Revert "feat: Add uris field for identifiers (#103)"

This reverts commit 0f766e5.

Author: MicPie

pyproject.toml

@@ -30,7 +30,6 @@ dev = [
         "pre-commit",
         "pydantic_yaml",
         "pytest",
-        "pubchempy"
 ]
 
 # [project.optional-dependencies]

src/chemnlp/data_val/model.py

@@ -1,7 +1,5 @@
 from typing import Dict, List, Optional
 
-import pubchempy as pcp
-import requests
 from pydantic import root_validator, validator
 from pydantic_yaml import YamlModel, YamlStrEnum
 
@@ -21,8 +19,6 @@ class Identifier(YamlModel):
     """Identifier information."""
 
     id: str
-
-    """A description of the field"""
     description: Optional[str]
     type: IdentifierEnum
     names: Optional[List[str]]
@@ -47,80 +43,17 @@ class ColumnTypes(YamlStrEnum):
     continuous = "continuous"
     categorical = "categorical"
     ordinal = "ordinal"
-    boolean = "boolean"
 
 
 class Target(YamlModel):
     """Target information."""
 
     id: str
-
-    """A english description of the field"""
     description: str
-
-    """The units of the field. None if unitless."""
-    units: Optional[str]
-
-    """The type of the field. Can be one of `continuous`, `categorical`, `ordinal`, `boolean`."""
+    units: str
     type: ColumnTypes
-
-    """A list of names describing the field.
-
-    Note that this will be used in building the prompts. Some example for prompts:
-
-    - Boolean variables
-
-        - `Is <name> <identifier>?`
-        - ```
-        What molecules in the list are <name>?
-        - <identifier_1>
-        - <identifier_2>
-        - <identifier_3>
-        ```
-
-
-    - Continuous variables
-
-        - `What is <name> of <identifier>?`
-        - ```
-        What is the molecule with largest <name> in the following list?
-        - <identifier_1>
-        - <identifier_2>
-        - <identifier_3>
-        ```
-    """
     names: List[str]
 
-    """A URI or multiple (consitent ) URIs for the field.
-
-    Ideally this would be a link to an entry in an ontrology or controlled
-    vocabulary that can also provide a canonical description for the field.
-    """
-    uris: Optional[List[str]]
-
-    """A PubChem assay IDs or multiple (consistent) PubChem assay IDs.
-
-    Make sure that the first assay ID is the primary assay ID.
-    """
-    pubchem_aids: Optional[List[int]]
-
-    @validator("pubchem_aids")
-    def uris_resolves(cls, values):
-        if values is not None:
-            for uri in values.get("uris"):
-                # perform a request to the URI and check if it resolves
-                response = requests.get(uri)
-                if response.status_code != 200:
-                    raise ValueError(f"URI {uri} does not resolve")
-
-    @validator("pubchem_aids")
-    def pubchem_assay_ids_resolve(cls, values):
-        if values is not None:
-            for aid in values:
-                assays = pcp.get_assays(aid)
-                if len(assays) == 0:
-                    raise ValueError(f"PubChem assay ID {aid} does not resolve")
-
 
 class Template(YamlModel):
     prompt: str
@@ -162,12 +95,3 @@ class Dataset(YamlModel):
     def num_points_must_be_positive(cls, v):
         if v < 0:
             raise ValueError("num_points must be positive")
-
-    @validator("links")
-    def links_must_resolve(cls, v):
-        if v is not None:
-            for link in v:
-                response = requests.get(link.url)
-                if response.status_code != 200:
-                    if not (("acs" in response.text) or ("sage" in response.text)):
-                        raise ValueError(f"Link {link.url} does not resolve")