#!/usr/bin/env perl


# SCF: fasta_lwp.pl is now returning internal server error. Maybe it has become obsolete. Now trying this code which i found at:
# https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/FASTA+Help+and+Documentation#FASTAHelpandDocumentation-WebServices


=head1 NAME

fasta.pl

=head1 DESCRIPTION

FASTA (REST) web service Perl client using L<LWP>.

Tested with:

=over

=item *
L<LWP> 6.35, L<XML::Simple> 2.25 and Perl 5.22.0 (MacOS 10.13.6)

=back

For further information see:

=over

=item *
L<https://www.ebi.ac.uk/Tools/webservices/>

=back

=head1 LICENSE

Copyright 2012-2018 EMBL - European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

Perl Client Automatically generated with:
https://github.com/ebi-wp/webservice-clients-generator

=cut

# ======================================================================
# Enable Perl warnings
use strict;
use warnings;

# Load libraries
use English;
use LWP;
use XML::Simple;
use Getopt::Long qw(:config no_ignore_case bundling);
use File::Basename;
use Data::Dumper;
use Time::HiRes qw(usleep);

# Base URL for service
my $baseUrl = 'https://www.ebi.ac.uk/Tools/services/rest/fasta';
my $version = '2020-02-28 14:43';

# Set interval for checking status
my $checkInterval = 3;

# Set maximum number of 'ERROR' status calls to call job failed.
my $maxErrorStatusCount = 3;

# Output level
my $outputLevel = 1;

# Process command-line options
my $numOpts = scalar(@ARGV);
my %params = (
    'debugLevel' => 0,
    'maxJobs'    => 1
);
my @database;
# Default parameter values (should get these from the service)
GetOptions(
    # Tool specific options
    'program=s'       => \$params{'program'},        # The FASTA program to be used for the Sequence Similarity Search
    'stype=s'         => \$params{'stype'},          # Indicates if the query sequence is protein, DNA or RNA. Used to force FASTA to interpret the input sequence as specified type of sequence (via. the '-p', '-n' or '-U' options), this prevents issues when using nucleotide sequences that contain many ambiguous residues.
    'matrix=s'        => \$params{'matrix'},         # (Protein searches) The substitution matrix used for scoring alignments when searching the database. Target identity is the average alignment identity the matrix would produce in the absence of homology and can be used to compare different matrix types. Alignment boundaries are more accurate when the alignment identity matches the target identity percentage.
    'match_scores=s'  => \$params{'match_scores'},   # (Nucleotide searches) The match score is the bonus to the alignment score when matching the same base. The mismatch is the penalty when failing to match.
    'gapopen=i'       => \$params{'gapopen'},        # Score for the first residue in a gap.
    'gapext=i'        => \$params{'gapext'},         # Score for each additional residue in a gap.
    'hsps'            => \$params{'hsps'},           # Turn on/off the display of all significant alignments between query and library sequence.
    'expupperlim=f'   => \$params{'expupperlim'},    # Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.
    'explowlim=f'     => \$params{'explowlim'},      # Limit the number of scores and alignments reported based on the expectation value. This is the minimum number of times the match is expected to occur by chance. This allows closely related matches to be excluded from the result in favor of more distant relationships.
    'strand=s'        => \$params{'strand'},         # For nucleotide sequences specify the sequence strand to be used for the search. By default both upper (provided) and lower (reverse complement of provided) strands are used, for single stranded sequences searching with only the upper or lower strand may provide better results.
    'hist'            => \$params{'hist'},           # Turn on/off the histogram in the FASTA result. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.
    'scores=i'        => \$params{'scores'},         # Maximum number of match score summaries reported in the result output.
    'alignments=i'    => \$params{'alignments'},     # Maximum number of match alignments reported in the result output.
    'scoreformat=s'   => \$params{'scoreformat'},    # Different score report formats.
    'stats=s'         => \$params{'stats'},          # The statistical routines assume that the library contains a large sample of unrelated sequences. Options to select what method to use include regression, maximum likelihood estimates, shuffles, or combinations of these.
    'annotfeats'      => \$params{'annotfeats'},     # Turn on/off annotation features. Annotation features shows features from UniProtKB, such as variants, active sites, phospho-sites and binding sites that have been found in the aligned region of the database hit. To see the annotation features in the results after this has been enabled, select sequences of interest and click to 'Show' Alignments. This option also enables a new result tab (Domain Diagrams) that highlights domain regions.
    'annotsym=s'      => \$params{'annotsym'},       # Specify the annotation symbols.
    'dbrange=s'       => \$params{'dbrange'},        # Specify the sizes of the sequences in a database to search against. For example: 100-250 will search all sequences in a database with length between 100 and 250 residues, inclusive.
    'seqrange=s'      => \$params{'seqrange'},       # Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell FASTA to only use residues 34 to 89, inclusive.
    'filter=s'        => \$params{'filter'},         # Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather then meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.
    'transltable=i'   => \$params{'transltable'},    # Query Genetic code to use in translation
    'sequence=s'      => \$params{'sequence'},       # The query sequence can be entered directly into this form. The sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.
    'database=s'      => \@database,                 # The databases to run the sequence similarity search against. Multiple databases can be used at the same time
    'ktup=i'          => \$params{'ktup'},           # FASTA uses a rapid word-based lookup strategy to speed the initial phase of the similarity search. The KTUP is used to control the sensitivity of the search. Lower values lead to more sensitive, but slower searches.
    # Generic options
    'email=s'         => \$params{'email'},          # User e-mail address
    'title=s'         => \$params{'title'},          # Job title
    'outfile=s'       => \$params{'outfile'},        # Output file name
    'outformat=s'     => \$params{'outformat'},      # Output file type
    'jobid=s'         => \$params{'jobid'},          # JobId
    'help|h'          => \$params{'help'},           # Usage help
    'asyncjob'        => \$params{'asyncjob'},       # Asynchronous submission
    'polljob'         => \$params{'polljob'},        # Get results
    'pollFreq=f'      => \$params{'pollFreq'},       # Poll Frequency
    'resultTypes'     => \$params{'resultTypes'},    # Get result types
    'status'          => \$params{'status'},         # Get status
    'params'          => \$params{'params'},         # List input parameters
    'paramDetail=s'   => \$params{'paramDetail'},    # Get details for parameter
    'multifasta'      => \$params{'multifasta'},     # Multiple fasta input
    'useSeqId'        => \$params{'useSeqId'},       # Seq Id file name
    'maxJobs=i'       => \$params{'maxJobs'},        # Max. parallel jobs

