Nested Attributes Query and Checker by krish69212 · Pull Request #66 · rcsb/py-rcsb-api

krish69212 · 2025-06-09T20:31:08Z

Creation of a nested attribute schema which is a dictionary with a tuple as a key that holds adjacent nested attributes and values as true.

Creation of nested attribute class which checks if two values are nested and groups them together.

Creation of nested attribute checker which checks if there are incorrectly nested attributes.

Switched from request.get to request.post in the search query.

Add dataclass field method to const

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v1.1.3 - Fix: Update regex pattern for instances in `const.py`

piehld

Thank you @krish69212! This is great work. I'm still in the process of reviewing everything, but I figured I would leave my "half review" now with some changes that I see at this point.

piehld · 2025-06-12T15:20:25Z

 list(query())
 ```

+Some attributes in the RCSB schema are part of a nested indexing context, meaning they must be queried together to ensure correct matching behavior. These include attributes like rcsb_binding_affinity.type and rcsb_binding_affinity.value, which are associated with the same underlying object (e.g., an EC50 measurement).


Whenever you reference an attribute or code element, you should wrap them in single tick marks so they appear like this. Makes things look super polished 😛 .

For a full list of markdown, checkout: https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax

Great things to know for any future work and projects you work on, so definitely worth the time to learn.

piehld

Excellent work and bug fixes, @krish69212! I've left a handful of other small comments and suggestions.

While you address those, I'm going to try testing out the package locally a bit and ensure we didn't miss any cracks 😄 .

piehld · 2025-06-12T19:06:45Z

        if self.operator == "and":
            if isinstance(other, Group):
-                # If keep_nested set to True, don't combine groups
+                # # If keep_nested set to True, don't combine groups


Suggested change

# # If keep_nested set to True, don't combine groups

# If keep_nested set to True, don't combine groups

piehld · 2025-06-12T19:49:37Z

        """URL to view this query on the RCSB PDB website query builder"""
+
+        # --- Warning ---
+        logging.warning("Warning: For complex queries, Advanced Search links are incompatible and may not work. Please use .get_editor_link to access the Search API Query Editor")


Suggested change

logging.warning("Warning: For complex queries, Advanced Search links are incompatible and may not work. Please use .get_editor_link to access the Search API Query Editor")

logging.warning("Warning: For complex queries, the Advanced Search builder page may not be compatible and so links may not render correctly. Please use the `.get_editor_link()` method to access the Search API Query Editor instead.")

piehld · 2025-06-12T20:13:04Z

+    Args:
+        AttributeQuery (AttributeQuery): Two attribute-level queries that must all belong to the same nested context group.


Can you actually make this two separate lines, to make it more clear/explicit that two AttributeQuery arguments are required?

piehld · 2025-06-12T20:14:58Z

+        AttributeQuery (AttributeQuery): Two attribute-level queries that must all belong to the same nested context group.
+
+    Raises:
+        Warning: If queries do not all belong to a valid and consistent nested attribute group.


Does it raise a warning or an error? Can you please confirm if logger.error actually raises an error and interrupts the process, or if it just logs and error and continues? If the latter, we should raise an error.

piehld · 2025-06-12T20:22:28Z

+        EXAMPLE QUERY:
+        query1 = AttributeQuery(attribute="rcsb_chem_comp_related.resource_name", operator="exact_match", value="DrugBank")
+        query2 = AttributeQuery(attribute="rcsb_chem_comp_related.resource_accession_code", operator="exact_match", value="DB00114")
+        NestedAttributeQuery(query1,query2)


Suggested change

