Files
DefinitelyTyped/types/gapi.client.genomics/gapi.client.genomics-tests.ts
Alexey Bolisov 4f8a3d571b Add Google APIs typings (#19083)
* Add Google APIs typings

* [gapi.cliebt.* ] Add version as part of typings name and fix gapi.client tslint errors

* versions should not get their own folders
fixing a few typos
using /** syntax so comments show up in editors
export only actual (last) version for now

* export only actual (last) version for now

* merge namespaces and remove unnecessary namespace qualifiers

* remove namespace qualifier for gapi.client.Request from nested namespaces and change Request base interface to Promise

* disable await-promise rule

* fix collision between gapi.client.Request and Request from nested namespace
disable no-irregular-whitespace rule

* sort properties and namespace resources

* remove empty comments
sort resources amd methods in tests and readme.md

* update 'this is autogenerated file' banner to remove this text from gapi.client namespace hint
use multiline comments when comment has several lines

* implement no-trailing-whitespace, no-padding, max-line-length, await-promise, no-irregular-whitespace rules

* add strictFunctionTypes to tsconfig

* fix "Whitespace within parentheses is not allowed" rule

* fix ts-lint rules

* fixes

* remove deprecated replicapool and replicapoolupdater api

* fix no-irregular-whitespace

* fix no-irregular-whitespace
2017-10-09 14:55:04 -07:00

751 lines
30 KiB
TypeScript

/* This is stub file for gapi.client.{{=it.name}} definition tests */
/* IMPORTANT.
* This file was automatically generated by https://github.com/Bolisov/google-api-typings-generator. Please do not edit it manually.
* In case of any problems please post issue to https://github.com/Bolisov/google-api-typings-generator
**/
gapi.load('client', () => {
/** now we can use gapi.client */
gapi.client.load('genomics', 'v1', () => {
/** now we can use gapi.client.genomics */
/** don't forget to authenticate your client before sending any request to resources: */
/** declare client_id registered in Google Developers Console */
const client_id = '<<PUT YOUR CLIENT ID HERE>>';
const scope = [
/** View and manage your data in Google BigQuery */
'https://www.googleapis.com/auth/bigquery',
/** View and manage your data across Google Cloud Platform services */
'https://www.googleapis.com/auth/cloud-platform',
/** Manage your data in Google Cloud Storage */
'https://www.googleapis.com/auth/devstorage.read_write',
/** View and manage Genomics data */
'https://www.googleapis.com/auth/genomics',
/** View Genomics data */
'https://www.googleapis.com/auth/genomics.readonly',
];
const immediate = true;
gapi.auth.authorize({ client_id, scope, immediate }, authResult => {
if (authResult && !authResult.error) {
/** handle succesfull authorization */
run();
} else {
/** handle authorization error */
}
});
run();
});
async function run() {
/**
* Creates one or more new annotations atomically. All annotations must
* belong to the same annotation set. Caller must have WRITE
* permission for this annotation set. For optimal performance, batch
* positionally adjacent annotations together.
*
* If the request has a systemic issue, such as an attempt to write to
* an inaccessible annotation set, the entire RPC will fail accordingly. For
* lesser data issues, when possible an error will be isolated to the
* corresponding batch entry in the response; the remaining well formed
* annotations will be created normally.
*
* For details on the requirements for each individual annotation resource,
* see
* CreateAnnotation.
*/
await gapi.client.annotations.batchCreate({
});
/**
* Creates a new annotation. Caller must have WRITE permission
* for the associated annotation set.
*
* The following fields are required:
*
* &#42; annotationSetId
* &#42; referenceName or
* referenceId
*
* ### Transcripts
*
* For annotations of type TRANSCRIPT, the following fields of
* transcript must be provided:
*
* &#42; exons.start
* &#42; exons.end
*
* All other fields may be optionally specified, unless documented as being
* server-generated (for example, the `id` field). The annotated
* range must be no longer than 100Mbp (mega base pairs). See the
* Annotation resource
* for additional restrictions on each field.
*/
await gapi.client.annotations.create({
});
/**
* Deletes an annotation. Caller must have WRITE permission for
* the associated annotation set.
*/
await gapi.client.annotations.delete({
annotationId: "annotationId",
});
/**
* Gets an annotation. Caller must have READ permission
* for the associated annotation set.
*/
await gapi.client.annotations.get({
annotationId: "annotationId",
});
/**
* Searches for annotations that match the given criteria. Results are
* ordered by genomic coordinate (by reference sequence, then position).
* Annotations with equivalent genomic coordinates are returned in an
