using folder for each herb

Author: emptymalei

dataherb/command.py

@@ -96,9 +96,24 @@ def configure(show, locate):
 
         config = {
             "workdir": answers.get("workdir"),
-            "default": {"flora": answers.get("default_flora")},
+            "default": {
+                "flora": answers.get("default_flora"),
+                "aggregrated": False # if false, we will use folders for each herb.
+            },
         }
 
+        flora_path_workdir = answers.get("workdir", "")
+        if flora_path_workdir.startswith("~"):
+            home = Path.home()
+            flora_path_workdir = str(home / flora_path_workdir[2:])
+
+        flora_path = Path(flora_path_workdir) / "flora" / f"{answers.get('default_flora')}"
+        if not flora_path.exists():
+            click.secho(f"{flora_path} doesn't exist. Creating {flora_path}...", fg="red")
+            flora_path.mkdir(parents=True)
+        else:
+            click.secho(f"{flora_path} exists, using the folder directly.", fg="green")
+
         logger.debug(f"config: {config}")
 
         with open(config_path, "w") as f:
@@ -387,7 +402,7 @@ def remove(flora, herb_id):
     to_remove = click.confirm(f"Remove {herb_id} from the flora?", default=False)
     if to_remove:
         fl.remove(herb_id)
-        click.echo(f"Removed {herb_id} into the flora.")
+        click.echo(f"Removed {herb_id} from the flora.")
     else:
         click.echo("We did nothing.")
 

dataherb/flora.py

@@ -99,7 +99,10 @@ def add(self, herb):
                 raise Exception(f"herb id = {herb.id} already exists")
 
         self.flora.append(herb)
-        self.save()
+        if self.is_aggregated:
+            self.save()
+        else:
+            self.save(herb=herb)
 
     def remove(self, herb_id):
         """
@@ -116,12 +119,15 @@ def remove(self, herb_id):
         else:
             self.remove_herb_from_flora(herb_id)
 
-    def save(self, path=None, id=None):
+    def save(self, path=None, id=None, herb=None):
         """save flora metadata to json file"""
 
         if path is None:
             path = self.flora_config
 
+        if isinstance(path, str):
+            path = Path(path)
+
         logger.debug(
             f"type of a herb in flora: {type(self.flora[0])}\n{self.flora[0].metadata}"
         )
@@ -137,8 +143,15 @@ def save(self, path=None, id=None):
                     serialized_flora, fp, sort_keys=True, indent=4, separators=(",", ": ")
                 )
         else:
-            if not id:
+            if (not id) and (not herb):
                 raise Exception("dataherb id must be provided")
+            elif herb:
+                logger.debug(f"Saving herb using herb object")
+                self.save_herb_meta(herb.id, path / f"{herb.id}")
+            elif id:
+                logger.debug(f"Saving herb using herb id")
+                self.save_herb_meta(id, path / f"{id}")
+
 
     def save_herb_meta(self, id, path=None):
         """Save a herb metadata to json file"""

dataherb/utils/configs.py

@@ -10,7 +10,12 @@
 class Config:
     """Config system for Dataherb"""
 
-    def __init__(self, config_path=None, no_config_error=False):
+    def __init__(self, is_aggregated=None, config_path=None, no_config_error=False):
+
+        if is_aggregated is None:
+            is_aggregated = False
+
+        self.is_aggregated = is_aggregated
 
         self.config_path = config_path
         self.no_config_error = no_config_error
@@ -33,7 +38,10 @@ def _flora_path(self, flora, workdir=None):
         if workdir is None:
             workdir = self.config["WD"]
 
-        which_flora_path = Path(workdir) / "flora" / Path(flora + ".json")
+        if self.is_aggregated:
+            which_flora_path = Path(workdir) / "flora" / Path(flora + ".json")
+        else:
+            which_flora_path = Path(workdir) / "flora" / Path(flora)
         logger.debug(f"Using flora path: {which_flora_path}")
         if not which_flora_path.exists():
             raise Exception(f"flora config {which_flora_path} does not exist")