NestedAttributeQuery(query1,query2)

nestedQuery = NestedAttributeQuery(query1, query2)

piehld · 2025-06-12T20:23:14Z

+nested = NestedAttributeQuery(q1, q2)
+
+query = nested & q3


Suggested change

nested = NestedAttributeQuery(q1, q2)

query = nested & q3

nestedQuery = NestedAttributeQuery(q1, q2)

query = nestedQuery & q3

piehld · 2025-06-12T20:49:00Z

+            expected_tuple = ('rcsb_uniprot_annotation.name', 'rcsb_uniprot_annotation.type')
+            self.assertIn(expected_tuple, SEARCH_SCHEMA.nested_attribute_schema)
+
+            not_expected_tuple = ('rcsb_uniprot_annotation.name.asdlkfjaskdjfaskldjf', 'rcsb_uniprot_annotation.type')


I appreciate the creativity lol, but can you use a pair of real attributes (but which do not have nested context) for this check?

piehld · 2025-06-19T18:17:48Z

Hi @krish69212, so I did some more testing, and overall things seem to be working as expected. However, I did notice a somewhat peculiar behavior when using parentheses which I'm curious about...

For example, the below two query constructors should produce the same query JSON; but the second one ends up looking a bit different:

from rcsbapi.search import AttributeQuery
from rcsbapi.search.search_query import NestedAttributeQuery

q1n = NestedAttributeQuery(AttributeQuery("rcsb_binding_affinity.type", "exact_match", "EC50"), AttributeQuery("rcsb_binding_affinity.value", "equals", 2.0))
q2 = AttributeQuery("rcsb_entry_info.selected_polymer_entity_types", "exists")
q3 = AttributeQuery("rcsb_nonpolymer_entity_container_identifiers.nonpolymer_comp_id", "exists")
q4a = AttributeQuery("rcsb_entry_info.structure_determination_methodology", "exact_match", "experimental")
q5 = AttributeQuery("rcsb_entry_info.deposited_polymer_monomer_count", "greater", 1000)

# Quer: q2 & q3 & q4a & q5 & q1n
{
    'type': 'group',
    'logical_operator': 'and',
    'nodes': [
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_entry_info.selected_polymer_entity_types', 'operator': 'exists', 'negation': False}, 'node_id': 0},
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_nonpolymer_entity_container_identifiers.nonpolymer_comp_id', 'operator': 'exists', 'negation': False}, 'node_id': 0},
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_entry_info.structure_determination_methodology', 'operator': 'exact_match', 'negation': False, 'value': 'experimental'}, 'node_id': 0},
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_entry_info.deposited_polymer_monomer_count', 'operator': 'greater', 'negation': False, 'value': 1000}, 'node_id': 0},
        {
            'type': 'group',
            'logical_operator': 'and',
            'nodes': [
                {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_binding_affinity.type', 'operator': 'exact_match', 'negation': False, 'value': 'EC50'}, 'node_id': 0},
                {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_binding_affinity.value', 'operator': 'equals', 'negation': False, 'value': 2.0}, 'node_id': 0}
            ]
        }
    ]
}


# Query: (q2 & q3) & (q4a & (q5 & q1n))
{
    'type': 'group',
    'logical_operator': 'and',
    'nodes': [
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_entry_info.selected_polymer_entity_types', 'operator': 'exists', 'negation': False}, 'node_id': 0},
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_nonpolymer_entity_container_identifiers.nonpolymer_comp_id', 'operator': 'exists', 'negation': False}, 'node_id': 0},
        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_entry_info.structure_determination_methodology', 'operator': 'exact_match', 'negation': False, 'value': 'experimental'}, 'node_id': 0},
        {
            'type': 'group',
            'logical_operator': 'and',
            'nodes': [
                {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_entry_info.deposited_polymer_monomer_count', 'operator': 'greater', 'negation': False, 'value': 1000}, 'node_id': 0},
                {
                    'type': 'group',
                    'logical_operator': 'and',
                    'nodes': [
