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rename "geneset" to "gene set" in CLI (#2088)

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* remove dead code

* rename geneset to gene_set
This commit is contained in:
Bruce Martin
2021-03-02 15:36:01 -08:00
committed by GitHub
parent b00496198d
commit c037f4eaa6
14 changed files with 101 additions and 102 deletions
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local_server/test/unit/common/test_api.py
+14 -14
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@@ -388,7 +388,7 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
[
f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
"--disable-annotations",
"--disable-genesets-save",
"--disable-gene-sets-save",
"--experimental-enable-reembedding",
],
)
@@ -465,7 +465,7 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
[
f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
"--disable-annotations",
"--genesets-file",
"--gene-sets-file",
genesets_file,
],
)
@@ -496,7 +496,7 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
{"gene_description": "", "gene_symbol": "SRM"},
],
"geneset_description": "a description",
"geneset_name": "first geneset name",
"geneset_name": "first gene set name",
},
{
"genes": [
@@ -504,10 +504,10 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
{"gene_description": "", "gene_symbol": "SIK1"},
],
"geneset_description": "",
"geneset_name": "second geneset",
"geneset_name": "second gene set",
},
{"genes": [], "geneset_description": "", "geneset_name": "third geneset"},
{"genes": [], "geneset_description": "fourth description", "geneset_name": "fourth_geneset"},
{"genes": [], "geneset_description": "", "geneset_name": "third gene set"},
{"genes": [], "geneset_description": "fourth description", "geneset_name": "fourth_gene_set"},
{"genes": [], "geneset_description": "", "geneset_name": "fifth_dataset"},
],
"tid": 0,
@@ -522,14 +522,14 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
self.assertEqual(result.headers["Content-Type"], "text/csv")
self.assertEqual(
result.text,
"""geneset_name,geneset_description,gene_symbol,gene_description\r
first geneset name,a description,F5,a gene_description\r
first geneset name,a description,SUMO3,\r
first geneset name,a description,SRM,\r
second geneset,,RER1,\r
second geneset,,SIK1,\r
third geneset,,,\r
fourth_geneset,fourth description,,\r
"""gene_set_name,gene_set_description,gene_symbol,gene_description\r
first gene set name,a description,F5,a gene_description\r
first gene set name,a description,SUMO3,\r
first gene set name,a description,SRM,\r
second gene set,,RER1,\r
second gene set,,SIK1,\r
third gene set,,,\r
fourth_gene_set,fourth description,,\r
fifth_dataset,,,\r
""",
)