feat: Onboard GBIF dataset (#355)

* yaml config files * generate terraform * generate DAG
GoogleCloudPlatform · May 12, 2022 · ab4e208 · ab4e208
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diff --git a/datasets/gbif/infra/gbif_dataset.tf b/datasets/gbif/infra/gbif_dataset.tf
@@ -0,0 +1,40 @@
+/**
+ * Copyright 2021 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.
+ */
+
+
+resource "google_bigquery_dataset" "gbif" {
+ dataset_id = "gbif"
+ project = var.project_id
+ description = "The Global Biodiversity Information Facility is an international network and data infrastructure funded by the world\u0027s governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."
+}
+
+data "google_iam_policy" "bq_ds__gbif" {
+ dynamic "binding" {
+ for_each = var.iam_policies["bigquery_datasets"]["gbif"]
+ content {
+ role = binding.value["role"]
+ members = binding.value["members"]
+ }
+ }
+}
+
+resource "google_bigquery_dataset_iam_policy" "gbif" {
+ dataset_id = google_bigquery_dataset.gbif.dataset_id
+ policy_data = data.google_iam_policy.bq_ds__gbif.policy_data
+}
+output "bigquery_dataset-gbif-dataset_id" {
+ value = google_bigquery_dataset.gbif.dataset_id
+}
diff --git a/datasets/gbif/infra/gcs_to_bq_pipeline.tf b/datasets/gbif/infra/gcs_to_bq_pipeline.tf
@@ -0,0 +1,34 @@
+/**
+ * Copyright 2021 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.
+ */
+
+
+resource "google_bigquery_table" "gbif_occurrences" {
+ project = var.project_id
+ dataset_id = "gbif"
+ table_id = "occurrences"
+ description = "Evidence of the occurrence of a species (or other taxon) at a particular place on a specified date."
+ depends_on = [
+ google_bigquery_dataset.gbif
+ ]
+}
+
+output "bigquery_table-gbif_occurrences-table_id" {
+ value = google_bigquery_table.gbif_occurrences.table_id
+}
+
+output "bigquery_table-gbif_occurrences-id" {
+ value = google_bigquery_table.gbif_occurrences.id
+}
diff --git a/datasets/gbif/infra/provider.tf b/datasets/gbif/infra/provider.tf
@@ -0,0 +1,28 @@
+/**
+ * Copyright 2021 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.
+ */
+
+
+provider "google" {
+ project = var.project_id
+ impersonate_service_account = var.impersonating_acct
+ region = var.region
+}
+
+data "google_client_openid_userinfo" "me" {}
+
+output "impersonating-account" {
+ value = data.google_client_openid_userinfo.me.email
+}
diff --git a/datasets/gbif/infra/variables.tf b/datasets/gbif/infra/variables.tf
@@ -0,0 +1,26 @@
+/**
+ * Copyright 2021 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.
+ */
+
+
+variable "project_id" {}
+variable "bucket_name_prefix" {}
+variable "impersonating_acct" {}
+variable "region" {}
+variable "env" {}
+variable "iam_policies" {
+ default = {}
+}
+
diff --git a/datasets/gbif/pipelines/dataset.yaml b/datasets/gbif/pipelines/dataset.yaml
@@ -0,0 +1,26 @@
+# Copyright 2021 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.
+
+dataset:
+ name: gbif
+ friendly_name: gbif
+ description: ~
+ dataset_sources: ~
+ terms_of_use: ~
+
+resources:
+ - type: bigquery_dataset
+ dataset_id: gbif
+ description: |-
+ The Global Biodiversity Information Facility is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.
diff --git a/datasets/gbif/pipelines/gcs_to_bq/gcs_to_bq_dag.py b/datasets/gbif/pipelines/gcs_to_bq/gcs_to_bq_dag.py
@@ -0,0 +1,47 @@
+# Copyright 2021 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.
+
+
+from airflow import DAG
+from airflow.providers.google.cloud.transfers import gcs_to_bigquery
+
+default_args = {
+ "owner": "Google",
+ "depends_on_past": False,
+ "start_date": "2022-03-31",
+}
+
+
+with DAG(
+ dag_id="gbif.gcs_to_bq",
+ default_args=default_args,
+ max_active_runs=1,
+ schedule_interval="0 0 2 * *",
+ catchup=False,
+ default_view="graph",
+) as dag:
+
+ # Load Parquet files to BQ
+ load_parquet_files_to_bq = gcs_to_bigquery.GCSToBigQueryOperator(
+ task_id="load_parquet_files_to_bq",
+ bucket="{{ var.json.gbif.source_bucket }}",
+ source_objects=[
+ "occurrence/{{ execution_date.strftime('%Y-%m-01') }}/occurrence.parquet/*"
+ ],
+ source_format="PARQUET",
+ destination_project_dataset_table="gbif.occurrences",
+ write_disposition="WRITE_TRUNCATE",
+ )
+
+ load_parquet_files_to_bq
diff --git a/datasets/gbif/pipelines/gcs_to_bq/pipeline.yaml b/datasets/gbif/pipelines/gcs_to_bq/pipeline.yaml
@@ -0,0 +1,47 @@
+# Copyright 2021 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: occurrences
+ description: "Evidence of the occurrence of a species (or other taxon) at a particular place on a specified date."
+
+dag:
+ airflow_version: 2
+ initialize:
+ dag_id: gcs_to_bq
+ default_args:
+ owner: "Google"
+ depends_on_past: False
+ start_date: "2022-03-31"
+ max_active_runs: 1
+ schedule_interval: "0 0 2 * *" # Every 2nd day of the month
+ catchup: False
+ default_view: graph
+
+ tasks:
+ - operator: "GoogleCloudStorageToBigQueryOperator"
+ description: "Load Parquet files to BQ"
+ args:
+ task_id: "load_parquet_files_to_bq"
+ bucket: "{{ var.json.gbif.source_bucket }}"
+ source_objects: ["occurrence/{{ execution_date.strftime('%Y-%m-01') }}/occurrence.parquet/*"]
+ source_format: "PARQUET"
+ destination_project_dataset_table: "gbif.occurrences"
+ write_disposition: "WRITE_TRUNCATE"
+
+ graph_paths:
+ - "load_parquet_files_to_bq"