                        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_binding_affinity.type', 'operator': 'exact_match', 'negation': False, 'value': 'EC50'}, 'node_id': 0},
                        {'type': 'terminal', 'service': 'text', 'parameters': {'attribute': 'rcsb_binding_affinity.value', 'operator': 'equals', 'negation': False, 'value': 2.0}, 'node_id': 0}
                    ]
                }
            ]
        }
    ]
}

Technically, both of those should produce the same JSON query structure. In fact, even the query (q2 & q3) & q4a & (q5 & q1n) produces the same JSON as q2 & q3 & q4a & q5 & q1n; so, it's peculiar to me why (q2 & q3) & (q4a & (q5 & q1n)) does not.

Although the above still lead to the same result set, I think it would be good to understand why they are differing, in case some other use case arises in which this behavior does impact the set of results. Would you be able to look into what's going on here?

piehld · 2025-06-19T18:21:17Z

@krish69212 Oh, also—one other very small thing—would you be able to add NestedAttributeQuery to the search __init__.py file, similar to how AttributeQuery is added there?

Doing so would allow you to simplify your import of NestedAttributeQuery, i.e.:

# OLD: 
from rcsbapi.search.search_query import NestedAttributeQuery
# NEW:
from rcsbapi.search import NestedAttributeQuery

piehld

Thanks again @krish69212! I'm going to merge this now.

ivana-truong and others added 10 commits March 20, 2025 16:09

Merge pull request #57 from rcsb/staging

0064fb8

Add dataclass field method to const

Merge pull request #59 from rcsb/staging

9d79341

Update code metadata and FAIR badges

Merge pull request #60 from rcsb/staging

45eb56c

update badges

Merge pull request #62 from rcsb/staging

e853606

add zenodo doi badge

Merge pull request #63 from rcsb/staging

20478cf

v1.1.3 - Fix: Update regex pattern for instances in `const.py`

Nested Attribute Addition

96eb5a7

Nested Attrs Azure Tests

892389d

Nested Attrs Import Statement

51206a2

Nested Attribute Checker

de0f30e

Azure Tests

1536c72

krish69212 requested a review from piehld June 9, 2025 20:31

krish69212 added 7 commits June 10, 2025 13:48

Fixing Grouping Class

e15c8d5

Fixing Group Class

ee48c7c

Updating Error Messages

36f6b37

Azure Tests Update

6153c53

Updated Azure Tests

51a52e7

Azure Test Fix

6ca231c

Nested Attributes Docs

acf89ad

krish69212 requested a review from brindakv June 12, 2025 15:16

piehld requested changes Jun 12, 2025

View reviewed changes

krish69212 added 2 commits June 12, 2025 14:57

Test, Request, Documentation Fixes

5abb85f

Azure Test Fix

d3b372a

piehld requested changes Jun 12, 2025

View reviewed changes

krish69212 added 2 commits June 13, 2025 09:27

Linting Fixes

e1c2a51

Linting Fixes

60b913a

search init fix

ab16724

piehld changed the base branch from master to staging July 8, 2025 10:02

update docs

1c1fde0

piehld approved these changes Jul 8, 2025

View reviewed changes

piehld merged commit 30a1053 into staging Jul 8, 2025
2 of 6 checks passed

piehld mentioned this pull request Jul 8, 2025

v1.2.0 - Addition of Sequence Coordinates API support and Nested Attributes #69

Merged

	# # If keep_nested set to True, don't combine groups
	# If keep_nested set to True, don't combine groups

	logging.warning("Warning: For complex queries, Advanced Search links are incompatible and may not work. Please use .get_editor_link to access the Search API Query Editor")
	logging.warning("Warning: For complex queries, the Advanced Search builder page may not be compatible and so links may not render correctly. Please use the `.get_editor_link()` method to access the Search API Query Editor instead.")

		Args:
		AttributeQuery (AttributeQuery): Two attribute-level queries that must all belong to the same nested context group.

	NestedAttributeQuery(query1,query2)
	nestedQuery = NestedAttributeQuery(query1, query2)

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piehld commented Jun 19, 2025

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krish69212 commented Jun 9, 2025 •

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