* unspecified order. This order is consistent, such that two queries for the
* same content (regardless of page size) yield annotations in the same order
* across their respective streams of paginated responses. Caller must have
* READ permission for the queried annotation sets.
*/
await gapi.client.annotations.search({
});
/**
* Updates an annotation. Caller must have
* WRITE permission for the associated dataset.
*/
await gapi.client.annotations.update({
annotationId: "annotationId",
updateMask: "updateMask",
});
/**
* Creates a new annotation set. Caller must have WRITE permission for the
* associated dataset.
*
* The following fields are required:
*
* &#42; datasetId
* &#42; referenceSetId
*
* All other fields may be optionally specified, unless documented as being
* server-generated (for example, the `id` field).
*/
await gapi.client.annotationsets.create({
});
/**
* Deletes an annotation set. Caller must have WRITE permission
* for the associated annotation set.
*/
await gapi.client.annotationsets.delete({
annotationSetId: "annotationSetId",
});
/**
* Gets an annotation set. Caller must have READ permission for
* the associated dataset.
*/
await gapi.client.annotationsets.get({
annotationSetId: "annotationSetId",
});
/**
* Searches for annotation sets that match the given criteria. Annotation sets
* are returned in an unspecified order. This order is consistent, such that
* two queries for the same content (regardless of page size) yield annotation
* sets in the same order across their respective streams of paginated
* responses. Caller must have READ permission for the queried datasets.
*/
await gapi.client.annotationsets.search({
});
/**
* Updates an annotation set. The update must respect all mutability
* restrictions and other invariants described on the annotation set resource.
* Caller must have WRITE permission for the associated dataset.
*/
await gapi.client.annotationsets.update({
annotationSetId: "annotationSetId",
updateMask: "updateMask",
});
/**
* Creates a new call set.
*
* For the definitions of call sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.callsets.create({
});
/**
* Deletes a call set.
*
* For the definitions of call sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.callsets.delete({
callSetId: "callSetId",
});
/**
* Gets a call set by ID.
*
* For the definitions of call sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.callsets.get({
callSetId: "callSetId",
});
/**
* Updates a call set.
*
* For the definitions of call sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* This method supports patch semantics.
*/
await gapi.client.callsets.patch({
callSetId: "callSetId",
updateMask: "updateMask",
});
/**
* Gets a list of call sets matching the criteria.
*
* For the definitions of call sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
*/
await gapi.client.callsets.search({
});
/**
* Creates a new dataset.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.datasets.create({
});
/**
* Deletes a dataset and all of its contents (all read group sets,
* reference sets, variant sets, call sets, annotation sets, etc.)
* This is reversible (up to one week after the deletion) via
* the
* datasets.undelete
* operation.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.datasets.delete({
datasetId: "datasetId",
});
/**
* Gets a dataset by ID.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.datasets.get({
datasetId: "datasetId",
});
/**
* Gets the access control policy for the dataset. This is empty if the
* policy or resource does not exist.
*
* See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
* Policy</a> for more information.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.datasets.getIamPolicy({
resource: "resource",
});
/**
* Lists datasets within a project.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.datasets.list({
pageSize: 1,
pageToken: "pageToken",
projectId: "projectId",
});
/**
* Updates a dataset.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* This method supports patch semantics.
*/
await gapi.client.datasets.patch({
datasetId: "datasetId",
updateMask: "updateMask",
});
/**
* Sets the access control policy on the specified dataset. Replaces any
* existing policy.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
* Policy</a> for more information.
*/
await gapi.client.datasets.setIamPolicy({
resource: "resource",
});
/**
* Returns permissions that a caller has on the specified resource.
* See <a href="/iam/docs/managing-policies#testing_permissions">Testing
* Permissions</a> for more information.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.datasets.testIamPermissions({
resource: "resource",
});
/**
* Undeletes a dataset by restoring a dataset which was deleted via this API.
*
