Replaced https://zfin.org/downloads_genotype_to_phenotype.nt.gz with …

…zfin_genotype_to_phenotype in all files (using vscode)

.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": "[email protected]",

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",
 )

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')")

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'

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"