include rules (exclude and requiredIf) in workflows

src/jflow/rules.py

@@ -174,7 +174,6 @@ class Exclude(LinkRule):
             if exclude in self.user_args and self.user_args[exclude] is not None and self.user_args[exclude] and \
                     self.user_args[exclude] != self.get_parameter(exclude).default:
                 # The target is found, is not None and is not False
-                print(self.user_args)
                 self.error("Parameters '" + self.parameter_name + "' and '" + exclude + "' are mutually excluded")
 
 

workflows/addanalysis/__init__.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/>.
 #
@@ -26,37 +26,37 @@ from ng6.run import Run
 from ng6.analysis import Analysis
 
 class AddAnalysis (BasicNG6Workflow):
-    
+
     def get_description(self):
         return "Add a brand new analysis to a run or a project"
-    
+
     def define_parameters(self, function="process"):
         self.add_input_file_list("data_file", " Which data files should be added to the analysis", required = True)
         self.add_parameter("compression", "How should data be compressed once archived", choices = ['none', 'gz', 'bz2'], default = 'none')
         self.add_parameter("delete", "Should the input data be deleted once the process is over", type = bool , default = False)
         self.add_parameter("archive_name", "Give a name to the final archive", default = 'ng6_archive')
         self.add_parameter("project_id", "The project id the analysis belongs to", type = 'int', rules="Exclude=run_id;RequiredIf?ALL[run_id=None]")
-        self.add_parameter("run_id", "The run id the run belongs to", type = 'int', rules = "Exclude=project_id;RequiredIf?ALL[project_id=None]")
+        self.add_parameter("run_id", "The run id the run belongs to", type = 'int')
         self.add_parameter("analysis_name", "Give a name to your analysis", required = True)
         self.add_parameter("analysis_description", "Give a description to your analysis", required = True)
         self.add_parameter("analysis_software", "Which software was used for this analysis", required = True)
         self.add_parameter("analysis_software_options", "Which software options were used for this analysis", required = True)
         self.add_parameter("analysis_software_version", "analysis_software_version", required = True)
         self.add_parameter("parent_analysis", "The id of an analysis to be used as a parent analysis", type= 'int')
-        
-    
+
+
     def process(self):
         self.runobj = None
         self.project = None
         # First check if files provided exists
-        files_to_save = [] 
+        files_to_save = []
         for file in self.data_file:
             if os.path.isfile(file):
                 files_to_save.append(file)
             else:
                 display_error_message("error: %s file does not exists\n" % (file))
-        
-        # Check if user provided a project or a run        
+
+        # Check if user provided a project or a run
         if self.project_id :
             self.project = Project.get_from_id(self.project_id)
             self.metadata.append("project_id="+str(self.project_id))
@@ -68,9 +68,9 @@ class AddAnalysis (BasicNG6Workflow):
             self.metadata.append("run_id="+str(self.run_id))
         else :
             display_error_message("One of run_id or project_id parameter is required!\n")
-        
+
         addto = "project" if self.project else "run"
-        
+
         parent = None
         if self.parent_analysis :
             parent = Analysis.get_from_id(self.parent_analysis)
@@ -80,11 +80,11 @@ class AddAnalysis (BasicNG6Workflow):
                 analyses_ids = [ o.id for o in self.runobj.get_analysis()]
             if parent.id not in analyses_ids :
                     display_error_message("The parent analysis associated with id '%s' does not belong to the %s id '%s' " % (parent.id, addto, self.project_id or self.run_id) )
-        
-        basicanalysis = self.add_component("BasicAnalysis", [files_to_save, self.analysis_name, 
-                        self.analysis_description, self.analysis_software, self.analysis_software_options, 
-                        self.analysis_software_version, self.compression, self.delete, 
-                        self.archive_name], addto=addto, parent = parent)        
+
+        basicanalysis = self.add_component("BasicAnalysis", [files_to_save, self.analysis_name,
+                        self.analysis_description, self.analysis_software, self.analysis_software_options,
+                        self.analysis_software_version, self.compression, self.delete,
+                        self.archive_name], addto=addto, parent = parent)
 
