fetchSequenceChecksums.ts 2.72 KB
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/**
 * See the NOTICE file distributed with this work for additional information
 * regarding copyright ownership.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

import { gql } from '@apollo/client';

import { client } from 'src/gql-client';

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export type TranscriptSequenceMetadata = {
  cdna?: {
    checksum: string;
    label: string;
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  };
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  cds?: {
    checksum: string;
    label: string;
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  };
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  protein?: {
    checksum: string;
    label: string;
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  };
};

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type TranscriptQueryResult = {
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  transcript: {
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    product_generating_contexts: Array<{
      cdna: {
        sequence_checksum: string;
      };
      cds: {
        sequence_checksum: string;
      };
      product: {
        stable_id: string;
        sequence_checksum: string;
      };
    }>;
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  };
};

const transcriptChecksumsQuery = gql`
  query Transcript($genomeId: String!, $transcriptId: String!) {
    transcript(byId: { genome_id: $genomeId, stable_id: $transcriptId }) {
      product_generating_contexts {
        cds {
          sequence_checksum
        }
        cdna {
          sequence_checksum
        }
        product {
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          stable_id
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          sequence_checksum
        }
      }
    }
  }
`;

type Variables = {
  genomeId: string;
  transcriptId: string;
};

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export const fetchTranscriptSequenceMetadata = (
  variables: Variables
): Promise<TranscriptSequenceMetadata> => {
  const { transcriptId } = variables;

  return client
    .query<TranscriptQueryResult>({
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      query: transcriptChecksumsQuery,
      variables
    })
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    .then(({ data }) => {
      // TODO: expect to fetch genomic sequence here as well when checksum becomes available
      const productGeneratingContext =
        data.transcript.product_generating_contexts[0];
      if (!productGeneratingContext) {
        return {};
      }

      return {
        cdna: {
          checksum: productGeneratingContext.cdna.sequence_checksum,
          label: `${transcriptId} cdna`
        },
        cds: {
          checksum: productGeneratingContext.cds.sequence_checksum,
          label: `${transcriptId} cds`
        },
        protein: {
          checksum: productGeneratingContext.product.sequence_checksum,
          label: `${productGeneratingContext.product.stable_id} pep`
        }
      };
    });
};