Moon david edit get method

README.md

@@ -75,7 +75,7 @@ The `result` is a pandas DataFrame containing the mapped IDs (see below), while
 
 ## Retrieving Information
 
-All [supported return fields](https://david-araripe.github.io/UniProtMapper/stable/field_reference.html#supported-fields) are both accessible through the attribute `ProtMapper.fields_table`:
+A DataFrame with the [supported return fields](https://david-araripe.github.io/UniProtMapper/stable/field_reference.html#supported-fields) is accessible through the attribute `ProtMapper.fields_table`:
 
 ```Python
 from UniProtMapper import ProtMapper
@@ -86,11 +86,11 @@ df.head()
 ```
 |    | label                | returned_field   | field_type       | has_full_version   | type          |
 |---:|:---------------------|:-----------------|:-----------------|:-------------------|:--------------|
-|  0 | Entry                | accession        | Names & Taxonomy | yes                | uniprot_field |
-|  1 | Entry Name           | id               | Names & Taxonomy | yes                | uniprot_field |
-|  2 | Gene Names           | gene_names       | Names & Taxonomy | yes                | uniprot_field |
-|  3 | Gene Names (primary) | gene_primary     | Names & Taxonomy | yes                | uniprot_field |
-|  4 | Gene Names (synonym) | gene_synonym     | Names & Taxonomy | yes                | uniprot_field |
+|  0 | Entry                | accession        | Names & Taxonomy | -                  | uniprot_field |
+|  1 | Entry Name           | id               | Names & Taxonomy | -                  | uniprot_field |
+|  2 | Gene Names           | gene_names       | Names & Taxonomy | -                  | uniprot_field |
+|  3 | Gene Names (primary) | gene_primary     | Names & Taxonomy | -                  | uniprot_field |
+|  4 | Gene Names (synonym) | gene_synonym     | Names & Taxonomy | -                  | uniprot_field |
 
 From the DataFrame, all `return_field` entries can be used to access UniProt data programmatically:
 