     def post_process(self):
         if self.runobj:

workflows/addfiles/__init__.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/>.
 #
@@ -24,41 +24,41 @@ from ng6.run import Run
 from ng6.analysis import Analysis
 
 class AddFiles (BasicNG6Workflow):
-    
+
     def get_description(self):
         return "Add files to an existing analysis or run"
-    
+
     def define_parameters(self, function="process"):
         self.add_input_file_list("data_file", " Which data files should be added to the analysis or the run", required = True)
         self.add_parameter("compression", "How should data be compressed once archived", choices = ['none', 'gz', 'bz2'], default = 'none')
         self.add_parameter("delete", "Should the input data be deleted once the process is over", type = bool , default = False)
-        self.add_parameter("analysis_id", "The id of the analysis", type = int) #, required = True)
-        self.add_parameter("run_id", "The run id the run belongs to", type = int)#, required = True)
-        #TODO Exclude self.add_exclusion_rule( "analysis_id", "run_id" )
-    
+        self.add_parameter("analysis_id", "The id of the analysis", type = int, rules="Exclude=run_id;RequiredIf?ALL[run_id=None]")
+        self.add_parameter("run_id", "The run id the run belongs to", type = 'int')
+
     def process(self):
         # check if files provided exists
-        files_to_save = [] 
+
+        files_to_save = []
         for file in self.data_file:
             if os.path.isfile(file):
                 files_to_save.append(file)
             else:
                 sys.exit("error: %s file does not exists\n" % (file))
-        
+
         self.runobj = None
         self.analysisobj = None
         self.project = None
-        
+
         if self.run_id :
             self.runobj = Run.get_from_id(self.run_id)
             self.project = Project.get_from_run_id(self.run_id)
             if self.project is not None and not self.project.is_admin(self.admin_login):
                 sys.stderr.write( "The user login '" + self.admin_login + "' is not allowed to add data on project '" + self.project.name + "'.\n" )
                 sys.exit()
-            
+
             self.metadata.append("run_id="+str(self.run_id))
             add = self.add_component("AddRawFiles", [ self.runobj, files_to_save, self.compression ] )
-        
+
         elif self.analysis_id :
             self.analysisobj = Analysis.get_from_id(self.analysis_id)
             self.project = self.analysisobj.project
@@ -71,11 +71,10 @@ class AddFiles (BasicNG6Workflow):
         else :
             sys.stderr.write("One of --run-id or --analysis-id parameter is required!\n")
             sys.exit()
-        
+
     def post_process(self):
         # once everything done, sync directories
         if self.runobj:
             self.runobj.sync()
         elif self.analysisobj:
             self.analysisobj.sync()
-    

workflows/radseq/__init__.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/>.
 #
@@ -23,7 +23,7 @@ from ng6.ng6workflow import NG6Workflow
 from ng6.utils import Utils
 
 class RADseq (NG6Workflow):
-    
+
     ENZYMES = {
               'sbfI' : {
                         'rad'    : 'CCTGCAGG',
@@ -39,28 +39,29 @@ class RADseq (NG6Workflow):
 	        }
     }
 
