preprocess fuction call was missing in case of no input in sign0.fit, added...

preprocess fuction call was missing in case of no input in sign0.fit, added call, relocated preprocess function to preprocess class as classmethods

package/chemicalchecker/core/chemcheck.py

@@ -52,7 +52,6 @@ from glob import glob
 
 from .molkit import Mol
 from .data import DataFactory
-from .preprocess import Preprocess
 from .signature_data import DataSignature
 
 from chemicalchecker.database import Dataset, Molecule
@@ -406,60 +405,6 @@ class ChemicalChecker():
             return None
         return DataSignature(data.data_path)
 
-    def preprocess(self, sign):
-        """Return the file with the raw data preprocessed.
-
-        Args:
-            sign: signature object obtained from cc.get_signature)
-        Returns:
-            datafile(str): The name of the file where the data in pairs is
-                saved.
-        """
-
-        prepro = Preprocess(sign.signature_path, sign.dataset)
-        if not prepro.is_fit():
-            self.__log.info(
-                "No preprocessed file found, calling the preprocessing script")
-            prepro.fit()
-        else:
-            self.__log.info("Found {}".format(prepro.data_path))
-        return prepro.data_path
-
-        # ex:os.path.join(self.raw_path, "preprocess.h5")
-
-    def preprocess_predict(self, sign, input_file, destination):
-        """Runs the preprocessing script 'predict'.
-
-        Run on an input file of raw data formatted correctly for the space of
-        interest
-
-        Args:
-            sign: signature object obtained from cc.get_signature)
-            input_file(str): path to the h5 file containning the data on which
-                to apply 'predict'
-            destination(str): Path to a .h5 file where the predicted signature
-                will be saved.
-        Returns:
-            datafile(str): The h5 file containing the predicted data after
-                preprocess
-        """
-
-        input_file = os.path.abspath(input_file)
-        destination = os.path.abspath(destination)
-
-        # Checking the provided paths
-
-        if not os.path.exists(input_file):
-            raise Exception("Error, {} does not exist!".format(input_file))
-
-        ext = destination[-2:].lower()
-        if not ext == 'h5':
-            destination += '.h5'
-
-        prepro = Preprocess(sign.signature_path, sign.dataset)
-        prepro.predict(input_file, destination)
-
-        return destination
 
     def signature(self, dataset, cctype):
         return self.get_signature(cctype=cctype, molset="full",

package/chemicalchecker/core/preprocess.py

@@ -161,6 +161,64 @@ class Preprocess():
             result.append(dict(zip(keys, values)))
         return result
 
+    @classmethod
+    def preprocess(cls, sign):
+        """Return the file with the raw data preprocessed.
+
+        Args:
+            sign: signature object (e.g. obtained from cc.get_signature)
+        Returns:
+            datafile(str): The name of the file where the data is saved.
+        
+        ex:
+        os.path.join(self.raw_path, "preprocess.h5")
+        """
+
+        prepro = cls(sign.signature_path, sign.dataset)
+        if not prepro.is_fit():
+            cls.__log.info(
+                "No preprocessed file found, calling the preprocessing script")
+            prepro.fit()
+        else:
+            cls.__log.info("Found {}".format(prepro.data_path))
+        return prepro.data_path
+
+
+    @classmethod
+    def preprocess_predict(cls, sign, input_file, destination):
+        """Runs the preprocessing script 'predict'.
+
+        Run on an input file of raw data formatted correctly for the space of
+        interest
+
+        Args:
+            sign: signature object ( e.g. obtained from cc.get_signature)
+            input_file(str): path to the h5 file containning the data on which
+                to apply 'predict'
+            destination(str): Path to a .h5 file where the predicted signature
+                will be saved.
+        Returns:
+            datafile(str): The h5 file containing the predicted data after
+                preprocess
+        """
+
+        input_file = os.path.abspath(input_file)
+        destination = os.path.abspath(destination)
+
+        # Checking the provided paths
+
+        if not os.path.exists(input_file):
+            raise Exception("Error, {} does not exist!".format(input_file))
+
+        ext = destination[-2:].lower()
+        if not ext == 'h5':
+            destination += '.h5'
+
+        prepro = cls(sign.signature_path, sign.dataset)
+        prepro.predict(input_file, destination)
+
+        return destination
+    
     @staticmethod
     def get_parser():
         description = 'Run preprocess script.'

package/chemicalchecker/core/sign0.py

@@ -13,6 +13,7 @@ import numpy as np
 
 from .signature_data import DataSignature
 from .signature_base import BaseSignature
+from .preprocess import Preprocess
 
 from chemicalchecker.util import logged
 from chemicalchecker.util.sanitize import Sanitizer
@@ -305,6 +306,10 @@ class sign0(BaseSignature, DataSignature):
         BaseSignature.fit(self,  **params)
         self.clear()
         self.update_status("Getting data")
+        if pairs is None and X is None and data_file is None:
+            self.__log.debug("Runnning preprocess")
+            data_file = Preprocess.preprocess(self)
+
         self.__log.debug("data_file is {}".format(data_file))
         res = self.get_data(pairs=pairs, X=X, keys=keys, features=features,
                             data_file=data_file, key_type=key_type,