REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6
This API client was generated by the OpenAPI Generator project. By using the OpenAPI spec from a remote server, you can easily generate an API client.
Install the dependencies
install.packages("jsonlite")
install.packages("httr")
install.packages("base64enc")
git clone https://github.com/GIT_USER_ID/GIT_REPO_ID
cd GIT_REPO_ID
R CMD build .
R CMD check RSirius_6.5.4.tar.gz --no-manual
R CMD INSTALL --preclean RSirius_6.5.4.tar.gz
install.packages("RSirius")
To install directly from Github, use devtools:
install.packages("devtools")
library(devtools)
install_github("GIT_USER_ID/GIT_REPO_ID")
To install the package from a local file:
install.packages("RSirius_6.5.4.tar.gz", repos = NULL, type = "source")
library(RSirius)
To reformat code using styler, please run the following in the R console:
install.packages("remotes")
remotes::install_github("r-lib/styler@v1.7.0.9003")
library("styler")
style_dir()
All URIs are relative to http://localhost:8080
| Class | Method | HTTP request | Description |
|---|---|---|---|
| ActuatorApi | Health | GET /actuator/health | Actuator web endpoint 'health' |
| ActuatorApi | Shutdown | POST /actuator/shutdown | Actuator web endpoint 'shutdown' |
| CompoundsApi | AddCompounds | POST /api/projects/{projectId}/compounds | Import compounds and their contained features. |
| CompoundsApi | DeleteCompound | DELETE /api/projects/{projectId}/compounds/{compoundId} | Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. |
| CompoundsApi | GetCompound | GET /api/projects/{projectId}/compounds/{compoundId} | Get compound (group of ion identities) with the given identifier from the specified project-space. |
| CompoundsApi | GetCompoundQuantTable | GET /api/projects/{projectId}/compounds/quant-table | Returns the full quantification table of compounds |
| CompoundsApi | GetCompounds | GET /api/projects/{projectId}/compounds | [DEPRECATED] List of all available compounds (group of ion identities) in the given project-space |
| CompoundsApi | GetCompoundsPage | GET /api/projects/{projectId}/compounds/page | Page of available compounds (group of ion identities) in the given project-space |
| CompoundsApi | GetCompoundsSearchableFields | GET /api/projects/{projectId}/compounds/searchable-fields | Get all fields that can be used in the searchQuery parameter of compound endpoints |
| FeaturesApi | AddAlignedFeatures | POST /api/projects/{projectId}/aligned-features | Import (aligned) features into the project. |
| FeaturesApi | DeleteAlignedFeature | DELETE /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Delete feature (aligned over runs) with the given identifier from the specified project-space. |
| FeaturesApi | DeleteAlignedFeatures | PUT /api/projects/{projectId}/aligned-features/delete | Delete feature (aligned over runs) with the given identifier from the specified project-space. |
| FeaturesApi | DeleteAlignedFeaturesByQuery | PUT /api/projects/{projectId}/aligned-features/delete-by-query | Delete all features (aligned over runs) that match the given lucene search query from the specified project-space. |
| FeaturesApi | GetAlignedFeature | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Get feature (aligned over runs) with the given identifier from the specified project-space. |
| FeaturesApi | GetAlignedFeatures | GET /api/projects/{projectId}/aligned-features | [DEPRECATED] Get all available features (aligned over runs) in the given project-space |
| FeaturesApi | GetAlignedFeaturesPage | GET /api/projects/{projectId}/aligned-features/page | Get features (aligned over runs) in the given project-space |
| FeaturesApi | GetAlignedFeaturesSearchableFields | GET /api/projects/{projectId}/aligned-features/searchable-fields | Get all fields that can be used in the searchQuery parameter of feature (aligned over runs) endpoints |
| FeaturesApi | GetBestMatchingCompoundClasses | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes | Return Best matching compound classes for given formulaId |
| FeaturesApi | GetCanopusPrediction | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction | All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, |
| FeaturesApi | GetDeNovoStructureCandidates | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | [DEPRECATED] List of de novo structure candidates (e |
| FeaturesApi | GetDeNovoStructureCandidatesByFormula | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures | [DEPRECATED] List of de novo structure candidates (e |
| FeaturesApi | GetDeNovoStructureCandidatesByFormulaPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. |
| FeaturesApi | GetDeNovoStructureCandidatesPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. |
| FeaturesApi | GetFeatureQuantTable | GET /api/projects/{projectId}/aligned-features/quant-table | Returns the full quantification table of features |
| FeaturesApi | GetFeatures | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/features | [DEPRECATED] Get all features the given feature (aligned over runs) was aligned from |
| FeaturesApi | GetFeaturesPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/features/page | Page of features the given feature (aligned over runs) was aligned from, one per run it has been detected in |