    'verbose'         => \$params{'verbose'},        # Increase output level
    'version'         => \$params{'version'},        # Prints out the version of the Client and exit.
    'quiet'           => \$params{'quiet'},          # Decrease output level
    'debugLevel=i'    => \$params{'debugLevel'},     # Debugging level
    'baseUrl=s'       => \$baseUrl,                  # Base URL for service.
);
if ($params{'verbose'}) {$outputLevel++}
if ($params{'quiet'}) {$outputLevel--}
if ($params{'pollFreq'}) {$checkInterval = $params{'pollFreq'} * 1000 * 1000}
if ($params{'baseUrl'}) {$baseUrl = $params{'baseUrl'}}
$params{"database"} = [@database];

# Debug mode: LWP version
&print_debug_message('MAIN', 'LWP::VERSION: ' . $LWP::VERSION,
    1);

# Debug mode: print the input parameters
&print_debug_message('MAIN', "params:\n" . Dumper(\%params), 11);

# LWP UserAgent for making HTTP calls (initialised when required).
my $ua;

# Get the script filename for use in usage messages
my $scriptName = basename($0, ());

# Print usage and exit if requested
if ($params{'help'} || $numOpts == 0) {
    &usage();
    exit(0);
}

# Debug mode: show the base URL
&print_debug_message('MAIN', 'baseUrl: ' . $baseUrl, 1);
if (
    !(
        $params{'polljob'}
            || $params{'resultTypes'}
            || $params{'status'}
            || $params{'params'}
            || $params{'paramDetail'}
            || $params{'version'}
    )
        && !(defined($ARGV[0]) || defined($params{'sequence'}))
) {

    # Bad argument combination, so print error message and usage
    print STDERR 'Error: bad option combination', "\n";
    &usage();
    exit(1);
}
# Get parameters list
elsif ($params{'params'}) {
    &print_tool_params();
}

# Get parameter details
elsif ($params{'paramDetail'}) {
    &print_param_details($params{'paramDetail'});
}

# Print Client version
elsif ($params{'version'}) {
  print STDOUT 'Revision: ' . $version, "\n";
  exit(1);
}

# Job status
elsif ($params{'status'} && defined($params{'jobid'})) {
    &print_job_status($params{'jobid'});
}

# Result types
elsif ($params{'resultTypes'} && defined($params{'jobid'})) {
    &print_result_types($params{'jobid'});
}

