mkdir ./submission_files; 
#set $studies_table_path = './submission_files/studies.tsv'
#set $samples_table_path =   './submission_files/samples.tsv'
#set $experiments_table_path = './submission_files/experiments.tsv'
#set $runs_table_path =  './submission_files/runs.tsv'
        
#set $studies_table_path_updated = './submission_files/studies_updated.tsv'
#set $samples_table_path_updated =   './submission_files/samples_updated.tsv'
#set $experiments_table_path_updated = './submission_files/experiments_updated.tsv'
#set $runs_table_path_updated =  './submission_files/runs_updated.tsv'

#set working_dir = os.getcwd()
#if $action_options.input_format_conditional.input_format == "build_tables":
  python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json;
#end if
        
credentials_path='test_fake_path';
echo "username: test_user" > \$credentials_path;
echo "password: test_password" >> \$credentials_path;


#if $action_options.input_format_conditional.input_format == "build_tables":
    cp $studies_table_path $studies_table_out &&
    cp $samples_table_path $samples_table_out &&
    cp $experiments_table_path $experiments_table_out &&
    cp $runs_table_path $runs_table_out &&
#end if
#if $action_options.input_format_conditional.input_format == "user_generated_tables":
    ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
    ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
    ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
    ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
#end if
#if $action_options.input_format_conditional.input_format == "excel_tables":
    ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
#end if
#if $action_options.input_format_conditional.input_format == "isa_json":
    ln -s '$action_options.input_format_conditional.isa_json_file' ./isa_json_input.json &&
#end if
#if $action_options.test_submit_parameters.dry_run == "False":
    webin_id=`grep 'username' $credentials`;
    if [ "\$webin_id" = "" ]; then
      ## No credentials in user defined preferences    
      ## Fallback to global defined credentials (if exist)   
      #import os
      #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
          credentials_path=\${GALAXY_ENA_SECRETS};     
          webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
          if [ "\$webin_id" = "" ]; then
                echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
              exit 1;
          fi;
      #else:
          echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
          exit 1;
      #end if
    else
      credentials_path='$credentials';
    fi;
#end if


## create the list of files to upload and make the symlinks 
#import re      
#set $files_to_upload = list()
#if $action_options.input_format_conditional.input_format == "build_tables":
    #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study:
      #for $sample in $study.rep_sample:
        #for $experiment in $sample.rep_experiment:
          #for $run in $experiment.rep_runs:
            #for $file in $run.upload_files:
                #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
                #if $action_options.input_format_conditional.add_extension == "True":
                    #set $extension = '.fastq'
                #else
                    #set $extension = ''
                #end if
                #if $file.is_of_type('fastq', 'fastqsanger'):
                    ## compression output is defined as safename_reads_file so no need to symlink
                    #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
                    gzip -c '$file' > $safename_reads_file &&
                #else:
                    #if $action_options.input_format_conditional.add_extension == "True":
                        #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
                            #set $compression = '.gz' 
                        #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                            #set $compression = '.bz2' 
                        #end if
                        #set $safename_reads_file = $safename_reads_file + $extension + $compression 
                    #end if
                    ln -s '$file' $safename_reads_file &&
                #end if
                $files_to_upload.append(str($safename_reads_file))
            #end for
          #end for
        #end for
      #end for
    #end for
#else:
    #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list':
        #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection:
            #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
            ## Always need to add .fastq + compression suffix because the name is based on the pair name which has no extensions
            #if $pair.forward.is_of_type('fastq', 'fastqsanger'):
                ## compress the file, no need to create the link then
                ## always add the compression suffix (.gz)
                #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz'
                gzip -c '$file' > $safename_fwd_reads_file &&
            #else
                #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
                    #set $compression = '.gz'
                #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                    #set $compression = '.bz2'
                #end if
                #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression
                ln -s '$pair.forward' $safename_fwd_reads_file &&
            #end if