| FeaturesApi | GetFingerprintPrediction | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint | Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) |
| FeaturesApi | GetFormulaAnnotatedMsMsData | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata | Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId |
| FeaturesApi | GetFormulaAnnotatedSpectrum | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum | Returns a fragmentation spectrum (e |
| FeaturesApi | GetFormulaCandidate | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId} | FormulaResultContainers for the given 'formulaId' with minimal information. |
| FeaturesApi | GetFormulaCandidates | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas | [DEPRECATED] List of FormulaResultContainers available for this feature with minimal information |
| FeaturesApi | GetFormulaCandidatesPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page | Page of FormulaResultContainers available for this feature with minimal information. |
| FeaturesApi | GetFragTree | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree | Returns fragmentation tree (SIRIUS) for the given formula result identifier |
| FeaturesApi | GetIsotopePatternAnnotation | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern | Returns Isotope pattern information for given formulaId |
| FeaturesApi | GetLipidAnnotation | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation | Returns Lipid annotation (ElGordo) for the given formulaId |
| FeaturesApi | GetMsData | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data | Mass Spec data (input data) for the given 'alignedFeatureId' . |
| FeaturesApi | GetSpectralLibraryMatch | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId} | Spectral library match for the given 'alignedFeatureId'. |
| FeaturesApi | GetSpectralLibraryMatches | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches | [DEPRECATED] List of spectral library matches for the given 'alignedFeatureId' |
| FeaturesApi | GetSpectralLibraryMatchesPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page | Page of spectral library matches for the given 'alignedFeatureId'. |
| FeaturesApi | GetSpectralLibraryMatchesSummary | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary | Summarize matched reference spectra for the given 'alignedFeatureId'. |
| FeaturesApi | GetStructureCandidates | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures | [DEPRECATED] List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information |
| FeaturesApi | GetStructureCandidatesByFormula | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures | [DEPRECATED] List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information |
| FeaturesApi | GetStructureCandidatesByFormulaPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page | Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. |
| FeaturesApi | GetStructureCandidatesPage | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page | Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. |
| GuiApi | CloseGui | DELETE /api/projects/{projectId}/gui | Close GUI instance of given project-space if available. |
| GuiApi | GetGuis | GET /api/guis | Get list of currently running gui windows, managed by this SIRIUS instance. |
| GuiApi | OpenGui | POST /api/projects/{projectId}/gui | Open GUI instance on specified project-space and bring the GUI window to foreground. |
| InfoApi | GetConnectionCheck | GET /api/connection-status | |
| InfoApi | GetInfo | GET /api/info | |
| JobsApi | DeleteJob | DELETE /api/projects/{projectId}/jobs/{jobId} | Delete job. |
| JobsApi | DeleteJobConfig | DELETE /api/job-configs/{name} | Delete job configuration with given name. |
| JobsApi | DeleteJobs | DELETE /api/projects/{projectId}/jobs | Delete ALL jobs. |
| JobsApi | GetCommand | POST /api/job-configs/get-command | Get a CLI command for the given job configuration. |
| JobsApi | GetDefaultJobConfig | GET /api/default-job-config | Request default job configuration |
| JobsApi | GetJob | GET /api/projects/{projectId}/jobs/{jobId} | Get job information and its current state and progress (if available). |
| JobsApi | GetJobConfig | GET /api/job-configs/{name} | Request job configuration with given name. |
| JobsApi | GetJobConfigNames | GET /api/job-config-names | [DEPRECATED] Get all (non-default) job configuration names |
| JobsApi | GetJobConfigs | GET /api/job-configs | Request all available job configurations |
| JobsApi | GetJobs | GET /api/projects/{projectId}/jobs | [DEPRECATED] Get list of all available jobs with information such as current state and progress (if available) |
| JobsApi | GetJobsPage | GET /api/projects/{projectId}/jobs/page | Get Page of jobs with information such as current state and progress (if available). |
| JobsApi | HasJobs | GET /api/projects/{projectId}/has-jobs | |
| JobsApi | SaveJobConfig | POST /api/job-configs/{name} | Add new job configuration with given name. |
| JobsApi | StartJob | POST /api/projects/{projectId}/jobs | Start computation for given compounds and with given parameters. |
