Zenodo and downloads (#328)

* updated zenodo doi in config

* got downloading working with new data

* updated autodownloader

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

geneplexus/_config/config.py

@@ -14,20 +14,18 @@
 MAX_RETRY = 10 # maximum number of retries for downloading
 
 URL_DICT = {
- "Zenodo": "https://zenodo.org/record/6383205/files/",
- "Wasabi": "http://s3.us-east-2.wasabisys.com/geneplexus/v0.1dev/PyGenePlexusDataZip/",
+ "Zenodo": "https://zenodo.org/records/13844808/files/",
 }
 
 CONFIG_PATH = pathlib.Path(__file__).parent.absolute()
 DATA_FILENAMES_PATH = osp.join(CONFIG_PATH, "data_filenames.txt")
 
 LOG_LEVELS = ["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"]
 
-ALL_TASKS = ["IDconversion", "MachineLearning", "Similarities", "NetworkGraph", "OriginalGSCs"]
 ALL_NETWORKS = ["BioGRID", "STRING", "IMP"]
 ALL_FEATURES = ["SixSpeciesN2V"]
 ALL_GSCS = ["GO", "Monarch", "Mondo", "Combined"]
-ALL_SPECIES = ["Human", "Mouse", "Fly", "Worm", "Fish", "Yeast"]
+ALL_SPECIES = ["Human", "Mouse", "Fly", "Worm", "Zebrafish", "Yeast"]
 
 DEFAULT_LOGREG_KWARGS: Dict[str, Any] = {
  "max_iter": 10000,
@@ -50,13 +48,11 @@
  ("Entrez", "Symbol"),
 }
 
-TASK_TYPE = Literal["IDconversion", "MachineLearning", "Similarities", "NetworkGraph", "OriginalGSCs"]
 NET_TYPE = Literal["BioGRID", "STRING", "IMP"]
 FEATURE_TYPE = Literal["SixSpeciesN2V"]
 GSC_TYPE = Literal["GO", "Monarch", "Mondo", "Combined"]
 SPECIES_TYPE = Literal["Human", "Mouse", "Fly", "Worm", "Fish", "Yeast"]
 
-TASK_SELECTION_TYPE = Union[Literal["All"], TASK_TYPE, List[TASK_TYPE]]
 NET_SELECTION_TYPE = Union[Literal["All"], NET_TYPE, List[NET_TYPE]]
 FEATURE_SELECTION_TYPE = Union[Literal["All"], FEATURE_TYPE, List[FEATURE_TYPE]]
 GSC_SELECTION_TYPE = Union[Literal["All"], GSC_TYPE, List[GSC_TYPE]]
@@ -71,7 +67,6 @@
  "URL_DICT",
  "CONFIG_PATH",
  "DATA_FILENAMES_PATH",
- "ALL_TASKS",
  "ALL_NETWORKS",
  "ALL_FEATURES",
  "ALL_GSCS",
@@ -80,12 +75,10 @@
  "ID_SRC_TYPE",
  "ID_DST_TYPE",
  "VALID_ID_CONVERSION",
- "TASK_TYPE",
  "NET_TYPE",
  "FEATURE_TYPE",
  "GSC_TYPE",
  "SPECIES_TYPE",
- "TASK_SELECTION_TYPE",
  "NET_SELECTION_TYPE",
  "FEATURE_SELECTION_TYPE",
  "GSC_SELECTION_TYPE",

geneplexus/_geneplexus.py

@@ -70,7 +70,7 @@ def _initial_id_convert(input_genes, file_loc, species):
  agene,
  converted_gene or "Could Not be mapped to Entrez",
  converted_gene_name or "Could Not be mapped to Entrez",
- ]
+ ],
  )
 
  column_names = ["Original ID", "Entrez ID", "Gene Name"]