From 4333fca7aea2343ff8ed53c7436e477544a27e39 Mon Sep 17 00:00:00 2001 From: gkodukula <95613561+gkodukula@users.noreply.github.com> Date: Wed, 24 Aug 2022 01:14:27 +0530 Subject: [PATCH] Feat: Onboard MERFISH Mouse Brain Receptor Map dataset (#457) --- .../merfish/infra/cell_by_gene_pipeline.tf | 34 + .../merfish/infra/cell_metadata_pipeline.tf | 34 + .../infra/detected_transcripts_pipeline.tf | 34 + datasets/merfish/infra/merfish_dataset.tf | 25 + datasets/merfish/infra/provider.tf | 28 + datasets/merfish/infra/variables.tf | 26 + .../cell_by_gene/cell_by_gene_dag.py | 1758 +++++++++++ .../pipelines/cell_by_gene/pipeline.yaml | 2655 +++++++++++++++++ .../cell_metadata/cell_metadata_dag.py | 96 + .../pipelines/cell_metadata/pipeline.yaml | 87 + datasets/merfish/pipelines/dataset.yaml | 25 + .../detected_transcripts_dag.py | 87 + .../detected_transcripts/pipeline.yaml | 91 + 13 files changed, 4980 insertions(+) create mode 100644 datasets/merfish/infra/cell_by_gene_pipeline.tf create mode 100644 datasets/merfish/infra/cell_metadata_pipeline.tf create mode 100644 datasets/merfish/infra/detected_transcripts_pipeline.tf create mode 100644 datasets/merfish/infra/merfish_dataset.tf create mode 100644 datasets/merfish/infra/provider.tf create mode 100644 datasets/merfish/infra/variables.tf create mode 100644 datasets/merfish/pipelines/cell_by_gene/cell_by_gene_dag.py create mode 100644 datasets/merfish/pipelines/cell_by_gene/pipeline.yaml create mode 100644 datasets/merfish/pipelines/cell_metadata/cell_metadata_dag.py create mode 100644 datasets/merfish/pipelines/cell_metadata/pipeline.yaml create mode 100644 datasets/merfish/pipelines/dataset.yaml create mode 100644 datasets/merfish/pipelines/detected_transcripts/detected_transcripts_dag.py create mode 100644 datasets/merfish/pipelines/detected_transcripts/pipeline.yaml diff --git a/datasets/merfish/infra/cell_by_gene_pipeline.tf b/datasets/merfish/infra/cell_by_gene_pipeline.tf new file mode 100644 index 000000000..7f10bc0a9 --- /dev/null +++ b/datasets/merfish/infra/cell_by_gene_pipeline.tf @@ -0,0 +1,34 @@ +/** + * 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. + */ + + +resource "google_bigquery_table" "merfish_cell_by_gene" { + project = var.project_id + dataset_id = "merfish" + table_id = "cell_by_gene" + description = "The Merfish Mouse Brain Dataset" + depends_on = [ + google_bigquery_dataset.merfish + ] +} + +output "bigquery_table-merfish_cell_by_gene-table_id" { + value = google_bigquery_table.merfish_cell_by_gene.table_id +} + +output "bigquery_table-merfish_cell_by_gene-id" { + value = google_bigquery_table.merfish_cell_by_gene.id +} diff --git a/datasets/merfish/infra/cell_metadata_pipeline.tf b/datasets/merfish/infra/cell_metadata_pipeline.tf new file mode 100644 index 000000000..afba589ab --- /dev/null +++ b/datasets/merfish/infra/cell_metadata_pipeline.tf @@ -0,0 +1,34 @@ +/** + * 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. + */ + + +resource "google_bigquery_table" "merfish_cell_metadata" { + project = var.project_id + dataset_id = "merfish" + table_id = "cell_metadata" + description = "The Merfish Mouse Brain Dataset" + depends_on = [ + google_bigquery_dataset.merfish + ] +} + +output "bigquery_table-merfish_cell_metadata-table_id" { + value = google_bigquery_table.merfish_cell_metadata.table_id +} + +output "bigquery_table-merfish_cell_metadata-id" { + value = google_bigquery_table.merfish_cell_metadata.id +} diff --git a/datasets/merfish/infra/detected_transcripts_pipeline.tf b/datasets/merfish/infra/detected_transcripts_pipeline.tf new file mode 100644 index 000000000..f33a73539 --- /dev/null +++ b/datasets/merfish/infra/detected_transcripts_pipeline.tf @@ -0,0 +1,34 @@ +/** + * 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. + */ + + +resource "google_bigquery_table" "merfish_detected_transcripts" { + project = var.project_id + dataset_id = "merfish" + table_id = "detected_transcripts" + description = "The Merfish Mouse Brain Dataset" + depends_on = [ + google_bigquery_dataset.merfish + ] +} + +output "bigquery_table-merfish_detected_transcripts-table_id" { + value = google_bigquery_table.merfish_detected_transcripts.table_id +} + +output "bigquery_table-merfish_detected_transcripts-id" { + value = google_bigquery_table.merfish_detected_transcripts.id +} diff --git a/datasets/merfish/infra/merfish_dataset.tf b/datasets/merfish/infra/merfish_dataset.tf new file mode 100644 index 000000000..4eaa58fd4 --- /dev/null +++ b/datasets/merfish/infra/merfish_dataset.tf @@ -0,0 +1,25 @@ +/** + * 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. + */ + + +resource "google_bigquery_dataset" "merfish" { + dataset_id = "merfish" + project = var.project_id +} + +output "bigquery_dataset-merfish-dataset_id" { + value = google_bigquery_dataset.merfish.dataset_id +} diff --git a/datasets/merfish/infra/provider.tf b/datasets/merfish/infra/provider.tf new file mode 100644 index 000000000..dfb989c88 --- /dev/null +++ b/datasets/merfish/infra/provider.tf @@ -0,0 +1,28 @@ +/** + * 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. + */ + + +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/merfish/infra/variables.tf b/datasets/merfish/infra/variables.tf new file mode 100644 index 000000000..46c6dacda --- /dev/null +++ b/datasets/merfish/infra/variables.tf @@ -0,0 +1,26 @@ +/** + * 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. + */ + + +variable "project_id" {} +variable "bucket_name_prefix" {} +variable "impersonating_acct" {} +variable "region" {} +variable "env" {} +variable "iam_policies" { + default = {} +} + diff --git a/datasets/merfish/pipelines/cell_by_gene/cell_by_gene_dag.py b/datasets/merfish/pipelines/cell_by_gene/cell_by_gene_dag.py new file mode 100644 index 000000000..769993271 --- /dev/null +++ b/datasets/merfish/pipelines/cell_by_gene/cell_by_gene_dag.py @@ -0,0 +1,1758 @@ +# 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. + + +from airflow import DAG +from airflow.providers.google.cloud.transfers import gcs_to_bigquery + +default_args = { + "owner": "Google", + "depends_on_past": False, + "start_date": "2022-08-20", +} + + +with DAG( + dag_id="merfish.cell_by_gene", + default_args=default_args, + max_active_runs=1, + schedule_interval="@weekly", + catchup=False, + default_view="graph", +) as dag: + + # Task to load CSV data to a BigQuery table + load_cell_by_gene_to_bq = gcs_to_bigquery.GCSToBigQueryOperator( + 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=[ + {"name": "Oxgr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr1a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr1b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr1d", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr1f", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr2a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr2b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr2c", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr5a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr5b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Htr7", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adora1", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Adora2a", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Adora2b", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Adora3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgra1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgra2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgra3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrb1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrb3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgre1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgre4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrf4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrf5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrl1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrl2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrl3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrl4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrd1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrf1