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[BIOMAGE-2015] Removed dynamo references #399

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merged 2 commits into from
Jul 25, 2022
Merged

[BIOMAGE-2015] Removed dynamo references #399

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1413555
removed dynamo references
kafkasl Jul 25, 2022
04ebb12
removed unused snapshot
kafkasl Jul 25, 2022
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4 changes: 2 additions & 2 deletions src/specs/models/work-request-bodies/WorkRequestDifferentialExpression.v2.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,12 @@ properties:
description: |-
The cell set for preliminary selection of cells to compare.

This must be a valid UUID of a cell set as found in DynamoDB. All operations in `DifferentialExpression` will only consider cells that are found in this cell set.
This must be a valid UUID of a cell set as found in the DB. All operations in `DifferentialExpression` will only consider cells that are found in this cell set.

If not specified, no preliminary selection is done and the entire experiment is used as a basis for computation.
cellSet:
type: string
description: The first cell set differential expression is run on. This must be a valid UUID of a cell set as found in DynamoDB.
description: The first cell set differential expression is run on. This must be a valid UUID of a cell set as found in the DB.
compareWith:
type: string
description: |-
Expand Down
6 changes: 3 additions & 3 deletions src/sql/migrations/20220304184711_schema.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@ CREATE OR REPLACE FUNCTION public.delete_sample_file_if_orphan()
AS $function$
BEGIN
DELETE FROM sample_file
WHERE
WHERE
sample_file.id = OLD.sample_file_id AND
NOT EXISTS(
SELECT FROM sample_to_sample_file_map sf_map
SELECT FROM sample_to_sample_file_map sf_map
WHERE sf_map.sample_file_id = OLD.sample_file_id AND NOT OLD.sample_id = sf_map.sample_id
);
RETURN OLD;
Expand Down Expand Up @@ -41,7 +41,7 @@ const setupEnums = async (knex) => {
await knex.raw('CREATE TYPE sample_technology AS ENUM (\'10x\', \'rhapsody\');');
await knex.raw('CREATE TYPE sample_file_type AS ENUM (\'features10x\', \'barcodes10x\', \'matrix10x\', \'rhapsody\');');
await knex.raw(
'CREATE TYPE upload_status AS ENUM (\'uploaded\', \'uploading\', \'compressing\', \'uploadError\', \'fileNotFound\', \'fileReadError\', \'fileReadAborted\');',
'CREATE TYPE upload_status AS ENUM (\'invalidFormat\', \'uploaded\', \'uploading\', \'compressing\', \'uploadError\', \'fileNotFound\', \'fileReadError\', \'fileReadAborted\');',
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I don't think we can do this change here, you need to add a new migration to add invalidFormat to the upload_status

);
await knex.raw('CREATE TYPE access_role AS ENUM (\'owner\', \'admin\', \'explorer\', \'viewer\');');
};
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74 changes: 0 additions & 74 deletions src/utils/dynamoDb.js
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This file was deleted.

109 changes: 0 additions & 109 deletions src/utils/safeBatchGetItem.js
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153 changes: 0 additions & 153 deletions tests/test-utils/mockAWSServices.js
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Expand Up @@ -2,150 +2,6 @@ const AWSMock = require('aws-sdk-mock');
const _ = require('lodash');
const AWS = require('../../src/utils/requireAWS');

const marshallTableResults = (entries) => entries.map(
(entry) => AWS.DynamoDB.Converter.marshall(entry),
);

const mockDynamoGetItem = (payload = {}, error = null) => {
const dynamodbData = {
Item: AWS.DynamoDB.Converter.marshall(payload),
};

const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB', 'getItem', (params, callback) => {
fnSpy(params);
callback(error, dynamodbData);
});
return fnSpy;
};

const mockDynamoBatchGetItem = (response = {}, error = null) => {
const dynamodbData = {
Responses: _.mapValues(response.Responses, marshallTableResults),
};

const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB', 'batchGetItem', (params, callback) => {
fnSpy(params);
callback(error, dynamodbData);
});
return fnSpy;
};

const mockDynamoDeleteItem = (payload = {}, error = null) => {
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB', 'deleteItem', (params, callback) => {
fnSpy(params);
callback(error, payload);
});
return fnSpy;
};

const mockDynamoQuery = (payload = [], error = null) => {
const payloadToReturn = !Array.isArray(payload) ? [payload] : payload;

const dynamodbData = {
Items: payloadToReturn.map((entry) => AWS.DynamoDB.Converter.marshall(entry)),
};
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB', 'query', (params, callback) => {
fnSpy(params);
callback(error, dynamodbData);
});
return fnSpy;
};

const mockDocClientPutItem = (payload = {}, error = null) => {
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB.DocumentClient', 'put', (params, callback) => {
fnSpy(params);
callback(error, payload);
});
return fnSpy;
};

const mockDocClientQuery = (payload = [], error = null) => {
const payloadToReturn = !Array.isArray(payload) ? [payload] : payload;

const dynamodbData = {
Items: payloadToReturn,
};
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB.DocumentClient', 'query', (params, callback) => {
fnSpy(params);
callback(error, dynamodbData);
});
return fnSpy;
};

const mockDocClientBatchWrite = (payload = {}, error = null) => {
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB.DocumentClient', 'batchWrite', (params, callback) => {
fnSpy(params);
callback(error, payload);
});
return fnSpy;
};

/**
* Mocks the scan operation in dynamodb
*
* @param {Array} payloadPages the payloads to return in each scan operation in order
* (for pagination, also returns the LastEvaluatedKey if it has more than one page)
* @returns An object containing descriptions of projects.
*/
const mockDynamoScan = (payloadPages, error = null) => {
const pagesLength = payloadPages.length;
const dynamodbDbDataPages = payloadPages.map((page, i) => {
const isLastPage = pagesLength === i + 1;

const lastKey = isLastPage ? null : AWS.DynamoDB.Converter.marshall(_.first(payloadPages[i + 1]));
const items = page.map((entry) => AWS.DynamoDB.Converter.marshall(entry));

const response = { Items: items };

if (!isLastPage) {
response.LastEvaluatedKey = lastKey;
}

return response;
});

const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);

let callNumber = 0;
AWSMock.mock('DynamoDB', 'scan', (params, callback) => {
fnSpy(params);

callback(error, dynamodbDbDataPages[callNumber]);

callNumber += 1;
});

return fnSpy;
};

const mockDynamoUpdateItem = (payload = {}, error = null) => {
const dynamodbData = {
Attributes: AWS.DynamoDB.Converter.marshall(payload),
};
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
AWSMock.mock('DynamoDB', 'updateItem', (params, callback) => {
fnSpy(params);
callback(error, dynamodbData);
});
return fnSpy;
};

const mockS3GetObject = (payload = {}, error = null) => {
const fnSpy = jest.fn((x) => x);
AWSMock.setSDKInstance(AWS);
Expand Down Expand Up @@ -213,19 +69,10 @@ const mockS3GetSignedUrl = (payload = {}, error = null) => {
};

module.exports = {
mockDynamoGetItem,
mockDynamoBatchGetItem,
mockDynamoQuery,
mockDynamoScan,
mockDynamoUpdateItem,
mockDynamoDeleteItem,
mockS3GetObject,
mockS3PutObject,
mockS3DeleteObject,
mockS3DeleteObjects,
mockS3GetSignedUrl,
mockS3GetObjectTagging,
mockDocClientQuery,
mockDocClientBatchWrite,
mockDocClientPutItem,
};
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