* For the definitions of datasets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* This operation is only possible for a week after the deletion occurred.
*/
await gapi.client.datasets.undelete({
datasetId: "datasetId",
});
/**
* Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed.
* Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite
* cancellation.
*/
await gapi.client.operations.cancel({
name: "name",
});
/**
* Gets the latest state of a long-running operation. Clients can use this
* method to poll the operation result at intervals as recommended by the API
* service.
*/
await gapi.client.operations.get({
name: "name",
});
/** Lists operations that match the specified filter in the request. */
await gapi.client.operations.list({
filter: "filter",
name: "name",
pageSize: 3,
pageToken: "pageToken",
});
/**
* Deletes a read group set.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.readgroupsets.delete({
readGroupSetId: "readGroupSetId",
});
/**
* Exports a read group set to a BAM file in Google Cloud Storage.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Note that currently there may be some differences between exported BAM
* files and the original BAM file at the time of import. See
* ImportReadGroupSets
* for caveats.
*/
await gapi.client.readgroupsets.export({
readGroupSetId: "readGroupSetId",
});
/**
* Gets a read group set by ID.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.readgroupsets.get({
readGroupSetId: "readGroupSetId",
});
/**
* Creates read group sets by asynchronously importing the provided
* information.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* The caller must have WRITE permissions to the dataset.
*
* ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
*
* - Tags will be converted to strings - tag types are not preserved
* - Comments (`@CO`) in the input file header will not be preserved
* - Original header order of references (`@SQ`) will not be preserved
* - Any reverse stranded unmapped reads will be reverse complemented, and
* their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
* - Unmapped reads will be stripped of positional information (reference name
* and position)
*/
await gapi.client.readgroupsets.import({
});
/**
* Updates a read group set.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* This method supports patch semantics.
*/
await gapi.client.readgroupsets.patch({
readGroupSetId: "readGroupSetId",
updateMask: "updateMask",
});
/**
* Searches for read group sets matching the criteria.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
*/
await gapi.client.readgroupsets.search({
});
/**
* Gets a list of reads for one or more read group sets.
*
* For the definitions of read group sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Reads search operates over a genomic coordinate space of reference sequence
* & position defined over the reference sequences to which the requested
* read group sets are aligned.
*
* If a target positional range is specified, search returns all reads whose
* alignment to the reference genome overlap the range. A query which
* specifies only read group set IDs yields all reads in those read group
* sets, including unmapped reads.
*
* All reads returned (including reads on subsequent pages) are ordered by
* genomic coordinate (by reference sequence, then position). Reads with
* equivalent genomic coordinates are returned in an unspecified order. This
* order is consistent, such that two queries for the same content (regardless
* of page size) yield reads in the same order across their respective streams
* of paginated responses.
*
* Implements
* [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
*/
await gapi.client.reads.search({
});
/**
* Gets a reference.
*
* For the definitions of references and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
*/
await gapi.client.references.get({
referenceId: "referenceId",
});
/**
* Searches for references which match the given criteria.
*
* For the definitions of references and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
*/
await gapi.client.references.search({
});
/**
* Gets a reference set.
*
* For the definitions of references and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
*/
await gapi.client.referencesets.get({
referenceSetId: "referenceSetId",
});
/**
* Searches for reference sets which match the given criteria.
*
* For the definitions of references and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
*/
await gapi.client.referencesets.search({
});
/**
* Creates a new variant.
*
* For the definitions of variants and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variants.create({
});
/**
* Deletes a variant.
*
* For the definitions of variants and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variants.delete({
variantId: "variantId",
});
/**
* Gets a variant by ID.
*