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrf2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "ADGRF3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrg1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrg2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrg4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrg5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrg6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrg7", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adgrv1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mc2r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adra1a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adra1b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adra1d", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adra2a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adra2b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adra2c", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Aplnr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ackr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ackr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ackr3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ackr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Bdkrb1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Bdkrb2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adrb1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adrb2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Adrb3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Brs3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr1l1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr10", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr7", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr8", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccr9", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ccrl2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cxcr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cxcr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cxcr3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cxcr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cxcr5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cxcr6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "C3ar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "C5ar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "C5ar2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Celsr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Celsr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Celsr3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Calcrl", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Calcr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cnr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cnr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Xcr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cmklr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cckar", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Crhr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Crhr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cx3cr1", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Cysltr1", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Cysltr2", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Drd1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Drd5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Drd2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Drd3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Drd4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Oprd1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ednrb", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ednra", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Casr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fpr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fshr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fpr_s1", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Fpr_rs3", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Ffar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ffar3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ffar4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd10", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd7", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd8", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Fzd9", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpbar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gper1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr135", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr143", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr15", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr157", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr161", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr176", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr182", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr183", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr20", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr22", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr26", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr3", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Gpr37l1", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Gpr39", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr52", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr55", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr61", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr62", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr84", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr87", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gprc5b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gprc5c", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gprc5d", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gprc6a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Galr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Galr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gabbr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gabbr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gipr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grpr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cckbr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gcgr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Glp1r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Glp2r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr119", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gnrhr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ghsr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ghrhr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hrh1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hrh2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hrh3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hrh4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hcar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hcar2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Oprk1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Kiss1r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lgr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lgr5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lgr6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ltb4r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ltb4r2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lhcgr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lpar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lpar2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lpar3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lpar4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Lpar6", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Mrgpra3", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Mrgprb1", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Mrgprb2", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Mrgprb4", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