feat: Consolidate CLI #650
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…wise skip endpoint for respective genome_release
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WalkthroughThis pull request introduces a comprehensive refactoring of the annotation system, focusing on command-line interface improvements and expanded server-side annotation capabilities. The changes centralize CLI argument handling by creating a new Changes
Sequence DiagramsequenceDiagram
participant CLI as Command Line Interface
participant Server as Annotation Server
participant Annotator as Variant Annotator
participant Database as Annotation Databases
CLI->>Server: Send Variant Query
Server->>Annotator: Initialize with Sources
Annotator->>Database: Retrieve Annotation Data
Database-->>Annotator: Return Annotation Results
Annotator-->>Server: Provide Annotation Details
Server-->>CLI: Return Annotated Variant Information
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Actionable comments posted: 3
🧹 Nitpick comments (27)
src/server/run/mod.rs (4)
1-6: Consider consolidating imports.There are numerous imports from adjacent modules (cli, csq, etc.). If you find yourself refactoring frequently or referencing these across files, consider grouping or re-exporting from a central location for easier management and to reduce repetitive import statements.
153-181: Enhance user guidance & maintain consistency with CLI parameters.These info logs display helpful endpoint URLs for the user. Given the PR objective is to consolidate CLI options across tools, ensure the displayed guidance accurately reflects any new or updated CLI parameters so as not to confuse users.
206-241: Extract repeated logic into modular functions.Inside the
runfunction, lines 206–241 deal with transcript database loading, merging, and building different predictors. Similar logic recurs for frequency/ClinVar as well, making the code somewhat lengthy. Extracting such repeated logic (e.g., merging DBs, building annotators) into dedicated helper functions would improve readability and testability.
285-285: Ensure consistent logs and finalize initialization message.The final logging statement mentions data loading but does not confirm readiness of new endpoints (ClinVar, frequencies, etc.). A clearer statement about which services/annotators are enabled would provide better diagnostics during server startup.
src/annotate/seqvars/csq.rs (4)
2-6: Revisit imports for clarity and redundancy.You import both
annsymbols andTranscriptSourcein quick succession. Verify there is no duplication or overshadowing occurring, especially asTranscriptSourcewas relocated from another file.
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1787-1788: Add doc comments forConsequencePredictorusage.Lines 1787-1788 reveal the new
ConsequenceAnnotatorstruct. Provide doc comments about how it internally usesConsequencePredictorand note any side effects or assumptions on the input data, so that future maintainers can quickly grasp its purpose.
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1796-1800: Suggest clarifying error messages.When reading from transcript DB or building the
ConsequencePredictor, any failure triggers a generic error. Consider providing more context (e.g., "failed to build predictor with x parameter"), to speed up root cause analysis.
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2072-2116: Streamline file path checks for assembly mismatch.When skipping DB loading if
path_component(a)is not in the RosksDB path (line 2079, 2103), consider centralizing these checks in a small utility function. That avoids duplication and helps if new types of DBs are added later.src/annotate/seqvars/mod.rs (4)
11-12: Align naming conventions.Lines 11–12 show that
use self::ann::{AnnField, Consequence, FeatureBiotype}is placed next topub use crate::annotate::cli::{Sources, TranscriptSettings}. Consistently naming re-exports or grouping them by domain can improve discoverability and maintainability.
1313-1313: Consider an enum or trait-based approach.
AnnotatorEnumlumps frequency, ClinVar, and Consequence. With further expansion (like coverage or variant quality), an enum might become lengthy. A trait-based approach for different “Annotator” types can keep the code open for extension while ensuring each new type implements consistent methods.
1526-1531: Plan for partial annotation returns.When calling
annotate_variant, you either returnSome(...)with the frequency data or an error if none is found. Decide if an empty result is truly an error or if you can returnOk(None)to gracefully handle the absence of data—especially if a partial annotation is acceptable.
2014-2148: Optimize repeated DB loads.Between lines 2024–2116, various databases are loaded or merged. In typical usage, repeated loading might cost time or memory. Evaluate whether to cache references, load them once at server startup, or share them across modules to reduce overhead.
src/server/run/actix_server/mod.rs (2)
14-16: Align module names & doc comments.You added
pub mod seqvars_clinvar;andpub mod seqvars_frequencies;. A short doc comment describing each module’s responsibility can help new contributors locate the relevant business logic quickly.
56-60: Check memory usage for HashMaps inWebServerData.
frequency_annotatorsandclinvar_annotatorsmight increase memory usage if multiple large DBs are opened. If usage grows, consider lazy loading or caching only the needed data per request to avoid overhead.src/annotate/cli.rs (5)
20-25: Consider consistent documentation for each database field.
