NMRpy data model.
 ### Experiment
 
 Rohdaten -> Zwischenschritte nur nennen + interessante Parameter -> Endergebnis; Peaklist + Rangelist; rapidly pulsed (if then +calibration factor) vs fully relaxed
-Also preparation of EnzymeML doc
+Also preparation of EnzymeML doc https://github.com/EnzymeML/enzymeml-specifications/@AbstractSpecies, https://github.com/EnzymeML/enzymeml-specifications/@Protein, https://github.com/EnzymeML/enzymeml-specifications/@Reactant
 
 - __name__
   - Type: string
   - Description: A descriptive name for the overarching experiment.
 - enzymeml_species
-  - Type: https://github.com/EnzymeML/enzymeml-specifications/@AbstractSpecies, https://github.com/EnzymeML/enzymeml-specifications/@Protein, https://github.com/EnzymeML/enzymeml-specifications/@Reactant
+  - Type: string
   - Description: A species object from an EnzymeML document.
   - Multiple: True
 - fid