Mrgprb5", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Mrgprb8", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Mrgprd", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mrgpre", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mrgprf", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mrgprg", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mrgprh", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Mrgprx2", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Mchr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mc3r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mc4r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mc5r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Opn4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mtnr1a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mtnr1b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr50", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Grm7", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Oprm1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Chrm1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Chrm2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Chrm3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Chrm4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Chrm5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr18", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Nmbr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tacr3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Nmur2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npffr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npsr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npy1r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npy2r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npy4r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npy6r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Npbwr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ntsr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ntsr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Opn3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Opn5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hcrtr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Hcrtr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Oxtr", "type": "string", "description": "", "mode": 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{"name": "Gpr160", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr162", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr171", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr173", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr174", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr21", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr27", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr33", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr34", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr45", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr63", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr75", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr82", "type": "string", "description": "", 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"description": "", "mode": "nullable"}, + {"name": "Ptger4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Ptgfr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "F2r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "F2rl1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "F2rl2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "F2rl3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mas1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr65", "type": "string", "description": "", "mode": "nullable"}, + {"name": "P2ry10", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Qrfpr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Rxfp1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Rxfp2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Rxfp3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Rxfp4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gprc5a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Rho", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sctr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Opn1sw", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Smo", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sstr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sstr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sstr3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sstr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sstr5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "S1pr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "S1pr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "S1pr3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "S1pr4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "S1pr5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tacr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tacr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Sucnr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tas1r1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tas1r2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tas1r3", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Tas2r135", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Tas2r7", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tbxa2r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tshr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Trhr", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar6", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar7a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar7b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar7d", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar7e", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar7f", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar8a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar8b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar8c", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Taar9", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Agtr1a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Agtr1b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Agtr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Gpr17", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Uts2r", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Vipr1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Vipr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Avpr1a", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Avpr1b", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Avpr2", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Rrh", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Vmn1r40", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r42", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r43", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r44", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r45", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r46", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r47", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r49", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r50", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r51", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r52", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r53", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Vmn1r54", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "V1ra8", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Vmn2r1", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Vmn2r26", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Gramd3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Plxnb3", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Tjap1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cspg5", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mki67", "type": "string", "description": "", "mode": 