While transcript and frequency databases are documented, adding explicit availability links or disclaimers for the ClinVar database can further align user expectations.
28-33: Validate default transcript source.
Defaultingtranscript_sourcetoBothcan lead to higher resource usage or less deterministic outputs. Confirm that a user truly benefits from including all sources by default or consider a domain-specific default (e.g.,Ensembl).
53-71: ExtendConsequenceByor rename theAllelevariant.
There may be future expansions likeVariantorHaplotype. If planned, clarifying the difference betweenAlleleand a potentialVariantvariant can preempt confusion.
73-94: Provide usage guidance for eachTranscriptPickType.
The enumerators such asManeSelect,Basic, etc., have domain-specific implications. Including short docs or references for each helps maintainers and users choose correctly.
96-101: Ensure consistent naming for picking strategies.
pick_transcript_modeusesFirstandAll, but some codebases might preferSinglevs.Allfor clarity. Consistency across the pipeline fosters readability.src/server/run/actix_server/seqvars_clinvar.rs (2)
53-99: Handle missing or partial annotations gracefully.
annotate_variantmay returnNoneif the variant is not found. You’re appending the annotation to the result array only if it exists. Consider returning an empty array or a descriptive placeholder in the response to inform clients about missing data.
112-132: Document endpoint differences in code comments.
You provide both a deprecated endpoint (/seqvars/clinvar) and a new endpoint (/api/v1/seqvars/clinvar). Clarify or cross-reference their differences to help maintainers track usage over time.src/server/run/actix_server/seqvars_frequencies.rs (2)
33-39: Future-proof theFrequencyResultEntryvariants.
Additional variant categories (e.g., plasmids) might be integrated. Consider whether a catch-all variant or forward-compatible design is needed.
160-180: Deprecate old frequency endpoint gracefully.
Similar to clinvar, you have a deprecated/seqvars/frequencyand the recommended/api/v1/seqvars/frequency. Add deprecation notices in the doc comments or logs to guide users to the new endpoint.src/verify/seqvars.rs (1)
10-10: Imports consolidated intoclimodule.
Switching these enums to be imported fromcliis clearer for the user-facing command-line logic. This change is good, but ensure that none of these imports are also needed by the olderseqvarsmodule for fallback or backward compatibility.src/annotate/strucvars/mod.rs (3)
88-88: Hardcoded default overlap threshold.
pub min_overlap: f32with default 0.8 might be too strict or loose in some downstream analyses. Consider whether a user-supplied range validation or a best-practice note in your docs would help.
92-92: Slack around break-ends.
Using a default of 50 bases makes sense for many use cases but might need adjustments in certain contexts. Possibly document or log a warning if results are unusual with large structural variants.
100-100: Optional date string.
file_datebeing optional is flexible. Consider pattern validation (e.g., YYYYMMDD) for clarity, or at least a log message if the user sets an unexpected format.
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📒 Files selected for processing (13)
src/annotate/cli.rs(1 hunks)src/annotate/mod.rs(1 hunks)src/annotate/seqvars/csq.rs(4 hunks)src/annotate/seqvars/mod.rs(27 hunks)src/annotate/seqvars/provider.rs(1 hunks)src/annotate/strucvars/mod.rs(2 hunks)src/common/noodles.rs(2 hunks)src/server/run/actix_server/mod.rs(3 hunks)src/server/run/actix_server/seqvars_clinvar.rs(1 hunks)src/server/run/actix_server/seqvars_csq.rs(3 hunks)src/server/run/actix_server/seqvars_frequencies.rs(1 hunks)src/server/run/mod.rs(8 hunks)src/verify/seqvars.rs(1 hunks)
🔇 Additional comments (26)
src/server/run/mod.rs (2)
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117-133: Encapsulate input validation.The
Argsstruct has multiple fields that expect external input (e.g.,listen_host,listen_port). Consider validating or sanitizing these fields to avoid potential misconfiguration (for example, verifying if the host is reachable or ensuring the port is in a valid range).
242-247: Proactively handle missing transcript DB scenario.When no transcripts are provided (
elsebranch at line 242), you log a warning. Consider throwing an explicit error or returning early if transcripts are absolutely required for certain endpoints. This could prevent runtime confusion and alert operators quickly about the missing data.src/annotate/seqvars/csq.rs (3)
64-64: Provider field visibility changed topub(crate).Making
provideraccessible within the crate can aid in testing or hooking additional code. Validate that external modules do not require direct access; otherwise, consider making a public getter.