@@ -105,6 +105,23 @@ result, failed = mapper.get(["Q02880"], fields=fields)
 >>> Fetched: 1 / 1
 ```
 
+Further, for the cross-referenced fields that have `has_full_version` set to `yes`, returning the same field with extra information is supported by passing `<field_name>_full`, such as `xref_pdb_full`.
+
+All available return fields are also accessible through the attribute `ProtMapper.supported_return_fields`:
+
+```python
+from UniProtMapper import ProtMapper
+mapper = ProtMapper()
+print(mapper.supported_return_fields)
+
+>>> ['accession',
+>>>  'id',
+>>>  'gene_names',
+>>>  ...
+>>>  'xref_smart_full',
+>>>  'xref_supfam_full']
+```
+
 ## Field-based Querying
 
 UniProtMapper supports complex field-based protein queries using boolean operators (AND, OR, NOT) through the `uniprotkb_fields` module. This allows you to create sophisticated searches combining multiple criteria. For example:

docs/source/field_reference.rst

@@ -24,10 +24,10 @@ The supported return fields are listed below. The columns contain different info
 - **label**: The label used by UniProt to represent this field. Also used as column names on the `pd.DataFrame` returned from `get` methods implemented on both APIs.
 - **returned_field**: Name used to specify which information to retrieve by the APIs. For examples, check below.
 - **field_type**: The category of the field, as listed above under `Field Categories`. Note that for `type=='cross_reference'`, the field_type is the category of the cross-referenced database.
-- **has_full_version**: Always `yes` for `type=='uniprot_field'`. Is used by UniProt to indicate whether a cross-referenced database is fully integrated.
+- **has_full_version**: Not available for `type=='uniprot_field'`. If `yes`, a "full" version of the return field is accessible by using ``<field_name>_full``.
 - **type**: Either "uniprot_field" or "cross_reference". The former indicates a field that is directly related to the protein, while the latter indicates a field that is a cross-reference to another database and not native to UniProt.
 
-For more up-to-date information on `has_full_version` of cross-referenced fields, check the official UniProt documentation: `Return Fields <https://www.uniprot.org/help/return_fields_databases>`_
+For more up-to-date information on `has_full_version` of cross-referenced fields, check the official UniProt documentation: `Return Fields <https://www.uniprot.org/help/return_fields_databases>`_. In case of discrepancies, issues or pull requests are welcome!
 
 .. csv-table:: Supported Return Fields
    :header-rows: 1

src/UniProtMapper/idmapping_api.py

@@ -60,20 +60,6 @@ def __init__(
             backoff_factor,
             api_url,
         )
-        self.default_fields = (
-            "accession",
-            "id",
-            "gene_names",
-            "protein_name",
-            "organism_name",
-            "organism_id",
-            "go_id",
-            "go_p",
-            "go_c",
-            "go_f",
-            "cc_subcellular_location",
-            "sequence",
-        )
 
     @property
     def _supported_dbs(self) -> list:
@@ -170,7 +156,7 @@ def get_id_mapping_results_search(self, fields: str, url: str, compressed: bool)
     def get(
         self,
         ids: Union[List[str], str],
-        fields: Optional[Union[str, List]] = "default",
+        fields: Optional[Union[str, List]] = None,
         from_db: str = "UniProtKB_AC-ID",
         to_db: str = "UniProtKB-Swiss-Prot",
         compressed: bool = True,
@@ -181,9 +167,10 @@ def get(
 
         Args:
             ids: list of IDs to be mapped or single string.
-            fields: list of UniProt fields to be retrieved. If None, will return the API's
-                default fields. `Note:` parameter not supported for datasets that aren't
-                strictly UniProtKB, e.g.: UniParc, UniRef... Defaults to None.
+            fields: list of UniProt return fields to be retrieved. If None, will return the
+                API's default fields. `default` can also be passsed to access `self.default_fields`.
+                **Note** parameter not supported for datasets that aren't strictly UniProtKB,
+                e.g.: UniParc, UniRef... Defaults to None.
             from_db: database for the ids. Defaults to "UniProtKB_AC-ID".
             to_db: UniProtDB to query to. For reviewed-only accessions, use default. If
                 you want to include unreviewed accessions, use "UniProtKB". Defaults to
@@ -207,10 +194,10 @@ def get(
                 fields = self.default_fields
             else:
                 fields = np.char.lower(np.array(fields))
-                if not np.isin(fields, self.fields_table["returned_field"]).all():
+                if not np.isin(fields, self.supported_return_fields).all():
                     raise ValueError(
                         "Invalid fields. Valid fields are: "
-                        f"{self.fields_table['returned_field'].values}"
+                        f"{self.supported_return_fields}"
                     )
         if to_db not in ["UniProtKB-Swiss-Prot", "UniProtKB"]:
             if fields is not None:

src/UniProtMapper/interface.py

@@ -22,6 +22,22 @@ class BaseUniProt(ABC):
     - BaseUniProt -> ProtKB (UniProtKB API)
     """
 
+    fields_table = read_fields_table()
+    default_fields = (
+        "accession",
+        "id",
+        "gene_names",
+        "protein_name",
+        "organism_name",
+        "organism_id",
+        "go_id",
+        "go_p",
+        "go_c",
+        "go_f",
+        "cc_subcellular_location",
+        "sequence",
+    )
+
     def __init__(
         self,
         pooling_interval: int = 3,
@@ -44,10 +60,20 @@ def __init__(
         self.session = requests.Session()
         self._setup_session()
         self._re_next_link = re.compile(r'<(.+)>; rel="next"')
+        self._cached_supported_return_fields = None
 
     @property
-    def fields_table(self) -> None:
-        return read_fields_table()
+    def supported_return_fields(self) -> list:
+        """Return a list of the supported fields in UniProtKB & ID mapping API."""
+        if self._cached_supported_return_fields is None:
+            full_version_fields = (
+                self.fields_table.query('has_full_version == "yes"')["returned_field"]
+                + "_full"
+            ).tolist()
+            self._cached_supported_return_fields = (
+                self.fields_table["returned_field"].tolist() + full_version_fields
+            )
+        return self._cached_supported_return_fields
 
     def _setup_retries(self, total_retries, backoff_factor) -> None:
         return Retry(