# Poll job and get results
elsif ($params{'polljob'} && defined($params{'jobid'})) {
    &get_results($params{'jobid'});
}

# Submit a job
else {
    # Multiple input sequence mode, assume fasta format.
    if (defined($params{'multifasta'}) && $params{'multifasta'}) {
        &multi_submit_job();
    }

    # Entry identifier list file.
    elsif ((defined($params{'sequence'}) && $params{'sequence'} =~ m/^\@/)
        || (defined($ARGV[0]) && $ARGV[0] =~ m/^\@/)) {
        my $list_filename = $params{'sequence'} || $ARGV[0];
        $list_filename =~ s/^\@//;
        &list_file_submit_job($list_filename);
    }
    # Default: single sequence/identifier.
    else {
        # Warn for invalid batch only option use.
        if (defined($params{'useSeqId'}) && $params{'useSeqId'}) {
            print STDERR "Warning: --useSeqId option ignored.\n";
            delete $params{'useSeqId'};
        }
        if (defined($params{'maxJobs'}) && $params{'maxJobs'} > 1) {
            print STDERR "Warning: --maxJobs option ignored.\n";
            $params{'maxJobs'} = 1;
        }
        # Load the sequence data and submit.
        &submit_job(&load_data());
    }
}



=head1 FUNCTIONS

=cut

### Wrappers for REST resources ###

=head2 rest_user_agent()

Get a LWP UserAgent to use to perform REST requests.

  my $ua = &rest_user_agent();

=cut

sub rest_user_agent() {
    print_debug_message('rest_user_agent', 'Begin', 21);
    # Create an LWP UserAgent for making HTTP calls.
    my $ua = LWP::UserAgent->new();
    # Set 'User-Agent' HTTP header to identifiy the client.
    my $revisionNumber = 0;
    $revisionNumber = "Revision: " . $version;
    $ua->agent("EBI-Sample-Client/$revisionNumber ($scriptName; $OSNAME) " . $ua->agent());
    # Configure HTTP proxy support from environment.
    $ua->env_proxy;
    print_debug_message('rest_user_agent', 'End', 21);
    return $ua;
}

=head2 rest_error()

Check a REST response for an error condition. An error is mapped to a die.

  &rest_error($response, $content_data);

=cut

sub rest_error() {
    print_debug_message('rest_error', 'Begin', 21);
    my $response = shift;
    my $contentdata;
    if (scalar(@_) > 0) {
        $contentdata = shift;
    }
    if (!defined($contentdata) || $contentdata eq '') {
        $contentdata = $response->content();
    }
    # Check for HTTP error codes
    if ($response->is_error) {
        my $error_message = '';
        # HTML response.
        if ($contentdata =~ m/<h1>([^<]+)<\/h1>/) {
            $error_message = $1;
        }
        #  XML response.
        elsif ($contentdata =~ m/<description>([^<]+)<\/description>/) {
            $error_message = $1;
        }
        # die 'http status: ' . $response->code . ' ' . $response->message . '  ' . $error_message;
    }
    print_debug_message('rest_error', 'End', 21);
}

=head2 rest_request()

Perform a REST request (HTTP GET).

  my $response_str = &rest_request($url);

=cut

sub rest_request {
    print_debug_message('rest_request', 'Begin', 11);
    my $requestUrl = shift;
    print_debug_message('rest_request', 'URL: ' . $requestUrl, 11);

    # Get an LWP UserAgent.
    $ua = &rest_user_agent() unless defined($ua);
    # Available HTTP compression methods.
    my $can_accept;
    eval {
        $can_accept = HTTP::Message::decodable();
    };
    $can_accept = '' unless defined($can_accept);
    # Perform the request
    my $response = $ua->get($requestUrl,
        'Accept-Encoding' => $can_accept, # HTTP compression.
    );
    print_debug_message('rest_request', 'HTTP status: ' . $response->code,
        11);
    print_debug_message('rest_request',
        'response length: ' . length($response->content()), 11);
    print_debug_message('rest_request',
        'request:' . "\n" . $response->request()->as_string(), 32);
    print_debug_message('rest_request',
        'response: ' . "\n" . $response->as_string(), 32);
    # Unpack possibly compressed response.
    my $retVal;
    if (defined($can_accept) && $can_accept ne '') {
        $retVal = $response->decoded_content();
    }
    # If unable to decode use orginal content.
    $retVal = $response->content() unless defined($retVal);
    # Check for an error.
    &rest_error($response, $retVal);
    print_debug_message('rest_request', 'retVal: ' . $retVal, 12);
    print_debug_message('rest_request', 'End', 11);

