datasets/merfish/pipelines/cell_by_gene/pipeline.yaml

# Copyright 2022 Google LLC
#
# 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.

---
resources:

  - type: bigquery_table
    table_id: cell_by_gene
    description: "The Merfish Mouse Brain Dataset"

dag:
  airflow_version: 2
  initialize:
    dag_id: cell_by_gene
    default_args:
      owner: "Google"
      depends_on_past: False
      start_date: '2022-08-20'
    max_active_runs: 1
    schedule_interval: "@weekly"
    catchup: False
    default_view: graph

  tasks:
    - operator: "GoogleCloudStorageToBigQueryOperator"
      description: "Task to load CSV data to a BigQuery table"
      args:
        task_id: "load_cell_by_gene_to_bq"
        bucket: "public-datasets-vizgen-merfish"
        source_objects: [
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate1/cell_by_gene_S1R1.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate2/cell_by_gene_S1R2.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate3/cell_by_gene_S1R3.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate1/cell_by_gene_S2R1.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate2/cell_by_gene_S2R2.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate3/cell_by_gene_S2R3.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate1/cell_by_gene_S3R1.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate2/cell_by_gene_S3R2.csv",
          "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate3/cell_by_gene_S3R3.csv"]
        source_format: "CSV"
        destination_project_dataset_table: "bigquery-public-data-dev.merfish.cell_by_gene"
        skip_leading_rows: 1
        allow_quoted_newlines: True
        write_disposition: "WRITE_TRUNCATE"
        schema_fields:
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  graph_paths:
    - "load_cell_by_gene_to_bq"