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fix(core): simple fix for timeout of FHIR reference extraction #3837
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fix(core): simple fix for timeout of FHIR reference extraction #3837
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…rely on regex matching metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
WalkthroughThe Changes
Sequence Diagram(s)sequenceDiagram
participant Caller
participant BundleUtils
Caller->>BundleUtils: getReferencesFromResources(resources)
BundleUtils->>BundleUtils: Store resource IDs in Set
BundleUtils->>BundleUtils: Check references using Set.has
BundleUtils-->>Caller: Return missing references
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metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
… data metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
To check if this is a valid premise (that JSON.stringify + regex is slower than a recursive object search) I added the following test but surprisingly this didn't work for the simple object I tested, likely because there are a lot of references. Will try again tomorrow with real data to compare the timing, but it seems like both methods are functionally the same for finding reference strings. |
metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
Thanks to @lucasdellabella I learned how to use It turns out that the bottleneck wasn't in In any case, this should speed up some resource ID extraction considerably (around 70x when we ran it on my laptop). I left the original JSON.stringify implementation in place so as to make the minimal code change possible to fix the ticket, but also left my deep search algorithm with test cases in case someone wants to optimize it further by incorporating the FHIR schemas for each resource type. That is, only recursively check down the path for a nested object if there is definitely something in the schema along that path which might have a reference string. |
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Actionable comments posted: 1
🧹 Nitpick comments (1)
packages/core/src/external/fhir/shared/__tests__/deep-search.test.ts (1)
51-66
: Comprehensive edge case testing.Great job testing the function with various edge cases including empty objects and non-plain objects like Date, Map, Set, Error, RegExp, and Promise. This ensures robustness in production scenarios.
- expect(deepSearchObjectForString(new RegExp(""), "reference")).toEqual([]); + expect(deepSearchObjectForString(/(?:)/, "reference")).toEqual([]);Use a regular expression literal instead of the RegExp constructor, which avoids some escaping required in string literals and is easier to analyze statically.
🧰 Tools
🪛 Biome (1.9.4)
[error] 57-57: Use a regular expression literal instead of the RegExp constructor.
Regular expression literals avoid some escaping required in a string literal, and are easier to analyze statically.
Safe fix: Use a literal notation instead.(lint/complexity/useRegexLiterals)
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📒 Files selected for processing (3)
packages/core/src/external/fhir/shared/__tests__/deep-search.test.ts
(1 hunks)packages/core/src/external/fhir/shared/bundle.ts
(4 hunks)packages/utils/src/fhir-converter/count-bundle-refs.ts
(1 hunks)
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📓 Path-based instructions (1)
`**/*.ts`: - Use the Onion Pattern to organize a package's code in layers - Try to use immutable code and avoid sharing state across different functions, objects, and systems - Try...
**/*.ts
: - Use the Onion Pattern to organize a package's code in layers
- Try to use immutable code and avoid sharing state across different functions, objects, and systems
- Try to build code that's idempotent whenever possible
- Prefer functional programming style functions: small, deterministic, 1 input, 1 output
- Minimize coupling / dependencies
- Avoid modifying objects received as parameter
- Only add comments to code to explain why something was done, not how it works
- Naming
- classes, enums:
PascalCase
- constants, variables, functions:
camelCase
- file names:
kebab-case
- table and column names:
snake_case
- Use meaningful names, so whoever is reading the code understands what it means
- Don’t use negative names, like
notEnabled
, preferisDisabled
- For numeric values, if the type doesn’t convey the unit, add the unit to the name
- Typescript
- Use types
- Prefer
const
instead oflet
- Avoid
any
and casting fromany
to other types- Type predicates: only applicable to narrow down the type, not to force a complete type conversion
- Prefer deconstructing parameters for functions instead of multiple parameters that might be of
the same type- Don’t use
null
inside the app, only on code interacting with external interfaces/services,
like DB and HTTP; convert toundefined
before sending inwards into the code- Use
async/await
instead of.then()
- Use the strict equality operator
===
, don’t use abstract equality operator==
- When calling a Promise-returning function asynchronously (i.e., not awaiting), use
.catch()
to
handle errors (seeprocessAsyncError
andemptyFunction
depending on the case)- Date and Time
- Always use
buildDayjs()
to createdayjs
instances- Prefer
dayjs.duration(...)
