check formats

src/jflow/parameter.py

@@ -28,8 +28,9 @@ import copy as _copy
 from urlparse import urlparse
 from jflow.config_reader import JFlowConfigReader
 
-# import custom types
+# import custom types and custom formats
 from workflows.types import *
+from workflows.formats import *
 
 
 # define all input type available
@@ -71,18 +72,6 @@ def inputfile(file):
     else:
         return urlfile(file)
 
-
-class Formats(object):
-    ANY = "any"
-    BAM = "bam"
-    FASTQ = "fastq"
-    FASTA = "fasta"
-    SFF = "sff"
-    QUAL = "qual"
-    FLOW = "flow"
-    HTML = "html"
-
-
 class MultipleParameters(object):
     def __init__(self, types, required, choices, excludes, default, actions):
         self.types = types
@@ -627,6 +616,9 @@ class AbstractInputFile(AbstractIOFile):
         except:
             return [input, False]
         
+    def check(self, ifile):
+        eval(self.file_format)(ifile)
+        
 
 class AbstractOutputFile(AbstractIOFile):
     """
@@ -667,6 +659,7 @@ class InputFile(StrParameter, AbstractInputFile):
             jflow_config_reader = JFlowConfigReader()
             new_path = os.path.join(jflow_config_reader.get_tmp_directory(), input)
         if is_local: new_path = input
+        self.check(new_path)
         return new_path
             
 
@@ -752,6 +745,9 @@ class InputFileList(ParameterList, AbstractInputFile):
             for path in path2test:
                 jflow_config_reader = JFlowConfigReader()
                 new_vals.append(os.path.join(jflow_config_reader.get_tmp_directory(), path))
+        # now that all files are downloaded and ok, check the format
+        for cfile in new_vals:
+            self.check(cfile)
         return new_vals
 
 class OutputFileList(ParameterList, AbstractOutputFile):

workflows/alignment/__init__.py

@@ -17,6 +17,8 @@
 
 from jflow.workflow import Workflow
 from jflow.parameter import InputFileList, InputFile
+from workflows.formats import Formats
+
 
 class Alignment (Workflow):
     
@@ -24,9 +26,9 @@ 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", required=True)
-        self.add_input_file_list("read_2", "Which read2 files should be used (if single end, leave empty)")
-        self.add_input_file("reference_genome", "Which genome should the read being align on", required=True)
+        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)
 
     def process(self):        
         # index the reference genome

workflows/components/bwa.py

@@ -19,7 +19,7 @@ import os
 from subprocess import Popen, PIPE
 
 from jflow.component import Component
-from jflow.parameter import Formats
+from workflows.formats import Formats
 
 from weaver.function import ShellFunction
 from weaver.abstraction import Map

workflows/components/bwaindex.py

@@ -19,7 +19,7 @@ import os
 from subprocess import Popen, PIPE
 
 from jflow.component import Component
-from jflow.parameter import Formats
+from workflows.formats import Formats
 from weaver.function import PythonFunction, ShellFunction
 
 

workflows/formats.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+from jflow import seqio
+import os
+import sys
+
+
+class Formats(object):
+    ANY = "any"
+    BAM = "bam"
+    FASTQ = "fastq"
+    FASTA = "fasta"
+    SFF = "sff"
+    
+
+def fastq(ifile):
+    try:
+        reader = seqio.FastqReader(ifile)
+        nb_seq = 0
+        for id, desc, seq, qualities in reader:
+            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)
+    
+def fasta(ifile):
+    try:
+        reader = seqio.FastaReader(ifile, wholefile=True)
+        nb_seq = 0
+        for id, desc, seq, qualities in reader:
+            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)
+    
+def sff(ifile):
+    try:
+        reader = seqio.SFFReader(ifile)
+        nb_seq = 0
+        for id, desc, seq, qualities in reader:
+            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)
+    
\ No newline at end of file