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152-184: Check boundary conditions for partial decoding.Methods like
normalize_variant,strip common suffixes/prefixes, oroverlaps(...)can risk edge-case failures (empty strings, negative positions, etc.). Ensure tests exist for corner cases to maintain robust boundary handling.
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2014-2022: Graceful fallback on unknown assemblies.
proto_assembly_from(assembly)returnsNoneif an assembly is not recognized. If the assembly is crucial for annotation, consider either logging a warning or returning an error. Otherwise, you risk silent failures where the annotation might remain incomplete.src/annotate/seqvars/mod.rs (2)
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1405-1455: Revisit error handling here.In
annotate_record_xy, lines 1415–1455 record potential database lookups (X or Y). If the data is missing or partial, consider whether you should fail silently or warn the user. Clarifying this would help debug missing frequency information on sex chromosomes.
1728-1732: Communicate the range of a known classification.
annotate_variantfor ClinVar returns classification details. If the classification set is limited (benign, likely benign, etc.), consider enumerating them or providing more context for how to interpret them. That could help consumers of your API handle classification consistently.src/annotate/mod.rs (1)
7-7: Visibility rationale forpub(crate) mod cli.Making
clia crate-private module is adequate if external applications do not require direct access to CLI structs. If you anticipate external crates hooking into your CLI, consider making it fully public or providing a public re-export.src/server/run/actix_server/mod.rs (2)
9-9: Validate concurrency & data races with new annotators.
ClinvarAnnotatorandFrequencyAnnotatorare introduced here. Confirm they safely support concurrent read operations from the DB (RocksDB) when registered for multiple endpoints in parallel requests. Typically, opening them in read-only mode is fine, but verifying concurrency safety is advised.
78-81: Endpoint expansions well-structured.Adding
.service(seqvars_frequencies::handle)and.service(seqvars_clinvar::handle)cleanly integrates new annotation endpoints. This approach fosters code separation and clarity in the overall Actix application architecture.src/annotate/cli.rs (3)
4-6: Clarify the usage of#[group(required = true, multiple = true)].
The Clap group annotation forces these options to be treated as a group, requiring at least one occurrence. However, havingmultiple = trueimplies multiple group members can be set. Confirm that this design meets user requirements for specifying multiple sources.
37-43: Ensure transcript picking is indeed optional.
pick_transcriptis aVec<TranscriptPickType>. An empty vector implies no picking, yet you must confirm that the logic in downstream code properly handles an empty pick list.
103-123: Confirm serialization expectations forTranscriptSource.
Enums exposed via CLI and JSON often need consistent casing or renaming. Verify ifBothshould remain capitalized or adapted for user-friendly input/output.src/server/run/actix_server/seqvars_clinvar.rs (2)
14-31: Validate required fields inClinvarQuery.
The fieldschromosome,position,reference, andalternativeare mandatory for queries. Confirm that user input or upstream code always provides them. You might want to enforce them as non-empty strings or valid numeric ranges forposition.
33-38: Confirm usage of multiple classification fields.
clinvar_germline_classificationis a vector. Does the database commonly return multiple classifications for a single variant? If so, ensure the UI or client code can handle multiple classifications properly.src/server/run/actix_server/seqvars_frequencies.rs (2)
14-31: Check uppercase/lowercase usage for SPDI parameters.
Some pipelines may pass contig IDs as “chr1” or plain “1.” Clarify whetherchromosomemust be stripped of a “chr” prefix or can it be upper/lower case. This helps prevent mismatch scenarios.
101-147: Guard against partial frequency data.
Whenannotate_variantreturns partial or no data, an empty vector is returned. Ensure you have appropriate fallback logic (like zero counts) and that no further steps break due to missing keys.src/common/noodles.rs (2)
63-63: Ensure backward compatibility with added lifetime parameter.
By adding'atoLocalBoxStream<'a, ...>, references to the stream are now bound to the function context. Check if existing downstream code that consumes these streams needs adjustments for the new lifetime constraints.
79-79: Leverage.record_bufs(header)consistently.
The logic forVcfcalls.record_bufs(header), whileBcfuses.records()andRecordBuf::try_from_variant_record(...). Verify that these calls remain in sync regarding returned fields, especially if extended.src/server/run/actix_server/seqvars_csq.rs (3)
76-77: Ensure correct usage of strand sign.
The newstrandfield is ani32, which allows for different sign conventions (e.g., -1 for minus, +1 for plus). Confirm that all places setting or reading this value interpret the strand consistently (e.g., no dependencies on 0 vs. ±1).
