improve the implementation a bit!

src/jflow/__init__.py

@@ -22,6 +22,9 @@ import os
 
 from jflow.config_reader import JFlowConfigReader
 
+# Define some Error classes
+class InvalidFormatError(Exception): pass
+
 jflowconf = JFlowConfigReader()
 
 # if log file directory does not exist, create it

src/jflow/parameter.py

@@ -16,6 +16,7 @@
 #
 
 import re
+import sys
 import types
 import datetime
 import logging
@@ -621,8 +622,15 @@ class AbstractInputFile(AbstractIOFile):
             eval(self.file_format)
             function_exists = True
         except: function_exists = False
-        if function_exists: eval(self.file_format)(ifile)
-        
+        if function_exists:
+            try: 
+                eval(self.file_format)(ifile)
+            except jflow.InvalidFormatError as e:
+                sys.stderr.write(str(e)+"\n")
+                sys.exit(1)
+        else:
+            sys.stderr.write("Error: Invalid file format '" + self.file_format + "'!\n")
+            sys.exit(1)
 
 class AbstractOutputFile(AbstractIOFile):
     """

workflows/alignment/__init__.py

@@ -17,7 +17,6 @@
 
 from jflow.workflow import Workflow
 from jflow.parameter import InputFileList, InputFile
-from workflows.formats import Formats
 
 
 class Alignment (Workflow):
@@ -26,9 +25,9 @@ class Alignment (Workflow):
         return "Align reads against a reference genome"
 
     def define_parameters(self, function="process"):
-        self.add_input_file_list("read_1", "Which read1 files should be used", file_format=Formats.FASTQ, required=True)
-        self.add_input_file_list("read_2", "Which read2 files should be used (if single end, leave empty)", file_format=Formats.FASTQ)
-        self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, file_format=Formats.FASTA)
+        self.add_input_file_list("read_1", "Which read1 files should be used", file_format="fastq", required=True)
+        self.add_input_file_list("read_2", "Which read2 files should be used (if single end, leave empty)", file_format="fastq")
+        self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, file_format="fasta")
 
     def process(self):        
         # index the reference genome

workflows/components/bwa.py

@@ -19,19 +19,18 @@ import os
 from subprocess import Popen, PIPE
 
 from jflow.component import Component
-from workflows.formats import Formats
+from jflow.abstraction import MultiMap
 
 from weaver.function import ShellFunction
 from weaver.abstraction import Map
-from jflow.abstraction import MultiMap
 
 
 class BWA (Component):
     
     def define_parameters(self, reference_genome, read1, read2=None, algorithm="aln"):
         self.add_input_file("reference_genome", "Which reference file should be used", default=reference_genome, required=True)
-        self.add_input_file_list("read1", "Which read1 files should be used", file_format=Formats.FASTQ, default=read1, required=True)
-        self.add_input_file_list("read2", "Which read2 files should be used", file_format=Formats.FASTQ, default=read2)
+        self.add_input_file_list("read1", "Which read1 files should be used", file_format="fastq", default=read1, required=True)
+        self.add_input_file_list("read2", "Which read2 files should be used", file_format="fastq", default=read2)
         self.add_parameter("algorithm", "Which algorithm should be used to align the reads", default=algorithm, choices=["aln", "bwasw"])
         if algorithm == "aln":
             self.add_output_file_list("sai1", "The BWA sai1 file", pattern='{basename_woext}.sai', items=self.read1)
@@ -42,10 +41,10 @@ class BWA (Component):
                 self.add_output_file_list("sai2", "The BWA sai2 file", pattern='{basename_woext}.sai', items=self.read2)
             else: 
                 self.sai2 = None
-            self.add_output_file_list("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', items=[self.read1, self.read2], file_format=Formats.BAM)
+            self.add_output_file_list("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', items=[self.read1, self.read2], file_format="bam")
         else:
             self.sai2 = None
-            self.add_output_file_list("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', items=self.read1, file_format=Formats.BAM)
+            self.add_output_file_list("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', items=self.read1, file_format="bam")
         self.add_output_file("stderr", "The BWA stderr file", filename='bwa.stderr')
         
     def process(self):        

workflows/components/bwaindex.py

@@ -19,7 +19,6 @@ import os
 from subprocess import Popen, PIPE
 
 from jflow.component import Component
-from workflows.formats import Formats
 from weaver.function import PythonFunction, ShellFunction
 
 
@@ -43,7 +42,7 @@ def bwa_index(exec_path, algorithm, input_fasta, databank, stdout_path, stderr_p
 class BWAIndex (Component):
     
     def define_parameters(self, input_fasta, algorithm="bwtsw"):
-        self.add_input_file("input_fasta", "Which fasta file should be indexed", file_format=Formats.FASTA, default=input_fasta, required=True)
+        self.add_input_file("input_fasta", "Which fasta file should be indexed", file_format="fasta", default=input_fasta, required=True)
         self.add_parameter("algorithm", "Which algorithm should be used to index the fasta file", default=algorithm, choices=["bwtsw", "div", "is"])
         self.add_output_file("databank", "The indexed databank to use with BWA", filename=os.path.basename(input_fasta))
         self.add_output_file("stdout", "The BWAIndex stdout file", filename="bwaindex.stdout")

workflows/formats.py

@@ -15,18 +15,14 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
+import jflow
 from jflow import seqio
 import os
 import sys
 
 
-class Formats(object):
-    ANY = "any"
-    BAM = "bam"
-    FASTQ = "fastq"
-    FASTA = "fasta"
-    SFF = "sff"
-    
+def any(ifile): pass
+def bam(ifile): pass
 
 def fastq(ifile):
     try:
@@ -36,9 +32,8 @@ def fastq(ifile):
             nb_seq += 1
             # only check the first 10 sequences
             if nb_seq == 10: break
-    except: 
-        sys.stderr.write("Error: The provided file '" + ifile + "' is not a fastq file!\n")
-        sys.exit(1)
+    except:
+        raise jflow.InvalidFormatError("Error: The provided file '" + ifile + "' is not a fastq file!")
     
 def fasta(ifile):
     try:
@@ -48,9 +43,8 @@ def fasta(ifile):
             nb_seq += 1
              # only check the first 10 sequences
             if nb_seq == 10: break
-    except: 
-        sys.stderr.write("Error: The provided file '" + ifile + "' is not a fasta file!\n")
-        sys.exit(1)
+    except:
+        raise jflow.InvalidFormatError("Error: The provided file '" + ifile + "' is not a fasta file!")
     
 def sff(ifile):
     try:
@@ -60,7 +54,6 @@ def sff(ifile):
             nb_seq += 1
             # only check the first 10 sequences
             if nb_seq == 10: break
-    except: 
-        sys.stderr.write("Error: The provided file '" + ifile + "' is not a sff file!\n")
-        sys.exit(1)
+    except:
+        raise jflow.InvalidFormatError("Error: The provided file '" + ifile + "' is not a sff file!")
     
\ No newline at end of file

workflows/types.py

@@ -20,5 +20,9 @@ import datetime
 
 
 def date(datestr):
-    return datetime.datetime.strptime(datestr, '%d/%m/%Y')
+    try:
+        return datetime.datetime.strptime(datestr, '%d/%m/%Y')
+    except:
+        raise argparse.ArgumentTypeError("'" + datestr + "' is an invalid date!")
+    
         
\ No newline at end of file