From f9e308646fec9885104a5d41e4d5c8a58d149e90 Mon Sep 17 00:00:00 2001 From: AO33 Date: Thu, 23 May 2024 18:16:00 -0600 Subject: [PATCH] Replaced https://zfin.org/downloads_genotype_to_phenotype.nt.gz with zfin_genotype_to_phenotype in all files (using vscode) --- .cruft.json | 2 +- scripts/generate-rdf.py | 8 ++++---- scripts/generate-report.py | 8 ++++---- src/zfin_genotype_to_phenotype_ingest/metadata.yaml | 2 +- tests/test_example.py | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.cruft.json b/.cruft.json index e69211c..4e103bc 100644 --- a/.cruft.json +++ b/.cruft.json @@ -12,7 +12,7 @@ "__project_url": "https://github.com/monarch-initiative/zfin-genotype-to-phenotype-ingest", "ingest_source": "https://zfin.org/downloads", "ingest_type": "genotype_to_phenotype", - "__ingest_name": "https://zfin.org/downloads_genotype_to_phenotype", + "__ingest_name": "zfin_genotype_to_phenotype", "min_python_version": "3.10", "full_name": "Aaron Odell", "email": "aaron@tislab.org", diff --git a/scripts/generate-rdf.py b/scripts/generate-rdf.py index 19ce378..5bf8fc3 100644 --- a/scripts/generate-rdf.py +++ b/scripts/generate-rdf.py @@ -3,11 +3,11 @@ from kgx.cli.cli_utils import transform as kgx_transform from loguru import logger -logger.info(f"Creating rdf output: output/https://zfin.org/downloads_genotype_to_phenotype.nt.gz ...") +logger.info(f"Creating rdf output: output/zfin_genotype_to_phenotype.nt.gz ...") src_files = [] -src_nodes = f"output/https://zfin.org/downloads_genotype_to_phenotype_nodes.tsv" -src_edges = f"output/https://zfin.org/downloads_genotype_to_phenotype_edges.tsv" +src_nodes = f"output/zfin_genotype_to_phenotype_nodes.tsv" +src_edges = f"output/zfin_genotype_to_phenotype_edges.tsv" if Path(src_nodes).is_file(): src_files.append(src_nodes) @@ -18,7 +18,7 @@ inputs=src_files, input_format="tsv", stream=True, - output=f"output/https://zfin.org/downloads_genotype_to_phenotype.nt.gz", + output=f"output/zfin_genotype_to_phenotype.nt.gz", output_format="nt", output_compression="gz", ) diff --git a/scripts/generate-report.py b/scripts/generate-report.py index 40abc6a..5f1e228 100644 --- a/scripts/generate-report.py +++ b/scripts/generate-report.py @@ -2,8 +2,8 @@ import duckdb -nodes_file = "output/https://zfin.org/downloads_genotype_to_phenotype_nodes.tsv" -edges_file = "output/https://zfin.org/downloads_genotype_to_phenotype_edges.tsv" +nodes_file = "output/zfin_genotype_to_phenotype_nodes.tsv" +edges_file = "output/zfin_genotype_to_phenotype_edges.tsv" # Nodes @@ -14,7 +14,7 @@ GROUP BY all ORDER BY all """ - duckdb.sql(f"copy ({query}) to 'output/https://zfin.org/downloads_genotype_to_phenotype_nodes_report.tsv' (header, delimiter '\t')") + duckdb.sql(f"copy ({query}) to 'output/zfin_genotype_to_phenotype_nodes_report.tsv' (header, delimiter '\t')") # Edges if Path(edges_file).exists(): @@ -25,4 +25,4 @@ GROUP BY all ORDER BY all """ - duckdb.sql(f"copy ({query}) to 'output/https://zfin.org/downloads_genotype_to_phenotype_edges_report.tsv' (header, delimiter '\t')") + duckdb.sql(f"copy ({query}) to 'output/zfin_genotype_to_phenotype_edges_report.tsv' (header, delimiter '\t')") diff --git a/src/zfin_genotype_to_phenotype_ingest/metadata.yaml b/src/zfin_genotype_to_phenotype_ingest/metadata.yaml index 5dd3893..b7f4783 100644 --- a/src/zfin_genotype_to_phenotype_ingest/metadata.yaml +++ b/src/zfin_genotype_to_phenotype_ingest/metadata.yaml @@ -3,7 +3,7 @@ # See metadata properties at https://koza.monarchinitiative.org/Ingests/source_config/ id: 'CURIE for the project' -name: 'https://zfin.org/downloads_genotype_to_phenotype' +name: 'zfin_genotype_to_phenotype' ingest_title: 'zfin_genotype_to_phenotype_ingest' ingest_url: 'https://github.com/monarch-initiative/zfin-genotype-to-phenotype-ingest' description: 'Zebrafish genotype to phenotype ingest' diff --git a/tests/test_example.py b/tests/test_example.py index 2adf145..36459bc 100644 --- a/tests/test_example.py +++ b/tests/test_example.py @@ -13,7 +13,7 @@ from koza.utils.testing_utils import mock_koza # Define the ingest name and transform script path -INGEST_NAME = "https://zfin.org/downloads_genotype_to_phenotype" +INGEST_NAME = "zfin_genotype_to_phenotype" TRANSFORM_SCRIPT = "./src/zfin_genotype_to_phenotype_ingest/transform.py"