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"type": "string", "description": "", "mode": "nullable"}, + {"name": "Amigo2", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Slc17a6", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Slc17a7", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Slc17a8", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Aqp4", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Mlc1", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Slc15a3", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Selplg", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "Slco1a4", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "Fn1", "type": "string", "description": "", "mode": "nullable"}, + {"name": "Cldn5", "type": "string", "description": "", "mode": "nullable"}, + {"name": 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"type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_158", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_159", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_160", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_161", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_162", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_163", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_164", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "Blank_165", + "type": "string", + "description": "", + "mode": "nullable", + }, + ], + ) + + load_cell_by_gene_to_bq diff --git a/datasets/merfish/pipelines/cell_by_gene/pipeline.yaml b/datasets/merfish/pipelines/cell_by_gene/pipeline.yaml new file mode 100644 index 000000000..e0e878338 --- /dev/null +++ b/datasets/merfish/pipelines/cell_by_gene/pipeline.yaml @@ -0,0 +1,2655 @@ +# 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: + - name: "Oxgr1" + type: "string" + description: "" + mode: "nullable" + - name: "Htr1a" + type: "string" + description: "" + mode: "nullable" + - name: "Htr1b" + type: "string" + description: "" + mode: "nullable" + - name: "Htr1d" + type: "string" + description: "" + mode: "nullable" + - name: "Htr1f" + type: "string" + description: "" + mode: "nullable" + - name: "Htr2a" + type: "string" + description: "" + mode: "nullable" + - name: "Htr2b" + type: "string" + description: "" + mode: "nullable" + - name: "Htr2c" + type: "string" + description: "" + mode: "nullable" + - name: "Htr4" + type: "string" + description: "" + mode: "nullable" + - name: "Htr5a" + type: "string" + description: "" + mode: "nullable" + - name: "Htr5b" + type: "string" + description: "" + mode: "nullable" + - name: "Htr6" + type: "string" + description: "" + mode: "nullable" + - name: "Htr7" + type: "string" + description: "" + mode: "nullable" + - name: "Adora1" + type: "string" + description: "" + mode: "nullable" + - name: "Adora2a" + type: "string" + description: "" + mode: "nullable" + - name: "Adora2b" + type: "string" + description: "" + mode: "nullable" + - name: "Adora3" + type: "string" + description: "" + mode: "nullable" + - name: "Adgra1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgra2" + type: "string" + description: "" + mode: "nullable" + - name: "Adgra3" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrb1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrb3" + type: "string" + description: "" + mode: "nullable" + - name: "Adgre1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgre4" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrf4" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrf5" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrl1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrl2" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrl3" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrl4" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrd1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrf1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrf2" + type: "string" + description: "" + mode: "nullable" + - name: "ADGRF3" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrg1" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrg2" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrg4" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrg5" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrg6" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrg7" + type: "string" + description: "" + mode: "nullable" + - name: "Adgrv1" + type: "string" + description: "" + mode: "nullable" + - name: "Mc2r" + type: "string" + description: "" + mode: "nullable" + - name: "Adra1a" + type: "string" + description: "" + mode: "nullable" + - name: "Adra1b" + type: "string" + description: "" + mode: "nullable" + - name: "Adra1d" + type: "string" + description: "" + mode: "nullable" + - name: "Adra2a" + type: "string" + description: "" + mode: "nullable" + - name: "Adra2b" + type: "string" + description: "" + mode: "nullable" + - name: "Adra2c" + type: "string" + description: "" + mode: "nullable" + - name: "Aplnr" + type: "string" + description: "" + mode: "nullable" + - name: "Ackr1" + type: "string" + description: "" + mode: "nullable" + - name: "Ackr2" + type: "string" + description: "" + mode: "nullable" + - name: "Ackr3" + type: "string" + description: "" + mode: "nullable" + - name: "Ackr4" + type: "string" + description: "" + mode: "nullable" + - name: "Bdkrb1" + type: "string" + description: "" + mode: "nullable" + - name: "Bdkrb2" + type: "string" + description: "" + mode: "nullable" + - name: "Adrb1" + type: "string" + description: "" + mode: "nullable" + - name: "Adrb2" + type: "string" + description: "" + mode: "nullable" + - name: "Adrb3" + type: "string" + description: "" + mode: "nullable" + - name: "Brs3" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr1l1" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr1" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr10" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr2" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr4" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr6" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr7" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr8" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr9" + type: "string" + description: "" + mode: "nullable" + - name: "Ccrl2" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcr1" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcr2" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcr3" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcr4" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcr5" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcr6" + type: "string" + description: "" + mode: "nullable" + - name: "C3ar1" + type: "string" + description: "" + mode: "nullable" + - name: "C5ar1" + type: "string" + description: "" + mode: "nullable" + - name: "C5ar2" + type: "string" + description: "" + mode: "nullable" + - name: "Celsr1" + type: "string" + description: "" + mode: "nullable" + - name: "Celsr2" + type: "string" + description: "" + mode: "nullable" + - name: "Celsr3" + type: "string" + description: "" + mode: "nullable" + - name: "Calcrl" + type: "string" + description: "" + mode: "nullable" + - name: "Calcr" + type: "string" + description: "" + mode: "nullable" + - name: "Cnr1" + type: "string" + description: "" + mode: "nullable" + - name: "Cnr2" + type: "string" + description: "" + mode: "nullable" + - name: "Xcr1" + type: "string" + description: "" + mode: "nullable" + - name: "Cmklr1" + type: "string" + description: "" + mode: "nullable" + - name: "Cckar" + type: "string" + description: "" + mode: "nullable" + - name: "Crhr1" + type: "string" + description: "" + mode: "nullable" + - name: "Crhr2" + type: "string" + description: "" + mode: "nullable" + - name: "Cx3cr1" + type: "string" + description: "" + mode: "nullable" + - name: "Cysltr1" + type: "string" + description: "" + mode: "nullable" + - name: "Cysltr2" + type: "string" + description: "" + mode: "nullable" + - name: "Drd1" + type: "string" + description: "" + mode: "nullable" + - name: "Drd5" + type: "string" + description: "" + mode: "nullable" + - name: "Drd2" + type: "string" + description: "" + mode: "nullable" + - name: "Drd3" + type: "string" + description: "" + mode: "nullable" + - name: "Drd4" + type: "string" + description: "" + mode: "nullable" + - name: "Oprd1" + type: "string" + description: "" + mode: "nullable" + - name: "Ednrb" + type: "string" + description: "" + mode: "nullable" + - name: "Ednra" + type: "string" + description: "" + mode: "nullable" + - name: "Casr" + type: "string" + description: "" + mode: "nullable" + - name: "Fpr1" + type: "string" + description: "" + mode: "nullable" + - name: "Fshr" + type: "string" + description: "" + mode: "nullable" + - name: "Fpr_s1" + type: "string" + description: "" + mode: "nullable" + - name: "Fpr_rs3" + type: "string" + description: "" + mode: "nullable" + - name: "Ffar1" + type: "string" + description: "" + mode: "nullable" + - name: "Ffar3" + type: "string" + description: "" + mode: "nullable" + - name: "Ffar4" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd1" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd10" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd2" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd3" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd4" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd5" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd6" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd7" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd8" + type: "string" + description: "" + mode: "nullable" + - name: "Fzd9" + type: "string" + description: "" + mode: "nullable" + - name: "Gpbar1" + type: "string" + description: "" + mode: "nullable" + - name: "Gper1" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr1" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr135" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr143" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr15" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr157" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr161" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr176" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr182" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr183" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr20" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr22" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr26" + type: "string" + description: "" + mode: 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+ - name: "Tacr3" + type: "string" + description: "" + mode: "nullable" + - name: "Nmur2" + type: "string" + description: "" + mode: "nullable" + - name: "Npffr2" + type: "string" + description: "" + mode: "nullable" + - name: "Npsr1" + type: "string" + description: "" + mode: "nullable" + - name: "Npy1r" + type: "string" + description: "" + mode: "nullable" + - name: "Npy2r" + type: "string" + description: "" + mode: "nullable" + - name: "Npy4r" + type: "string" + description: "" + mode: "nullable" + - name: "Npy6r" + type: "string" + description: "" + mode: "nullable" + - name: "Npbwr1" + type: "string" + description: "" + mode: "nullable" + - name: "Ntsr1" + type: "string" + description: "" + mode: "nullable" + - name: "Ntsr2" + type: "string" + description: "" + mode: "nullable" + - name: "Opn3" + type: "string" + description: "" + mode: "nullable" + - name: "Opn5" + type: "string" + description: "" + mode: "nullable" + - name: "Hcrtr1" + type: "string" + description: "" + mode: "nullable" + - name: "Hcrtr2" + type: "string" + description: "" + mode: "nullable" + - name: "Oxtr" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry1" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry12" + type: "string" + description: "" + mode: "nullable" + - name: "P2yr13" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry14" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry2" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry4" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry6" + type: "string" + description: "" + mode: "nullable" + - name: "Pth2r" + type: "string" + description: "" + mode: "nullable" + - name: "Pth1r" + type: "string" + description: "" + mode: "nullable" + - name: "Adcyap1r1" + type: "string" + description: "" + mode: "nullable" + - name: "Ptafr" + type: "string" + description: "" + mode: "nullable" + - name: "Ccr3" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr101" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr132" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr139" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr141" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr142" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr146" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr149" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr150" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr151" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr152" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr153" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr156" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr158" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr160" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr162" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr171" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr173" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr174" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr21" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr27" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr33" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr34" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr45" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr63" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr75" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr82" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr83" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr85" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr88" + type: "string" + description: "" + mode: "nullable" + - name: "Prokr1" + type: "string" + description: "" + mode: "nullable" + - name: "Prokr2" + type: "string" + description: "" + mode: "nullable" + - name: "Prlhr" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr37" + type: "string" + description: "" + mode: "nullable" + - name: "Ptgir" + type: "string" + description: "" + mode: "nullable" + - name: "Ptgdr" + type: "string" + description: "" + mode: "nullable" + - name: "Ptgdr2" + type: "string" + description: "" + mode: "nullable" + - name: "Ptger1" + type: "string" + description: "" + mode: "nullable" + - name: "Ptger2" + type: "string" + description: "" + mode: "nullable" + - name: "Ptger3" + type: "string" + description: "" + mode: "nullable" + - name: "Ptger4" + type: "string" + description: "" + mode: "nullable" + - name: "Ptgfr" + type: "string" + description: "" + mode: "nullable" + - name: "F2r" + type: "string" + description: "" + mode: "nullable" + - name: "F2rl1" + type: "string" + description: "" + mode: "nullable" + - name: "F2rl2" + type: "string" + description: "" + mode: "nullable" + - name: "F2rl3" + type: "string" + description: "" + mode: "nullable" + - name: "Mas1" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr65" + type: "string" + description: "" + mode: "nullable" + - name: "P2ry10" + type: "string" + description: "" + mode: "nullable" + - name: "Qrfpr" + type: "string" + description: "" + mode: "nullable" + - name: "Rxfp1" + type: "string" + description: "" + mode: "nullable" + - name: "Rxfp2" + type: "string" + description: "" + mode: "nullable" + - name: "Rxfp3" + type: "string" + description: "" + mode: "nullable" + - name: "Rxfp4" + type: "string" + description: "" + mode: "nullable" + - name: "Gprc5a" + type: "string" + description: "" + mode: "nullable" + - name: "Rho" + type: "string" + description: "" + mode: "nullable" + - name: "Sctr" + type: "string" + description: "" + mode: "nullable" + - name: "Opn1sw" + type: "string" + description: "" + mode: "nullable" + - name: "Smo" + type: "string" + description: "" + mode: "nullable" + - name: "Sstr1" + type: "string" + description: "" + mode: "nullable" + - name: "Sstr2" + type: "string" + description: "" + mode: "nullable" + - name: "Sstr3" + type: "string" + description: "" + mode: "nullable" + - name: "Sstr4" + type: "string" + description: "" + mode: "nullable" + - name: "Sstr5" + type: "string" + description: "" + mode: "nullable" + - name: "S1pr1" + type: "string" + description: "" + mode: "nullable" + - name: "S1pr2" + type: "string" + description: "" + mode: "nullable" + - name: "S1pr3" + type: "string" + description: "" + mode: "nullable" + - name: "S1pr4" + type: "string" + description: "" + mode: "nullable" + - name: "S1pr5" + type: "string" + description: "" + mode: "nullable" + - name: "Tacr2" + type: "string" + description: "" + mode: "nullable" + - name: "Tacr1" + type: "string" + description: "" + mode: "nullable" + - name: "Sucnr1" + type: "string" + description: "" + mode: "nullable" + - name: "Tas1r1" + type: "string" + description: "" + mode: "nullable" + - name: "Tas1r2" + type: "string" + description: "" + mode: "nullable" + - name: "Tas1r3" + type: "string" + description: "" + mode: "nullable" + - name: "Tas2r135" + type: "string" + description: "" + mode: "nullable" + - name: "Tas2r7" + type: "string" + description: "" + mode: "nullable" + - name: "Tbxa2r" + type: "string" + description: "" + mode: "nullable" + - name: "Tshr" + type: "string" + description: "" + mode: "nullable" + - name: "Trhr" + type: "string" + description: "" + mode: "nullable" + - name: "Taar1" + type: "string" + description: "" + mode: "nullable" + - name: "Taar2" + type: "string" + description: "" + mode: "nullable" + - name: "Taar3" + type: "string" + description: "" + mode: "nullable" + - name: "Taar4" + type: "string" + description: "" + mode: "nullable" + - name: "Taar6" + type: "string" + description: "" + mode: "nullable" + - name: "Taar7a" + type: "string" + description: "" + mode: "nullable" + - name: "Taar7b" + type: "string" + description: "" + mode: "nullable" + - name: "Taar7d" + type: "string" + description: "" + mode: "nullable" + - name: "Taar7e" + type: "string" + description: "" + mode: "nullable" + - name: "Taar7f" + type: "string" + description: "" + mode: "nullable" + - name: "Taar8a" + type: "string" + description: "" + mode: "nullable" + - name: "Taar8b" + type: "string" + description: "" + mode: "nullable" + - name: "Taar8c" + type: "string" + description: "" + mode: "nullable" + - name: "Taar9" + type: "string" + description: "" + mode: "nullable" + - name: "Agtr1a" + type: "string" + description: "" + mode: "nullable" + - name: "Agtr1b" + type: "string" + description: "" + mode: "nullable" + - name: "Agtr2" + type: "string" + description: "" + mode: "nullable" + - name: "Gpr17" + type: "string" + description: "" + mode: "nullable" + - name: "Uts2r" + type: "string" + description: "" + mode: "nullable" + - name: "Vipr1" + type: "string" + description: "" + mode: "nullable" + - name: "Vipr2" + type: "string" + description: "" + mode: "nullable" + - name: "Avpr1a" + type: "string" + description: "" + mode: "nullable" + - name: "Avpr1b" + type: "string" + description: "" + mode: "nullable" + - name: "Avpr2" + type: "string" + description: "" + mode: "nullable" + - name: "Rrh" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r40" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r42" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r43" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r44" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r45" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r46" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r47" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r49" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r50" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r51" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r52" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r53" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn1r54" + type: "string" + description: "" + mode: "nullable" + - name: "V1ra8" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn2r1" + type: "string" + description: "" + mode: "nullable" + - name: "Vmn2r26" + type: "string" + description: "" + mode: "nullable" + - name: "Gramd3" + type: "string" + description: "" + mode: "nullable" + - name: "Plxnb3" + type: "string" + description: "" + mode: "nullable" + - name: "Tjap1" + type: "string" + description: "" + mode: "nullable" + - name: "Cspg5" + type: "string" + description: "" + mode: "nullable" + - name: "Mki67" + type: "string" + description: "" + mode: "nullable" + - name: "Cenpe" + type: "string" + description: "" + mode: "nullable" + - name: "Man1a" + type: "string" + description: "" + mode: "nullable" + - name: "Sema4d" + type: "string" + description: "" + mode: "nullable" + - name: "Tmem108" + type: "string" + description: "" + mode: "nullable" + - name: "Traf4" + type: "string" + description: "" + mode: "nullable" + - name: "Gjc3" + type: "string" + description: "" + mode: "nullable" + - name: "Sox8" + type: "string" + description: "" + mode: "nullable" + - name: "Aldh1l1" + type: "string" + description: "" + mode: "nullable" + - name: "Olig1" + type: "string" + description: "" + mode: "nullable" + - name: "Pcdh15" + type: "string" + description: "" + mode: "nullable" + - name: "Gad1" + type: "string" + description: "" + mode: "nullable" + - name: "Syt4" + type: "string" + description: "" + mode: "nullable" + - name: "Baiap2" + type: "string" + description: "" + mode: "nullable" + - name: "Amigo2" + type: "string" + description: "" + mode: "nullable" + - name: "Slc17a6" + type: "string" + description: "" + mode: "nullable" + - name: "Slc17a7" + type: "string" + description: "" + mode: "nullable" + - name: "Slc17a8" + type: "string" + description: "" + mode: "nullable" + - name: "Aqp4" + type: "string" + description: "" + mode: "nullable" + - name: "Mlc1" + type: "string" + description: "" + mode: "nullable" + - name: "Slc15a3" + type: "string" + description: "" + mode: "nullable" + - name: "Selplg" + type: "string" + description: "" + mode: "nullable" + - name: "Slco1a4" + type: "string" + description: "" + mode: "nullable" + - name: "Fn1" + type: "string" + description: "" + mode: "nullable" + - name: "Cldn5" + type: "string" + description: "" + mode: "nullable" + - name: "Emcn" + type: "string" + description: "" + mode: "nullable" + - name: "Myh11" + type: "string" + description: "" + mode: "nullable" + - name: "Lmod1" + type: "string" + description: "" + mode: "nullable" + - name: "Atp13a5" + type: "string" + description: "" + mode: "nullable" + - name: "Kcnj8" + type: "string" + description: "" + mode: "nullable" + - name: "Abcc9" + type: "string" + description: "" + mode: "nullable" + - name: "Cd300c2" + type: "string" + description: "" + mode: "nullable" + - name: "C1qa" + type: "string" + description: "" + mode: "nullable" + - name: "C1qb" + type: "string" + description: "" + mode: "nullable" + - name: "Cxcl12" + type: "string" + description: "" + mode: "nullable" + - name: "Arhgap29" + type: "string" + description: "" + mode: "nullable" + - name: "Sox9" + type: "string" + description: "" + mode: "nullable" + - name: "Slc25a18" + type: "string" + description: "" + mode: "nullable" + - name: "Dlk1" + type: "string" + description: "" + mode: "nullable" + - name: "Peg10" + type: "string" + description: "" + mode: "nullable" + - name: "Dgkk" + type: "string" + description: "" + mode: "nullable" + - name: "Chat" + type: "string" + description: "" + mode: "nullable" + - name: "Grin2b" + type: "string" + description: "" + mode: "nullable" + - name: "Cx3cl1" + type: "string" + description: "" + mode: "nullable" + - name: "Igfbpl1" + type: "string" + description: "" + mode: "nullable" + - name: "Eomes" + type: "string" + description: "" + mode: "nullable" + - name: "Ascl1" + type: "string" + description: "" + mode: "nullable" + - name: "Slc32a1" + type: "string" + description: "" + mode: "nullable" + - name: "Th" + type: "string" + description: "" + mode: "nullable" + - name: "Top2a" + type: "string" + description: "" + mode: "nullable" + - name: "Acte1" + type: "string" + description: "" + mode: "nullable" + - name: "Ppp1r3g" + type: "string" + description: "" + mode: "nullable" + - name: "Gfap" + type: "string" + description: "" + mode: "nullable" + - name: "Timp4" + type: "string" + description: "" + mode: "nullable" + - name: "Anxa11" + type: "string" + description: "" + mode: "nullable" + - name: "Cldn19" + type: "string" + description: "" + mode: "nullable" + - name: "Rspo3" + type: "string" + description: "" + mode: "nullable" + - name: "Slc47a1" + type: "string" + description: "" + mode: "nullable" + - name: "Pln" + type: "string" + description: "" + mode: "nullable" + - name: "Foxd3" + type: "string" + description: "" + mode: "nullable" + - name: "Alk" + type: "string" + description: "" + mode: "nullable" + - name: "Axl" + type: "string" + description: "" + mode: "nullable" + - name: "Csf1r" + type: "string" + description: "" + mode: "nullable" + - name: "Ddr1" + type: "string" + description: "" + mode: "nullable" + - name: "Ddr2" + type: "string" + description: "" + mode: "nullable" + - name: "Efemp1" + type: "string" + description: "" + mode: "nullable" + - name: "Egfr" + type: "string" + description: "" + mode: "nullable" + - name: "Epha1" + type: "string" + description: "" + mode: "nullable" + - name: "Epha2" + type: "string" + description: "" + mode: "nullable" + - name: "Epha3" + type: "string" + description: "" + mode: "nullable" + - name: "Epha4" + type: "string" + description: "" + mode: "nullable" + - name: "Epha5" + type: "string" + description: "" + mode: "nullable" + - name: "Epha6" + type: "string" + description: "" + mode: "nullable" + - name: "Epha7" + type: "string" + description: "" + mode: "nullable" + - name: "Epha8" + type: "string" + description: "" + mode: "nullable" + - name: "Epha10" + type: "string" + description: "" + mode: "nullable" + - name: "Ephb1" + type: "string" + description: "" + mode: "nullable" + - name: "Ephb2" + type: "string" + description: "" + mode: "nullable" + - name: "Ephb3" + type: "string" + description: "" + mode: "nullable" + - name: "Ephb6" + type: "string" + description: "" + mode: "nullable" + - name: "Erbb2" + type: "string" + description: "" + mode: "nullable" + - name: "Erbb3" + type: "string" + description: "" + mode: "nullable" + - name: "Erbb4" + type: "string" + description: "" + mode: "nullable" + - name: "Fgfr2" + type: "string" + description: "" + mode: "nullable" + - name: "Fgfr3" + type: "string" + description: "" + mode: "nullable" + - name: "Fgfr4" + type: "string" + description: "" + mode: "nullable" + - name: "Fgfrl1" + type: "string" + description: "" + mode: "nullable" + - name: "Flt1" + type: "string" + description: "" + mode: "nullable" + - name: "Flt3" + type: "string" + description: "" + mode: "nullable" + - name: "Flt4" + type: "string" + description: "" + mode: "nullable" + - name: "Igf1r" + type: "string" + description: "" + mode: "nullable" + - name: "Insr" + type: "string" + description: "" + mode: "nullable" + - name: "Insrr" + type: "string" + description: "" + mode: "nullable" + - name: "Kdr" + type: "string" + description: "" + mode: "nullable" + - name: "Kit" + type: "string" + description: "" + mode: "nullable" + - name: "Lmtk2" + type: "string" + description: "" + mode: "nullable" + - name: "Mertk" + type: "string" + description: "" + mode: "nullable" + - name: "Met" + type: "string" + description: "" + mode: "nullable" + - name: "Musk" + type: "string" + description: "" + mode: "nullable" + - name: "Nrp1" + type: "string" + description: "" + mode: "nullable" + - name: "Nrp2" + type: "string" + description: "" + mode: "nullable" + - name: "Ntrk1" + type: "string" + description: "" + mode: "nullable" + - name: "Ntrk2" + type: "string" + description: "" + mode: "nullable" + - name: "Ntrk3" + type: "string" + description: "" + mode: "nullable" + - name: "Pdgfra" + type: "string" + description: "" + mode: "nullable" + - name: "Pdgfrb" + type: "string" + description: "" + mode: "nullable" + - name: "Ptk7" + type: "string" + description: "" + mode: "nullable" + - name: "Ret" + type: "string" + description: "" + mode: "nullable" + - name: "Ror1" + type: "string" + description: "" + mode: "nullable" + - name: "Ror2" + type: "string" + description: "" + mode: "nullable" + - name: "Ros1" + type: "string" + description: "" + mode: "nullable" + - name: "Ryk" + type: "string" + description: "" + mode: "nullable" + - name: "Tek" + type: "string" + description: "" + mode: "nullable" + - name: "Tie1" + type: "string" + description: "" + mode: "nullable" + - name: "Tyro3" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_0" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_1" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_2" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_3" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_4" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_5" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_6" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_7" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_8" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_9" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_10" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_11" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_12" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_13" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_14" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_15" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_16" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_17" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_18" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_19" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_20" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_21" + type: "string" + description: "" + mode: 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+ type: "string" + description: "" + mode: "nullable" + - name: "Blank_155" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_156" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_157" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_158" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_159" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_160" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_161" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_162" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_163" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_164" + type: "string" + description: "" + mode: "nullable" + - name: "Blank_165" + type: "string" + description: "" + mode: "nullable" + + graph_paths: + - "load_cell_by_gene_to_bq" diff --git a/datasets/merfish/pipelines/cell_metadata/cell_metadata_dag.py b/datasets/merfish/pipelines/cell_metadata/cell_metadata_dag.py new file mode 100644 index 000000000..c1c17f10f --- /dev/null +++ b/datasets/merfish/pipelines/cell_metadata/cell_metadata_dag.py @@ -0,0 +1,96 @@ +# 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. + + +from airflow import DAG +from airflow.providers.google.cloud.transfers import gcs_to_bigquery + +default_args = { + "owner": "Google", + "depends_on_past": False, + "start_date": "2022-08-20", +} + + +with DAG( + dag_id="merfish.cell_metadata", + default_args=default_args, + max_active_runs=1, + schedule_interval="@weekly", + catchup=False, + default_view="graph", +) as dag: + + # Task to load CSV data to a BigQuery table + load_cell_metadata_to_bq = gcs_to_bigquery.GCSToBigQueryOperator( + task_id="load_cell_metadata_to_bq", + bucket="public-datasets-vizgen-merfish", + source_objects=[ + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate1/cell_metadata_S1R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate2/cell_metadata_S1R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate3/cell_metadata_S1R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate1/cell_metadata_S2R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate2/cell_metadata_S2R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate3/cell_metadata_S2R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate1/cell_metadata_S3R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate2/cell_metadata_S3R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate3/cell_metadata_S3R3.csv", + ], + source_format="CSV", + destination_project_dataset_table="bigquery-public-data-dev.merfish.cell_metadata", + skip_leading_rows=1, + allow_quoted_newlines=True, + write_disposition="WRITE_TRUNCATE", + schema_fields=[ + {"name": "fov", "type": "string", "description": None, "mode": "nullable"}, + { + "name": "volume", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "center_x", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "center_y", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "min_x", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "min_y", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "max_y", + "type": "string", + "description": None, + "mode": "nullable", + }, + ], + ) + + load_cell_metadata_to_bq diff --git a/datasets/merfish/pipelines/cell_metadata/pipeline.yaml b/datasets/merfish/pipelines/cell_metadata/pipeline.yaml new file mode 100644 index 000000000..d85bc61d4 --- /dev/null +++ b/datasets/merfish/pipelines/cell_metadata/pipeline.yaml @@ -0,0 +1,87 @@ +# 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_metadata + description: "The Merfish Mouse Brain Dataset" + +dag: + airflow_version: 2 + initialize: + dag_id: cell_metadata + 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_metadata_to_bq" + bucket: "public-datasets-vizgen-merfish" + source_objects: [ + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate1/cell_metadata_S1R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate2/cell_metadata_S1R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate3/cell_metadata_S1R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate1/cell_metadata_S2R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate2/cell_metadata_S2R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate3/cell_metadata_S2R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate1/cell_metadata_S3R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate2/cell_metadata_S3R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate3/cell_metadata_S3R3.csv"] + source_format: "CSV" + destination_project_dataset_table: "bigquery-public-data-dev.merfish.cell_metadata" + skip_leading_rows: 1 + allow_quoted_newlines: True + write_disposition: "WRITE_TRUNCATE" + schema_fields: + - name: "fov" + type: "string" + description: "" + mode: "nullable" + - name: "volume" + type: "string" + description: "" + mode: "nullable" + - name: "center_x" + type: "string" + description: "" + mode: "nullable" + - name: "center_y" + type: "string" + description: "" + mode: "nullable" + - name: "min_x" + type: "string" + description: "" + mode: "nullable" + - name: "min_y" + type: "string" + description: "" + mode: "nullable" + - name: "max_y" + type: "string" + description: "" + mode: "nullable" + + graph_paths: + - "load_cell_metadata_to_bq" diff --git a/datasets/merfish/pipelines/dataset.yaml b/datasets/merfish/pipelines/dataset.yaml new file mode 100644 index 000000000..8cedc9f9b --- /dev/null +++ b/datasets/merfish/pipelines/dataset.yaml @@ -0,0 +1,25 @@ +# 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. + +dataset: + name: merfish + friendly_name: ~ + description: ~ + dataset_sources: ~ + terms_of_use: ~ + +resources: + - type: bigquery_dataset + dataset_id: merfish + description: ~ diff --git a/datasets/merfish/pipelines/detected_transcripts/detected_transcripts_dag.py b/datasets/merfish/pipelines/detected_transcripts/detected_transcripts_dag.py new file mode 100644 index 000000000..69db36c18 --- /dev/null +++ b/datasets/merfish/pipelines/detected_transcripts/detected_transcripts_dag.py @@ -0,0 +1,87 @@ +# 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. + + +from airflow import DAG +from airflow.providers.google.cloud.transfers import gcs_to_bigquery + +default_args = { + "owner": "Google", + "depends_on_past": False, + "start_date": "2022-08-20", +} + + +with DAG( + dag_id="merfish.detected_transcripts", + default_args=default_args, + max_active_runs=1, + schedule_interval="@weekly", + catchup=False, + default_view="graph", +) as dag: + + # Task to load CSV data to a BigQuery table + load_detected_transcripts_to_bq = gcs_to_bigquery.GCSToBigQueryOperator( + task_id="load_detected_transcripts_to_bq", + bucket="public-datasets-vizgen-merfish", + source_objects=[ + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate1/detected_transcripts_S1R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate2/detected_transcripts_S1R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate3/detected_transcripts_S1R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate1/detected_transcripts_S2R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate2/detected_transcripts_S2R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate3/detected_transcripts_S2R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate1/detected_transcripts_S3R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate2/detected_transcripts_S3R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate3/detected_transcripts_S3R3.csv", + ], + source_format="CSV", + destination_project_dataset_table="bigquery-public-data-dev.merfish.detected_transcripts", + skip_leading_rows=1, + allow_quoted_newlines=True, + write_disposition="WRITE_TRUNCATE", + schema_fields=[ + { + "name": "barcode_id", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "global_x", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "global_y", + "type": "string", + "description": None, + "mode": "nullable", + }, + { + "name": "global_z", + "type": "string", + "description": None, + "mode": "nullable", + }, + {"name": "x", "type": "string", "description": None, "mode": "nullable"}, + {"name": "y", "type": "string", "description": None, "mode": "nullable"}, + {"name": "fov", "type": "string", "description": None, "mode": "nullable"}, + {"name": "gene", "type": "string", "description": None, "mode": "nullable"}, + ], + ) + + load_detected_transcripts_to_bq diff --git a/datasets/merfish/pipelines/detected_transcripts/pipeline.yaml b/datasets/merfish/pipelines/detected_transcripts/pipeline.yaml new file mode 100644 index 000000000..760cee0bb --- /dev/null +++ b/datasets/merfish/pipelines/detected_transcripts/pipeline.yaml @@ -0,0 +1,91 @@ +# 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: detected_transcripts + description: "The Merfish Mouse Brain Dataset" + +dag: + airflow_version: 2 + initialize: + dag_id: detected_transcripts + 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_detected_transcripts_to_bq" + bucket: "public-datasets-vizgen-merfish" + source_objects: [ + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate1/detected_transcripts_S1R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate2/detected_transcripts_S1R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice1/Replicate3/detected_transcripts_S1R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate1/detected_transcripts_S2R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate2/detected_transcripts_S2R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice2/Replicate3/detected_transcripts_S2R3.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate1/detected_transcripts_S3R1.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate2/detected_transcripts_S3R2.csv", + "datasets/mouse_brain_map/BrainReceptorShowcase/Slice3/Replicate3/detected_transcripts_S3R3.csv"] + source_format: "CSV" + destination_project_dataset_table: "bigquery-public-data-dev.merfish.detected_transcripts" + skip_leading_rows: 1 + allow_quoted_newlines: True + write_disposition: "WRITE_TRUNCATE" + schema_fields: + - name: "barcode_id" + type: "string" + description: "" + mode: "nullable" + - name: "global_x" + type: "string" + description: "" + mode: "nullable" + - name: "global_y" + type: "string" + description: "" + mode: "nullable" + - name: "global_z" + type: "string" + description: "" + mode: "nullable" + - name: "x" + type: "string" + description: "" + mode: "nullable" + - name: "y" + type: "string" + description: "" + mode: "nullable" + - name: "fov" + type: "string" + description: "" + mode: "nullable" + - name: "gene" + type: "string" + description: "" + mode: "nullable" + + graph_paths: + - "load_detected_transcripts_to_bq"