Merge pull request #3 from TheJacksonLaboratory/G3-29-geneweaver-cli-…

…client-excel-parsing-tool-2

Fixing enum str formatting and batch parsing of special cases

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-core"
-version = "0.8.0a0"
+version = "0.8.0a1"
 description = "The core of the Jax-Geneweaver Python library"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"

src/geneweaver/core/enum.py

@@ -21,6 +21,10 @@ class GenesetScoreTypeStr(str, Enum):
     CORRELATION = "correlation"
     EFFECT = "effect"
 
+    def __str__(self) -> str:
+        """Render as a string."""
+        return "-".join(part.capitalize() for part in self.name.split("_"))
+
 
 class ScoreType(int, Enum):
     """Integer based Enum for the different types of geneset scores."""
@@ -31,6 +35,10 @@ class ScoreType(int, Enum):
     CORRELATION = 4
     EFFECT = 5
 
+    def __str__(self) -> str:
+        """Render as a string."""
+        return "-".join(part.capitalize() for part in self.name.split("_"))
+
 
 class GenesetAccess(str, Enum):
     """Enum for the different types of geneset access."""
@@ -72,7 +80,7 @@ class Species(int, Enum):
 
     def __str__(self) -> str:
         """Render as a string."""
-        return self.name
+        return self.name.replace("_", " ").capitalize()
 
 
 class GeneIdentifier(int, Enum):
@@ -97,6 +105,8 @@ class GeneIdentifier(int, Enum):
 
     def __str__(self) -> str:
         """Render as a string."""
+        if len(self.name) > 4:
+            return " ".join(part.capitalize() for part in self.name.split("_"))
         return self.name
 
 
@@ -151,4 +161,5 @@ class Microarray(int, Enum):
 
     def __str__(self) -> str:
         """Render as a string."""
-        return self.name
+        formatted = " ".join(part.capitalize() for part in self.name.split("_"))
+        return f"microarray {formatted}"

src/geneweaver/core/schema/batch.py

@@ -115,11 +115,15 @@ def initialize_score(cls, v) -> GenesetScoreType:
         """Initialize score type."""
         if isinstance(v, GenesetScoreType):
             return v
+        elif isinstance(v, dict):
+            return GenesetScoreType(**v)
         return parse_score(v)
 
     @validator("private", pre=True)
     def private_to_bool(cls, v) -> bool:
         """Convert private str to bool."""
+        if isinstance(v, bool):
+            return v
         return v.lower() != "public"
 
     @validator("curation_id", pre=True)