-   
+
     def get_enzyme (self, name):
         if name not in self.ENZYMES :
             raise ValueError("The enzyme name " + str(name) + " does not exists. Accepted names are " + str (list(self.ENZYMES.keys())))
-    
+
         return (self.ENZYMES[name]['rad'], self.ENZYMES[name]['radtag'])
-    
+
     def get_name(self):
         return 'radseq'
-    
+
     def get_description(self):
         return "RADseq data quality analysis workflow"
-    
+
     def define_parameters(self, function="process"):
-        
+
         # if metadata.barcode faire splitbc. Sinon liste read1 = liste des échantillons.
-        
+
         # split_bc
         self.add_multiple_parameter_list("pool", "Sequence pool", required = False)
         self.add_parameter("id", "Pool uniq identifier", add_to = "pool")
         # required = True que si pool précisé
-        self.add_input_file("read1", "Read 1 fastq file path", required = False, add_to = "pool")
+        #TODO check rules
+        self.add_input_file("read1", "Read 1 fastq file path", rules="RequiredIf?ALL[poll!=None]", add_to = "pool")
         self.add_input_file("read2", "Read 2 fastq file path", add_to = "pool")
         # options bougées dans process_radtag
         #self.add_parameter("enzyme", "Restriction enzyme name", required = True , choices = list(self.ENZYMES.keys()))
@@ -68,13 +69,12 @@ class RADseq (NG6Workflow):
         # option inutile maintenant, puisque potentiel rescue et check RAD dans process_radtag
         #self.add_parameter("tag_mismatch", "Max. number of mismatches allowed in the radTAG sequence",default = 0, type=int)
         self.add_parameter("mismatches", "Max. number of mismatches allowed.",default = 0, type=int)
-        self.add_parameter("trim_barcode", "Should the barecode be trimmed",default = True, type=bool)
+        self.add_parameter("trim_barcode", "Should the barecode be trimmed",default = True, type=bool, rules="Exclude=trim_reads2")
         self.add_parameter("trim_reads2", " Shoud the read 2 be trimmed to have the same length as the read1",default = False, type=bool)
-        #TODO Exclude self.add_exclusion_rule('trim_reads2', 'trim_barcode')        
-              
+
         #clone_filter
         self.add_parameter("dereplicate", "Should we remove PCR duplcat. Only for paired end - single RADSeq protocol",default = False, type=bool)
-        
+
         # process_radtag
         self.add_parameter("enzyme", "Restriction enzyme name", required = True , choices = list(self.ENZYMES.keys()))
         self.add_parameter("enzyme2", "Restriction enzyme 2 name", required = False, default="", choices = list(self.ENZYMES.keys()))
@@ -86,7 +86,7 @@ class RADseq (NG6Workflow):
         self.add_parameter("keep_discard_read", "capture discarded reads to a file.", default = True, type=bool)
         self.add_parameter("window_size", "set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).", default=0.15, type=float)
         self.add_parameter("limit_score", "set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).", default=10, type=int)
-       
+
         # ustacks
         self.add_parameter("min_cov", "stacks minimum coverage", type=int)
         self.add_parameter("primary_mismatch", "stacks max mismatch", type=int)
@@ -95,21 +95,21 @@ class RADseq (NG6Workflow):
         self.add_parameter("disable_removal_algo", "removal cluster correction algo", type=bool)
         self.add_parameter("disable_deleveraging_algo", "deleveraging cluster correction algo", type=bool)
         self.add_parameter("max_locus", "max stacks per cluster", type=int)
-        
+
         # cstacks
         self.add_parameter("batch_id", " batch_id of this radseq analysis",default = 1, type=int)
         self.add_parameter("catalog_mismatches", "How many mismatches allowed between sample to generate the cluster catalog",default = 1, type=int)
-        
+
         # ng6
         self.add_parameter("compression", "How should data be compressed once archived (none|gz|bz2)",default = 'gz', choices=['none', 'gz', 'bz2'])
         self.add_parameter("databank", "Which databank should be used to seek contamination (as to be nr databank)")
-        
-    
+
+
     def process(self):
-        
+
         read1_list=[]
         read2_list= []
-        
+
         # plus besoins on fait le check du rad dans process_radtag, sinon ça ne fonctionne pas dans le cas des double digest.
         # rad, rad_tag = self.get_enzyme(self.enzyme)
         # si aucun pool, alors données démultipléxées et donc les sample read1 sont les vraies sample read1
@@ -127,18 +127,18 @@ class RADseq (NG6Workflow):
                 if p["id"] in pools :
                     raise ValueError("Duplicated pool id." + p['id'])
                 pools[p["id"]] = (p, [])
-             
+
             for sample in self.samples :
                 pool_id = sample.get_metadata('pool_id')
                 if pool_id not in pools:
                     raise ValueError("The pool id " + pool_id + " does not exists in (individual " + sample.name + ")")
                 pools[pool_id][1].append(sample)
-             
-            # prepare fastq files 
+
+            # prepare fastq files
             fastq_files_1 = []
             fastq_files_2 = []
             barcode_files = []
-             
+
             for pool_id, data in pools.items() :
                 p = data[0]
                 samples = data[1]
@@ -147,18 +147,18 @@ class RADseq (NG6Workflow):
                 fastq_files_1.append(p['read1']);
                 if p['read2'] :
                     fastq_files_2.append(p['read2'])
-                 
+
                 # write barcode file
                 with open(tmp_barcode, "w") as ff:
                     for sample in samples :
                         ff.write(sample.name + "\t" + sample.get_metadata('barcode') +"\n")
-                 
+
             #splitbc = self.add_component("Splitbc", [ fastq_files_1, barcode_files, fastq_files_2, rad, rad_tag, self.mismatches, self.tag_mismatch, self.trim_barcode, self.trim_reads2])
             splitbc = self.add_component("Splitbc", [ fastq_files_1, barcode_files, fastq_files_2, self.mismatches, self.trim_barcode, self.trim_reads2])
             read1_list=splitbc.output_read1
             read2_list=splitbc.output_read2
 
