Merge branch 'main' of github.com:pachterlab/gget into main

merging main into local

docs/src/SUMMARY.md

@@ -9,9 +9,11 @@
 
 # Manual
 * [gget alphafold](en/alphafold.md)  
-* [gget archs4](en/archs4.md)  
+* [gget archs4](en/archs4.md)
+* [gget bgee](en/bgee.md)
 * [gget blast](en/blast.md)  
-* [gget blat](en/blat.md)  
+* [gget blat](en/blat.md)
+* [gget cbio](en/cbio.md)
 * [gget cellxgene](en/cellxgene.md)  
 * [gget cosmic](en/cosmic.md)  
 * [gget diamond](en/diamond.md)  
@@ -20,15 +22,13 @@
 * [gget gpt](en/gpt.md)  
 * [gget info](en/info.md)  
 * [gget muscle](en/muscle.md)
-* [gget mutate](en/mutate.md)  
+* [gget mutate](en/mutate.md)
+* [gget opentargets](en/opentargets.md) 
 * [gget pdb](en/pdb.md)  
 * [gget ref](en/ref.md)  
 * [gget search](en/search.md)  
 * [gget setup](en/setup.md)  
-* [gget seq](en/seq.md)  
-* [gget opentargets](en/opentargets.md)  
-* [gget cbio](en/cbio.md)  
-* [gget bgee](en/bgee.md)
+* [gget seq](en/seq.md)   
 
 ---
 

docs/src/en/cbio.md

@@ -13,7 +13,8 @@ Return format: JSON (command-line) or string list (Python).
 
 **Positional argument**     
 `keywords`  
-Space-separated list of keywords to search for, e.g. <code>breast&nbsp;lung</code>.
+Space-separated list of keywords to search for, e.g. <code>breast&nbsp;lung</code>.  
+Python: Pass keywords as a list of strings.
 
 ### `plot` subcommand (Python: `gget.cbio_plot`)
 Plot cancer genomics heatmaps using data from cBioPortal.
@@ -89,7 +90,7 @@ gget cbio search esophag ovary ovarian
 ```python
 # Python
 import gget
-gget.cbio_search('esophag', 'ovary', 'ovarian')
+gget.cbio_search(['esophag', 'ovary', 'ovarian'])
 ```
 &rarr; Returns a list of studies with cancer types matching the keywords `esophag`, `ovary`, or `ovarian`.
 

gget/gget_cbio.py

@@ -289,13 +289,12 @@ def _extract_study_name(name: str) -> str:
     return name
 
 
-def cbio_search(*key_words: str):
+def cbio_search(key_words):
     """
     Find cBioPortal study IDs by keyword.
 
     Args:
-
-    :param key_words:    list of keywords to search for
+    key_words           list of keywords to search for
 
     Return:
 
@@ -315,6 +314,9 @@ def cbio_search(*key_words: str):
         )
         return []
 
+    if isinstance(key_words, str):
+        key_words = [key_words]
+
     api = SwaggerClient.from_url(
         "https://www.cbioportal.org/api/v2/api-docs",
         config={

gget/main.py

@@ -58,7 +58,10 @@ def _get_help_string(self, action):
             help_str += " (default: %(default)s)"
         return help_str
 
-
+def convert_to_list(*args):
+    args_list = list(args)
+    return args_list
+
 def int_or_str(value):
     try:
         return int(value)
@@ -3314,7 +3317,7 @@ def main():
     ## cbio return
     if args.command == "cbio":
         if args.subcommand == "search":
-            cbio_results = cbio_search(*args.keywords)
+            cbio_results = cbio_search(convert_to_list(*args.keywords))
             print(json.dumps(cbio_results, ensure_ascii=False, indent=4))
         elif args.subcommand == "plot":
             cbio_plot(

tests/fixtures/test_cbio.json

@@ -27,7 +27,7 @@
             "/tmp/test_cbio_download/msk_impact_2017/sv.txt": "24ce260e03b417d47929f8fc34fc49a4",
 
             "/tmp/test_cbio_download/egc_msk_2023/clinical_patient.txt": "6fbd67c0eca7a24fa6918f37c989033f",
-            "/tmp/test_cbio_download/egc_msk_2023/clinical_sample.txt": "8469bcc199fc653afb867242b3ab6e00",
+            "/tmp/test_cbio_download/egc_msk_2023/clinical_sample.txt": "a4423dfa78788df1b9f49fef31f282a9",
             "/tmp/test_cbio_download/egc_msk_2023/cna.txt": "1acb67c06284754ee472402753e54263",
             "/tmp/test_cbio_download/egc_msk_2023/mutations.txt": "be28497d2f95d933ad8e14a04adc2beb",
             "/tmp/test_cbio_download/egc_msk_2023/sv.txt": "c1a0011480b533d2b659373ffd178c32"
@@ -42,4 +42,4 @@
         },
         "expected_result": false
     }
-}
+}

tests/fixtures/test_cbio_search.json

@@ -7,26 +7,29 @@
             "ovarian"
         ],
         "expected_result": [
+            "egc_tmucih_2015",
             "egc_msk_2017",
-            "egc_msk_2023",
-            "egc_msk_tp53_ccr_2022",
             "egc_mskcc_2020",
-            "egc_tmucih_2015",
-            "egc_trap_ccr_msk_2023",
-            "egc_trap_msk_2020",
+            "egc_msk_tp53_ccr_2022",
+            "escc_ucla_2014",
             "esca_broad",
-            "esca_tcga",
-            "esca_tcga_pan_can_atlas_2018",
             "escc_icgc",
-            "escc_ucla_2014",
+            "egc_trap_msk_2020",
             "hgsoc_msk_2021",
             "lgsoc_mapk_msk_2022",
-            "msk_spectrum_tme_2022",
-            "ov_tcga",
-            "ov_tcga_pan_can_atlas_2018",
             "ov_tcga_pub",
             "scco_mskcc",
-            "stes_tcga_pub"
+            "stes_tcga_pub",
+            "egc_trap_ccr_msk_2023",
+            "esca_tcga",
+            "egc_msk_2023",
+            "ov_tcga",
+            "msk_spectrum_tme_2022",
+            "esca_tcga_pan_can_atlas_2018",
+            "ov_tcga_pan_can_atlas_2018",
+            "esca_tcga_gdc",
+            "hgsoc_tcga_gdc",
+            "ovary_cptac_gdc"
         ]
     }
-}
+}

tests/fixtures/test_enrichr.json

@@ -5821,7 +5821,7 @@
             "species": "fish"
         },
         "expected_result": "ValueError",
-        "expected_msg": "Database 'pathway' is not supported for species 'fish'. Please select a database from the species-specific libraries listed at: https://maayanlab.cloud/FishEnrichr/#libraries."
+        "expected_msg": "Database 'pathway' is not supported for species 'fish'. Please select a database from the species-specific libraries listed at: https://maayanlab.cloud/FishEnrichr/#stats."
     },
     "test_enrichr_bad_background": {
         "type": "error",
@@ -6310,4 +6310,4 @@
             ]
         ]
     }
-}
+}