151-151: Confirm consistent extraction of strand value.
This code extractsstrandfromAnnField. Ensure that no panics occur ifann_fieldhas an unexpected strand value, and verify that any default or error behavior is properly handled.
179-179: Includestrandin sorting or grouping logic if needed.
As the code now includesstrandin eachSeqvarsCsqResultEntry, confirm whether sorting or grouping downstream might need to account for the strand sign. If it doesn’t, this is fine to leave as-is.src/annotate/seqvars/provider.rs (1)
5-5: Consistent referencing of transcript picking types.
ReferencingTranscriptPickModeandTranscriptPickTypefrom theclimodule keeps all command-line configurations centralized. Verify that no duplicate definitions remain inseqvarsto avoid confusion.src/annotate/strucvars/mod.rs (3)
64-64: Validate presence or content of the input PED file.
pub path_input_ped: Stringwith#[arg(long)]looks straightforward. Consider adding checks to ensure the file exists and is readable before proceeding to annotation.
68-68: Multiple VCF inputs.
pub path_input_vcf: Vec<String>supports multiple inputs. This is useful for merging or analyzing multiple VCF sources. Confirm that you handle possible collisions with sample names and that you address any potential concurrency in reading multiple VCFs.
72-72: Flattened subcommands intoPathOutput.
Neatly organizes different output paths under a single struct. This is a good approach. Check if any future expansions (e.g., writing both VCF and TSV at once) require adjusting the grouping constraint.
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Actionable comments posted: 1
🧹 Nitpick comments (1)
openapi.schema.yaml (1)
63-63: Fix incorrect summary in endpoint description.The summary for the ClinVar endpoint incorrectly mentions "gnomAD frequencies".
- summary: Query for gnomAD frequencies of a variant. + summary: Query for ClinVar information of a variant.
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openapi.schema.yaml(9 hunks)src/server/run/mod.rs(8 hunks)utils/docker/entrypoint.sh(2 hunks)
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🔇 Additional comments (5)
utils/docker/entrypoint.sh (1)
16-25: LGTM! Well-organized path structure.The new path organization clearly separates different data types (transcripts, frequencies, ClinVar) and genome builds (GRCh37, GRCh38) under a centralized location.
src/server/run/mod.rs (2)
249-265: Improved handling of multiple frequency databases.The code now properly handles multiple frequency databases by:
- Warning users when no databases are loaded
- Using only the first database when multiple are specified
- Warning users that multiple databases are not supported
However, consider documenting the selection behavior in user documentation.
267-281: Consistent handling of multiple ClinVar databases.The implementation mirrors the frequency database handling, providing consistent behavior and clear warnings.
openapi.schema.yaml (2)
59-110: LGTM! Well-designed ClinVar endpoint.The ClinVar endpoint follows REST best practices with:
- Consistent parameter naming with other endpoints
- Clear parameter descriptions
- Proper error responses
170-221: LGTM! Well-designed frequency endpoint.The frequency endpoint maintains consistency with:
- Same parameter structure as ClinVar endpoint
- Clear separation of autosomal/gonosomal/mitochondrial results
- Proper error handling
| $(test -e "$PATH_TRANSCRIPTS_37" && echo --transcripts "$PATH_TRANSCRIPTS_37") \ | ||
| $(test -e "$PATH_TRANSCRIPTS_38" && echo --transcripts "$PATH_TRANSCRIPTS_38") \ | ||
| $(test -e "$PATH_FREQUENCIES_37" && echo --frequencies "$PATH_FREQUENCIES_37") \ | ||
| $(test -e "$PATH_FREQUENCIES_38" && echo --frequencies "$PATH_FREQUENCIES_38") \ | ||
| $(test -e "$PATH_CLINVAR_37" && echo --clinvar "$PATH_CLINVAR_37") \ | ||
| $(test -e "$PATH_CLINVAR_38" && echo --clinvar "$PATH_CLINVAR_38") \ |
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Fix potential word splitting issues in command substitutions.
The current command substitutions could be vulnerable to word splitting if paths contain spaces.