    # Return the response data
    return $retVal;
}

=head2 rest_get_parameters()

Get list of tool parameter names.

  my (@param_list) = &rest_get_parameters();

=cut

sub rest_get_parameters {
    print_debug_message('rest_get_parameters', 'Begin', 1);
    my $url = $baseUrl . '/parameters/';
    my $param_list_xml_str = rest_request($url);
    my $param_list_xml = XMLin($param_list_xml_str);
    my (@param_list) = @{$param_list_xml->{'id'}};
    print_debug_message('rest_get_parameters', 'End', 1);
    return(@param_list);
}

=head2 rest_get_parameter_details()

Get details of a tool parameter.

  my $paramDetail = &rest_get_parameter_details($param_name);

=cut

sub rest_get_parameter_details {
    print_debug_message('rest_get_parameter_details', 'Begin', 1);
    my $parameterId = shift;
    print_debug_message('rest_get_parameter_details',
        'parameterId: ' . $parameterId, 1);
    my $url = $baseUrl . '/parameterdetails/' . $parameterId;
    my $param_detail_xml_str = rest_request($url);
    my $param_detail_xml = XMLin($param_detail_xml_str);
    print_debug_message('rest_get_parameter_details', 'End', 1);
    return($param_detail_xml);
}

=head2 rest_run()

Submit a job.

  my $job_id = &rest_run($email, $title, \%params );

=cut

sub rest_run {
    print_debug_message('rest_run', 'Begin', 1);
    my $email = shift;
    my $title = shift;
    my $params = shift;
    $email = '' if (!$email);
    print_debug_message('rest_run', 'email: ' . $email, 1);
    if (defined($title)) {
        print_debug_message('rest_run', 'title: ' . $title, 1);
    }
    print_debug_message('rest_run', 'params: ' . Dumper($params), 1);

    # Get an LWP UserAgent.
    $ua = &rest_user_agent() unless defined($ua);

    # Clean up parameters
    my (%tmp_params) = %{$params};
    $tmp_params{'email'} = $email;
    $tmp_params{'title'} = $title;
    foreach my $param_name (keys(%tmp_params)) {
        if (!defined($tmp_params{$param_name})) {
            delete $tmp_params{$param_name};
        }
    }

    # Submit the job as a POST
    my $url = $baseUrl . '/run';
    my $response = $ua->post($url, \%tmp_params);
    print_debug_message('rest_run', 'HTTP status: ' . $response->code, 11);
    print_debug_message('rest_run',
        'request:' . "\n" . $response->request()->as_string(), 11);
    print_debug_message('rest_run',
        'response: ' . length($response->as_string()) . "\n" . $response->as_string(), 11);

    # Check for an error.
    &rest_error($response);

    # The job id is returned
    my $job_id = $response->content();
    print_debug_message('rest_run', 'End', 1);
    return $job_id;
}

=head2 rest_get_status()

Check the status of a job.

  my $status = &rest_get_status($job_id);

=cut

sub rest_get_status {
    print_debug_message('rest_get_status', 'Begin', 1);
    my $job_id = shift;
    print_debug_message('rest_get_status', 'jobid: ' . $job_id, 2);
    my $status_str = 'UNKNOWN';
    my $url = $baseUrl . '/status/' . $job_id;
    $status_str = &rest_request($url);
    print_debug_message('rest_get_status', 'status_str: ' . $status_str, 2);
    print_debug_message('rest_get_status', 'End', 1);
    return $status_str;
}

=head2 rest_get_result_types()

Get list of result types for finished job.

  my (@result_types) = &rest_get_result_types($job_id);

=cut

sub rest_get_result_types {
    print_debug_message('rest_get_result_types', 'Begin', 1);
    my $job_id = shift;
    print_debug_message('rest_get_result_types', 'jobid: ' . $job_id, 2);
    my (@resultTypes);
    my $url = $baseUrl . '/resulttypes/' . $job_id;
    my $result_type_list_xml_str = &rest_request($url);
    my $result_type_list_xml = XMLin($result_type_list_xml_str);
    (@resultTypes) = @{$result_type_list_xml->{'type'}};
    print_debug_message('rest_get_result_types',
        scalar(@resultTypes) . ' result types', 2);
    print_debug_message('rest_get_result_types', 'End', 1);
    return(@resultTypes);
}

