-
Notifications
You must be signed in to change notification settings - Fork 33
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Synthesis endpoint now uses aggregation resource
- Loading branch information
Showing
6 changed files
with
261 additions
and
266 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| from typing import Optional, List, Dict, Union, Any | ||
| from fastapi import Query | ||
| from pymatgen.core import Composition | ||
| from maggma.api.query_operator import QueryOperator | ||
| from maggma.api.utils import STORE_PARAMS | ||
| from mp_api.routes.synthesis.models import SynthesisTypeEnum, OperationTypeEnum | ||
| from mp_api.routes.synthesis.utils import mask_highlights, mask_paragraphs | ||
|
|
||
|
|
||
| class SynthesisSearchQuery(QueryOperator): | ||
| """ | ||
| Method to generate a synthesis text search query | ||
| """ | ||
|
|
||
| def query( | ||
| self, | ||
| keywords: Optional[str] = Query( | ||
| None, | ||
| description="String keywords to search synthesis paragraph text with.", | ||
| ), | ||
| synthesis_type: Optional[List[SynthesisTypeEnum]] = Query( | ||
| None, description="Type of synthesis to include." | ||
| ), | ||
| target_formula: Optional[str] = Query( | ||
| None, description="Chemical formula of the target material." | ||
| ), | ||
| precursor_formula: Optional[str] = Query( | ||
| None, description="Chemical formula of the precursor material." | ||
| ), | ||
| operations: Optional[List[OperationTypeEnum]] = Query( | ||
| None, description="List of operations that syntheses must have." | ||
| ), | ||
| condition_heating_temperature_min: Optional[float] = Query( | ||
| None, description="Minimal heating temperature." | ||
| ), | ||
| condition_heating_temperature_max: Optional[float] = Query( | ||
| None, description="Maximal heating temperature." | ||
| ), | ||
| condition_heating_time_min: Optional[float] = Query( | ||
| None, description="Minimal heating time." | ||
| ), | ||
| condition_heating_time_max: Optional[float] = Query( | ||
| None, description="Maximal heating time." | ||
| ), | ||
| condition_heating_atmosphere: Optional[List[str]] = Query( | ||
| None, description='Required heating atmosphere, such as "air", "argon".' | ||
| ), | ||
| condition_mixing_device: Optional[List[str]] = Query( | ||
| None, description='Required mixing device, such as "zirconia", "Al2O3".' | ||
| ), | ||
| condition_mixing_media: Optional[List[str]] = Query( | ||
| None, description='Required mixing media, such as "alcohol", "water".' | ||
| ), | ||
| skip: int = Query(0, description="Number of entries to skip in the search"), | ||
| limit: int = Query( | ||
| 10, | ||
| description="Max number of entries to return in a single query. Limited to 10.", | ||
| ), | ||
| ): | ||
| project_dict: Dict[str, Union[Dict, int]] = { | ||
| "_id": 0, | ||
| "doi": 1, | ||
| "synthesis_type": 1, | ||
| "reaction": 1, | ||
| "reaction_string": 1, | ||
| "operations": 1, | ||
| "target": 1, | ||
| "targets_formula": 1, | ||
| "targets_formula_s": 1, | ||
| "precursors": 1, | ||
| "precursors_formula_s": 1, | ||
| "paragraph_string": 1, | ||
| } | ||
|
|
||
| pipeline: List[Any] = [] | ||
| if keywords: | ||
| pipeline.append( | ||
| { | ||
| "$search": { | ||
| # NOTICE to MongoDB admin: | ||
| # This MongoDB Atlas index should be created with: | ||
| # {"mappings": { "dynamic": false, | ||
| # "fields": { | ||
| # "paragraph_string": {"type": "string"} | ||
| # }}} | ||
| "index": "synth_descriptions", | ||
| "search": {"query": keywords, "path": "paragraph_string",}, | ||
| "highlight": { | ||
| "path": "paragraph_string", | ||
| # "maxNumPassages": 1 | ||
| }, | ||
| } | ||
| } | ||
| ) | ||
| project_dict.update( | ||
| { | ||
| "search_score": {"$meta": "searchScore"}, | ||
| "highlights": {"$meta": "searchHighlights"}, | ||
| } | ||
| ) | ||
| pipeline.append({"$project": project_dict}) | ||
|
|
||
| crit: Dict[str, Any] = {} | ||
| if synthesis_type: | ||
| crit["synthesis_type"] = {"$in": synthesis_type} | ||
| if target_formula: | ||
| reduced_formula = Composition( | ||
| target_formula | ||
| ).get_reduced_formula_and_factor()[0] | ||
| crit["targets_formula_s"] = reduced_formula | ||
| if precursor_formula: | ||
| reduced_formula = Composition( | ||
| precursor_formula | ||
| ).get_reduced_formula_and_factor()[0] | ||
| crit["precursors_formula_s"] = reduced_formula | ||
| if operations: | ||
| crit["operations.type"] = {"$all": operations} | ||
| if condition_heating_temperature_min: | ||
| crit["operations.conditions.heating_temperature.values"] = { | ||
| "$gte": condition_heating_temperature_min | ||
| } | ||
| if condition_heating_temperature_max: | ||
| crit["operations.conditions.heating_temperature.values"] = { | ||
| "$lte": condition_heating_temperature_max | ||
| } | ||
| if condition_heating_time_min: | ||
| crit["operations.conditions.heating_time.values"] = { | ||
| "$gte": condition_heating_time_min | ||
| } | ||
| if condition_heating_time_max: | ||
| crit["operations.conditions.heating_time.values"] = { | ||
| "$lte": condition_heating_time_max | ||
| } | ||
| if condition_heating_atmosphere: | ||
| crit["operations.conditions.heating_atmosphere"] = { | ||
| "$all": condition_heating_atmosphere | ||
| } | ||
| if condition_mixing_device: | ||
| crit["operations.conditions.mixing_device"] = { | ||
| "$all": condition_mixing_device | ||
| } | ||
| if condition_mixing_media: | ||
| crit["operations.conditions.mixing_media"] = { | ||
| "$all": condition_mixing_media | ||
| } | ||
|
|
||
| if crit: | ||
| pipeline.append({"$match": crit}) | ||
|
|
||
| # total = next( | ||
| # self.store._collection.aggregate( | ||
| # pipeline + [{"$count": "total"}], allowDiskUse=True | ||
| # ) | ||
| # )["total"] | ||
|
|
||
| pipeline.extend( | ||
| [{"$sort": {"search_score": -1}}, {"$skip": skip}, {"$limit": limit}] | ||
| ) | ||
|
|
||
| return {"pipeline": pipeline} | ||
|
|
||
| def post_process(self, docs): | ||
|
|
||
| for doc in docs: | ||
| mask_highlights(doc) | ||
| mask_paragraphs(doc) | ||
|
|
||
| return docs | ||
|
|
Oops, something went wrong.