Apply this diff to properly quote the command substitutions:
- $(test -e "$PATH_TRANSCRIPTS_37" && echo --transcripts "$PATH_TRANSCRIPTS_37") \
- $(test -e "$PATH_TRANSCRIPTS_38" && echo --transcripts "$PATH_TRANSCRIPTS_38") \
- $(test -e "$PATH_FREQUENCIES_37" && echo --frequencies "$PATH_FREQUENCIES_37") \
- $(test -e "$PATH_FREQUENCIES_38" && echo --frequencies "$PATH_FREQUENCIES_38") \
- $(test -e "$PATH_CLINVAR_37" && echo --clinvar "$PATH_CLINVAR_37") \
- $(test -e "$PATH_CLINVAR_38" && echo --clinvar "$PATH_CLINVAR_38") \
+ "$(test -e "$PATH_TRANSCRIPTS_37" && echo --transcripts "$PATH_TRANSCRIPTS_37")" \
+ "$(test -e "$PATH_TRANSCRIPTS_38" && echo --transcripts "$PATH_TRANSCRIPTS_38")" \
+ "$(test -e "$PATH_FREQUENCIES_37" && echo --frequencies "$PATH_FREQUENCIES_37")" \
+ "$(test -e "$PATH_FREQUENCIES_38" && echo --frequencies "$PATH_FREQUENCIES_38")" \
+ "$(test -e "$PATH_CLINVAR_37" && echo --clinvar "$PATH_CLINVAR_37")" \
+ "$(test -e "$PATH_CLINVAR_38" && echo --clinvar "$PATH_CLINVAR_38")" \📝 Committable suggestion
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| $(test -e "$PATH_TRANSCRIPTS_37" && echo --transcripts "$PATH_TRANSCRIPTS_37") \ | |
| $(test -e "$PATH_TRANSCRIPTS_38" && echo --transcripts "$PATH_TRANSCRIPTS_38") \ | |
| $(test -e "$PATH_FREQUENCIES_37" && echo --frequencies "$PATH_FREQUENCIES_37") \ | |
| $(test -e "$PATH_FREQUENCIES_38" && echo --frequencies "$PATH_FREQUENCIES_38") \ | |
| $(test -e "$PATH_CLINVAR_37" && echo --clinvar "$PATH_CLINVAR_37") \ | |
| $(test -e "$PATH_CLINVAR_38" && echo --clinvar "$PATH_CLINVAR_38") \ | |
| "$(test -e "$PATH_TRANSCRIPTS_37" && echo --transcripts "$PATH_TRANSCRIPTS_37")" \ | |
| "$(test -e "$PATH_TRANSCRIPTS_38" && echo --transcripts "$PATH_TRANSCRIPTS_38")" \ | |
| "$(test -e "$PATH_FREQUENCIES_37" && echo --frequencies "$PATH_FREQUENCIES_37")" \ | |
| "$(test -e "$PATH_FREQUENCIES_38" && echo --frequencies "$PATH_FREQUENCIES_38")" \ | |
| "$(test -e "$PATH_CLINVAR_37" && echo --clinvar "$PATH_CLINVAR_37")" \ | |
| "$(test -e "$PATH_CLINVAR_38" && echo --clinvar "$PATH_CLINVAR_38")" \ |
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What is the current layout of the database folder (--path-db)? What should it ideally be? One issue, for example, is that we do not provide a combined refseq+ensembl transcript db anymore in the mehari-data-tx releases. That means you either have to specify both the refseq and ensembl version of the txdb, or merge the DBs beforehand and supply that instead (or we provide the pre-merged versions in the mehari-data-tx workflow, too). Either option is fine for me. |
Harmonizes CLI between
annotate seqvars,annotate strucvarsandserver, thoughannotate seqvarsis the only one to actually make use of all of the options right now.For
server, we could add endpoints for frequencies and clinvar as well, while we're at it; otherwise there's no point in adding the--frequenciesand--clinvaroptions.annotate strucvarsactually does not use any of the provided databases at the moment, since it mainly performs broad consequence predictions (transcript_variant,exon_variant,splice_region_variant,intron_variant,(up|down)stream_variant,intergenic_variant+ some seqvars predictions for the breakpoint if the svtype is ins or bnd) (correct me if I'm wrong @holtgrewe), where transcripts usually are of no use.So: should we keep these options for "the future" or just get rid of them for strucvars altogether? The old
path_dbwasn't used anywhere either.Current state summary:
annotate seqvarsandserver runnow use the same options (--transcripts,--frequencies,--clinvar, as well as transcript picking configurations)annotate strucvarsno longer expects thepath-dbargument, since that was unused, but also does not accept any of the options mentioned above--transcriptsoptions) or from the file path in case of--frequenciesand--clinvar(which expects rocksdb folders, this needs to be documented). This is a bit ugly.server runnow also exposesseqvars/frequencyandseqvars/clinvarendpointsSummary by CodeRabbit
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