            #if $pair.reverse.is_of_type('fastq', 'fastqsanger'):
                ## compress the file, no need to create the link then
                #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz'
                gzip -c '$file' > $safename_rev_reads_file &&
            #else
                #if $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                    #set $compression = '.bz2'
                #elif $pair.reverse.is_of_type('fastqsanger.gz', 'fastq.gz'):
                    #set $compression = '.gz'
                #end if
                #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression
                ln -s '$pair.reverse' $safename_rev_reads_file &&
            #end if
            $files_to_upload.append(str($safename_fwd_reads_file))
            $files_to_upload.append(str($safename_rev_reads_file))
        #end for
    #end if
    #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
        #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
            #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
            #if $file.is_of_type('fastq', 'fastqsanger'):
                ## always compress add the gz extension
                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
                    #set $safename_reads_file = $safename_reads_file + '.fastq.gz'
                #else
                    #set $safename_reads_file = $safename_reads_file + '.gz'
                #end if
                gzip -c '$file' > $safename_reads_file &&
            #else
                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
                    #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
                        #set $extension = '.fastq.gz'
                    #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                        #set $extension = '.fastq.bz2'
                    #end if
                    #set $safename_reads_file = $safename_reads_file + $extension
                #end if
                ln -s '$file' $safename_reads_file &&
            #end if      
            $files_to_upload.append(str($safename_reads_file))
        #end for
    #end if
#end if

ena-upload-cli
    --tool 'ena-upload-cli v0.9.0 @ Galaxy'
    --action '$action_options.action'
    --center '$action_options.test_submit_parameters.center'
    --secret \${credentials_path}
    --data
#for $dataset in $files_to_upload:
    '$dataset'
#end for
#if $action_options.test_submit_parameters.dry_run == "True":
    --draft
#end if
#if $action_options.input_format_conditional.input_format == "excel_tables":
    --xlsx ./xlsx_input.xlsx 
#elif $action_options.input_format_conditional.input_format == "user_generated_tables" or $action_options.input_format_conditional.input_format == "build_tables":
    --experiment '$experiments_table_path'
    --study '$studies_table_path'
    --run '$runs_table_path'
    --sample '$samples_table_path'
#elif $action_options.input_format_conditional.input_format == "isa_json":
    --isa_json ./isa_json_input.json
    --isa_assay_stream '$action_options.input_format_conditional.isa_assay_stream'
#end if
#if $action_options.input_format_conditional.input_format == "build_tables":
    #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
        --checklist ERC000033
    #end if
#elif $action_options.input_format_conditional.input_format == "isa_json":
    --checklist ERC000011
#else:
    --checklist $action_options.input_format_conditional.checklist_id
#end if
#if $action_options.test_submit_parameters.submit_dev == "True":
    -d
#end if
>> '$output';


#if $action_options.test_submit_parameters.dry_run == "False":
    echo -e 'center_name\t$action_options.test_submit_parameters.center' >> '$output';
    echo -e 'action_option\t$action_options.action' >> '$output';
#end if
        
## copy updated files
#if $action_options.input_format_conditional.input_format == "excel_tables" or $action_options.input_format_conditional.input_format == "isa_json":
    ## for the excel/ISA json input case, copy the upload-cli generated tables to the output files
    ## this applies for both draft and real submissions
    cp './ENA_template_experiment_updated.tsv' $experiments_table_out;
    cp './ENA_template_sample_updated.tsv' $samples_table_out;
    cp './ENA_template_study_updated.tsv' $studies_table_out;
    cp './ENA_template_run_updated.tsv' $runs_table_out;
#else
    cp $studies_table_path_updated $studies_table_out 2>/dev/null;
    cp $samples_table_path_updated $samples_table_out 2>/dev/null;
    cp $experiments_table_path_updated $experiments_table_out 2>/dev/null;
    cp $runs_table_path_updated $runs_table_out 2>/dev/null;
#end if

python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output;