-        # PROCESS_RADTAG  
+        # PROCESS_RADTAG
         print("before process",read1_list,read2_list)
         process_radtag = self.add_component("ProcessRadtag", [read1_list, read2_list, self.dereplicate, self.enzyme, self.enzyme2, self.window_size, self.limit_score, self.quality_encode, self.max_length, self.uncall_remove, self.discard_low_qual, self.rescue_radtag, self.keep_discard_read ])
 """
@@ -169,32 +169,32 @@ class RADseq (NG6Workflow):
 #         read1_files = []
 #         read2_files = []
 #         # check non empty and MAJ sample_id
-#         for idx, read1 in enumerate(process_radtag.output_read_1): 
+#         for idx, read1 in enumerate(process_radtag.output_read_1):
 #             if os.path.getsize(read1) > 0:
 #                 read1_files.append(read1)
 #                 read2_files.append(process_radtag.output_read_2[idx])
 #                 samples_id.append(idx)
 #
         ustacks_opt={"samples_id":samples_id,"read1_files":read1_list}
-        
-        if self.min_cov : 
+
+        if self.min_cov :
             ustacks_opt["min_cov"] = self.min_cov
-        if self.primary_mismatch : 
+        if self.primary_mismatch :
             ustacks_opt["primary_mismatch"] = self.primary_mismatch
-        if self.secondary_mismatch : 
+        if self.secondary_mismatch :
             ustacks_opt["secondary_mismatch"] =  self.secondary_mismatch
-        if self.uncall_hap : 
+        if self.uncall_hap :
             ustacks_opt["uncall_hap"] = self.uncall_hap
-        if self.disable_removal_algo : 
+        if self.disable_removal_algo :
             ustacks_opt["removal_algo"] = False
-        if self.disable_deleveraging_algo : 
+        if self.disable_deleveraging_algo :
             ustacks_opt["deleveraging_algo"] = False
-        if self.max_locus : 
+        if self.max_locus :
             ustacks_opt["max_locus"] = self.max_locus
-        
+
         ustacks = self.add_component("Ustacks", [],ustacks_opt)
-        
+
         # CSTACKS
 #         cstacks = self.add_component("Cstacks", [ustacks.alleles, ustacks.snps, ustacks.tags, self.batch_id, self.catalog_mismatches])
-         
+
 """