| JobsApi | StartJobFromConfig | POST /api/projects/{projectId}/jobs/from-config | Start computation for given compounds and with parameters from a stored job-config. |
| LoginAndAccountApi | GetAccountInfo | GET /api/account/ | Get information about the account currently logged in. |
| LoginAndAccountApi | GetSignUpURL | GET /api/account/signUpURL | Get SignUp URL (For signUp via web browser) |
| LoginAndAccountApi | GetSubscriptions | GET /api/account/subscriptions | Get available subscriptions of the account currently logged in. |
| LoginAndAccountApi | IsLoggedIn | GET /api/account/isLoggedIn | Check if a user is logged in. |
| LoginAndAccountApi | Login | POST /api/account/login | Login into SIRIUS web services and activate default subscription if available. |
| LoginAndAccountApi | Logout | POST /api/account/logout | Logout from SIRIUS web services. |
| LoginAndAccountApi | OpenPortal | GET /api/account/openPortal | Open User portal in browser. |
| LoginAndAccountApi | SelectSubscription | PUT /api/account/subscriptions/select-active | Select a subscription as active subscription to be used for computations. |
| LoginAndAccountApi | SignUp | GET /api/account/signUp | Open SignUp window in system browser and return signUp link. |
| ProjectsApi | BuildSearchIndex | PUT /api/projects/{projectId}/index | Create a search index for the given project. |
| ProjectsApi | CloseProject | DELETE /api/projects/{projectId} | Close project-space and remove it from the application |
| ProjectsApi | Create | POST /api/projects/create | Create and open a new project with unique autogenerated projectId. |
| ProjectsApi | CreateProject | POST /api/projects/{projectId} | Create and open a new project-space at given location and make it accessible via the given projectId. |
| ProjectsApi | GetCanopusClassyFireData | GET /api/projects/{projectId}/cf-data | Get CANOPUS prediction vector definition for ClassyFire classes |
| ProjectsApi | GetCanopusNpcData | GET /api/projects/{projectId}/npc-data | Get CANOPUS prediction vector definition for NPC classes |
| ProjectsApi | GetFingerIdData | GET /api/projects/{projectId}/fingerid-data | Get CSI:FingerID fingerprint (prediction vector) definition |
| ProjectsApi | GetProject | GET /api/projects/{projectId} | Get project space info by its projectId. |
| ProjectsApi | GetProjects | GET /api/projects | List opened project spaces. |
| ProjectsApi | ImportMsRunData | POST /api/projects/{projectId}/import/ms-data-files | Import and align full MS runs from various formats into the specified project Possible formats: mzML, mzXML. |
| ProjectsApi | ImportMsRunDataAsJob | POST /api/projects/{projectId}/import/ms-data-files-job | Import and align full MS runs from various formats into the specified project as background job. |
| ProjectsApi | ImportPreprocessedData | POST /api/projects/{projectId}/import/preprocessed-data-files | Import already preprocessed ms/ms data from various formats into the specified project Possible formats: ms, mgf, cef, msp. |
| ProjectsApi | ImportPreprocessedDataAsJob | POST /api/projects/{projectId}/import/preprocessed-data-files-job | Import ms/ms data from the given format into the specified project-space as background job. |
| ProjectsApi | OpenProject | PUT /api/projects/{projectId} | Open an existing project-space and make it accessible via the given projectId. |
| RunsApi | GetRun | GET /api/projects/{projectId}/runs/{runId} | Get run with the given identifier from the specified project-space. |
| RunsApi | GetRunsPage | GET /api/projects/{projectId}/runs/page | Get runs in the given project-space |
| RunsApi | GetRunsSearchableFields | GET /api/projects/{projectId}/runs/searchable-fields | Get all fields that can be used in the searchQuery parameter of run endpoints |
| SearchableDatabasesApi | AddDatabases | POST /api/databases | [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. |
| SearchableDatabasesApi | CreateDatabase | POST /api/databases/{databaseId} | Create a new, empty custom database |
| SearchableDatabasesApi | GetCustomDatabases | GET /api/databases/custom | List only the custom databases, that is the structure databases and spectral libraries the user has created or added. |
| SearchableDatabasesApi | GetDatabase | GET /api/databases/{databaseId} | Get a single searchable database by its id. |
| SearchableDatabasesApi | GetDatabases | GET /api/databases | List all searchable databases, both the ones included in SIRIUS and the custom ones added by the user |
| SearchableDatabasesApi | GetIncludedDatabases | GET /api/databases/included | List only the databases that ship with SIRIUS, such as PubChem and the bio databases. |
| SearchableDatabasesApi | ImportIntoDatabase | POST /api/databases/{databaseId}/import/from-files | Start import of structure and spectra files into the specified database. |
| SearchableDatabasesApi | RemoveDatabase | DELETE /api/databases/{databaseId} | Remove a custom database from this SIRIUS instance, and optionally delete it from disk |
| SearchableDatabasesApi | UpdateDatabase | PUT /api/databases/{databaseId} | Change the settings of an existing custom database |
Endpoints do not require authorization.