to create duration consts and keep them asduration
- Prefer Nullish Coalesce (??) than the OR operator (||) to provide a default value
- Avoid creating arrow functions
- Use truthy syntax instead of
in
- i.e.,if (data.link)
notif ('link' in data)
- Error handling
- Pass the original error as the new one’s
cause
so the stack trace is persisted- Error messages should have a static message - add dynamic data to MetriportError's
additionalInfo
prop- Avoid sending multiple events to Sentry for a single error
- Global constants and variables
- Move literals to constants declared after imports when possible (avoid magic numbers)
- Avoid shared, global objects
- Avoid using
console.log
andconsole.error
in packages other than utils, infra and shared,
and try to useout().log
instead- Avoid multi-line logs
- don't send objects as a second parameter to
console.log()
orout().log()
- don't create multi-line strings when using
JSON.stringify()
- Use
eslint
to enforce code style- Use
prettier
to format code- max column length is 100 chars
- multi-line comments use
/** */
- scripts: top-level comments go after the import
packages/utils/src/fhir-converter/count-bundle-refs.ts
packages/core/src/external/fhir/shared/__tests__/deep-search.test.ts
packages/core/src/external/fhir/shared/bundle.ts
🪛 Biome (1.9.4)
packages/core/src/external/fhir/shared/__tests__/deep-search.test.ts
[error] 57-57: Use a regular expression literal instead of the RegExp constructor.
Regular expression literals avoid some escaping required in a string literal, and are easier to analyze statically.
Safe fix: Use a literal notation instead.
(lint/complexity/useRegexLiterals)
🔇 Additional comments (8)
packages/core/src/external/fhir/shared/bundle.ts (5)
78-78
: Excellent performance optimization using Set.Replacing array with Set for resource IDs is a great optimization. Sets have O(1) lookup time for membership checks compared to O(n) for arrays, which will significantly improve performance when checking if references exist in large collections.
Also applies to: 87-87
119-120
: LGTM - Clean code refactoring.Moving the variable initialization to the beginning of the function scope improves code readability and follows good practices.
128-132
: Useful documentation of alternative approach.The commented code provides valuable context about the alternative approach that was considered and tested. This follows the guideline of explaining why something was done, not how it works.
150-184
: Well-implemented recursive search function with proper safeguards.The
deepSearchObjectForString
function is well-implemented with:
- Proper type safety using generics
- Good handling of edge cases (null, Date, Set, Map)
- Efficient recursion for nested objects and arrays
- Clear structure following functional programming principles
This follows the coding guideline of building small, deterministic functions with clear inputs and outputs.
186-193
: Clean implementation of array search helper.The
deepSearchArrayForString
function is clean, concise, and efficiently leveragesflatMap
for array handling. This complementary function maintains the functional approach and supports the object search function well.packages/core/src/external/fhir/shared/__tests__/deep-search.test.ts (3)
4-49
: Good performance benchmark test.This test properly validates that both approaches correctly find all references and logs timing information for comparison. This helps validate the performance hypothesis behind the new implementation.
However, consider removing or uncommenting line 48 since leaving commented expectations can be confusing:
- // expect(jsonStringifyTime).toBeGreaterThanOrEqual(deepSearchTime); + // We don't enforce timing constraints in tests as they can be environment-dependent
68-115
: Thorough testing of nested object scenarios.The tests effectively cover multiple levels of nesting and combinations of objects and arrays, ensuring the deep search function correctly finds all references regardless of structure complexity.
117-137
: Good coverage of array search scenarios.These tests validate that the array search function correctly extracts references from various array structures, including arrays of objects and arrays with nested objects.
metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
metriport/metriport-internal#1040 refs. ENG-279 Signed-off-by: Keshav Saharia <keshav@metriport.com>
Issues:
Dependencies
Description
Simple fix to improve latency of searching large bundles - thanks to @lucasdellabella's brilliant help, we were able to profile this with
0x
and found this performance improvement almost by accident.It seems like the aggregation of
missingReferences
was actually the bottleneck - by switching to using aSet
, we eliminated some interesting VM behavior and improved performance by around 70x for some large bundles we tested.Testing
The
Set
is only being used locally within the function. We tested the performance improvement by loading some large bundles and running the test script (see commits) that counts references.