* For the definitions of variants and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variants.get({
variantId: "variantId",
});
/**
* Creates variant data by asynchronously importing the provided information.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* The variants for import will be merged with any existing variant that
* matches its reference sequence, start, end, reference bases, and
* alternative bases. If no such variant exists, a new one will be created.
*
* When variants are merged, the call information from the new variant
* is added to the existing variant, and Variant info fields are merged
* as specified in
* infoMergeConfig.
* As a special case, for single-sample VCF files, QUAL and FILTER fields will
* be moved to the call level; these are sometimes interpreted in a
* call-specific context.
* Imported VCF headers are appended to the metadata already in a variant set.
*/
await gapi.client.variants.import({
});
/**
* Merges the given variants with existing variants.
*
* For the definitions of variants and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Each variant will be
* merged with an existing variant that matches its reference sequence,
* start, end, reference bases, and alternative bases. If no such variant
* exists, a new one will be created.
*
* When variants are merged, the call information from the new variant
* is added to the existing variant. Variant info fields are merged as
* specified in the
* infoMergeConfig
* field of the MergeVariantsRequest.
*
* Please exercise caution when using this method! It is easy to introduce
* mistakes in existing variants and difficult to back out of them. For
* example,
* suppose you were trying to merge a new variant with an existing one and
* both
* variants contain calls that belong to callsets with the same callset ID.
*
* // Existing variant - irrelevant fields trimmed for clarity
* {
* "variantSetId": "10473108253681171589",
* "referenceName": "1",
* "start": "10582",
* "referenceBases": "G",
* "alternateBases": [
* "A"
* ],
* "calls": [
* {
* "callSetId": "10473108253681171589-0",
* "callSetName": "CALLSET0",
* "genotype": [
* 0,
* 1
* ],
* }
* ]
* }
*
* // New variant with conflicting call information
* {
* "variantSetId": "10473108253681171589",
* "referenceName": "1",
* "start": "10582",
* "referenceBases": "G",
* "alternateBases": [
* "A"
* ],
* "calls": [
* {
* "callSetId": "10473108253681171589-0",
* "callSetName": "CALLSET0",
* "genotype": [
* 1,
* 1
* ],
* }
* ]
* }
*
* The resulting merged variant would overwrite the existing calls with those
* from the new variant:
*
* {
* "variantSetId": "10473108253681171589",
* "referenceName": "1",
* "start": "10582",
* "referenceBases": "G",
* "alternateBases": [
* "A"
* ],
* "calls": [
* {
* "callSetId": "10473108253681171589-0",
* "callSetName": "CALLSET0",
* "genotype": [
* 1,
* 1
* ],
* }
* ]
* }
*
* This may be the desired outcome, but it is up to the user to determine if
* if that is indeed the case.
*/
await gapi.client.variants.merge({
});
/**
* Updates a variant.
*
* For the definitions of variants and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* This method supports patch semantics. Returns the modified variant without
* its calls.
*/
await gapi.client.variants.patch({
updateMask: "updateMask",
variantId: "variantId",
});
/**
* Gets a list of variants matching the criteria.
*
* For the definitions of variants and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
*/
await gapi.client.variants.search({
});
/**
* Creates a new variant set.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* The provided variant set must have a valid `datasetId` set - all other
* fields are optional. Note that the `id` field will be ignored, as this is
* assigned by the server.
*/
await gapi.client.variantsets.create({
});
/**
* Deletes a variant set including all variants, call sets, and calls within.
* This is not reversible.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variantsets.delete({
variantSetId: "variantSetId",
});
/**
* Exports variant set data to an external destination.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variantsets.export({
variantSetId: "variantSetId",
});
/**
* Gets a variant set by ID.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variantsets.get({
variantSetId: "variantSetId",
});
/**
* Updates a variant set using patch semantics.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*/
await gapi.client.variantsets.patch({
updateMask: "updateMask",
variantSetId: "variantSetId",
});
/**
* Returns a list of all variant sets matching search criteria.
*
* For the definitions of variant sets and other genomics resources, see
* [Fundamentals of Google
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
*
* Implements
* [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
*/
await gapi.client.variantsets.search({
});
}
});