=head2 rest_get_result()

Get result data of a specified type for a finished job.

  my $result = rest_get_result($job_id, $result_type);

=cut

sub rest_get_result {
    print_debug_message('rest_get_result', 'Begin', 1);
    my $job_id = shift;
    my $type = shift;
    print_debug_message('rest_get_result', 'jobid: ' . $job_id, 1);
    print_debug_message('rest_get_result', 'type: ' . $type, 1);
    my $url = $baseUrl . '/result/' . $job_id . '/' . $type;
    my $result = &rest_request($url);
    print_debug_message('rest_get_result', length($result) . ' characters',
        1);
    print_debug_message('rest_get_result', 'End', 1);
    return $result;
}

### Service actions and utility functions ###

=head2 print_debug_message()

Print debug message at specified debug level.

  &print_debug_message($method_name, $message, $level);

=cut

sub print_debug_message {
    my $function_name = shift;
    my $message = shift;
    my $level = shift;
    if ($level <= $params{'debugLevel'}) {
        print STDERR '[', $function_name, '()] ', $message, "\n";
    }
}

=head2 print_tool_params()

Print list of tool parameters.

  &print_tool_params();

=cut

sub print_tool_params {
    print_debug_message('print_tool_params', 'Begin', 1);
    my (@param_list) = &rest_get_parameters();
    foreach my $param (sort (@param_list)) {
        print $param, "\n";
    }
    print_debug_message('print_tool_params', 'End', 1);
}

=head2 print_param_details()

Print details of a tool parameter.

  &print_param_details($param_name);

=cut

sub print_param_details {
    print_debug_message('print_param_details', 'Begin', 1);
    my $paramName = shift;
    print_debug_message('print_param_details', 'paramName: ' . $paramName, 2);
    my $paramDetail = &rest_get_parameter_details($paramName);
    print $paramDetail->{'name'}, "\t", $paramDetail->{'type'}, "\n";
    print $paramDetail->{'description'}, "\n";
    if (defined($paramDetail->{'values'}->{'value'})) {
        if (ref($paramDetail->{'values'}->{'value'}) eq 'ARRAY') {
            foreach my $value (@{$paramDetail->{'values'}->{'value'}}) {
                &print_param_value($value);
            }
        }
        else {
            &print_param_value($paramDetail->{'values'}->{'value'});
        }
    }
    print_debug_message('print_param_details', 'End', 1);
}

=head2 print_param_value()

Print details of a tool parameter value.

  &print_param_details($param_value);

Used by print_param_details() to handle both singluar and array values.

=cut

sub print_param_value {
    my $value = shift;
    print $value->{'value'};
    if ($value->{'defaultValue'} eq 'true') {
        print "\t", 'default';
    }
    print "\n";
    print "\t", $value->{'label'}, "\n";
    if (defined($value->{'properties'})) {
        foreach
        my $key (sort ( keys(%{$value->{'properties'}{'property'}}) )) {
            if (ref($value->{'properties'}{'property'}{$key}) eq 'HASH'
                && defined($value->{'properties'}{'property'}{$key}{'value'})
            ) {
                print "\t", $key, "\t",
                    $value->{'properties'}{'property'}{$key}{'value'}, "\n";
            }
            else {
                print "\t", $value->{'properties'}{'property'}{'key'},
                    "\t", $value->{'properties'}{'property'}{'value'}, "\n";
                last;
            }
        }
    }
}

=head2 print_job_status()

Print status of a job.

  &print_job_status($job_id);

=cut

sub print_job_status {
    print_debug_message('print_job_status', 'Begin', 1);
    my $jobid = shift;
    print_debug_message('print_job_status', 'jobid: ' . $jobid, 1);
    if ($outputLevel > 0) {
        print STDERR 'Getting status for job ', $jobid, "\n";
    }
    my $result = &rest_get_status($jobid);
    print "$result\n";
    if ($result eq 'FINISHED' && $outputLevel > 0) {
        print STDERR "To get results: perl $scriptName --polljob --jobid " . $jobid
            . "\n";
    }
    print_debug_message('print_job_status', 'End', 1);
}

=head2 print_result_types()

Print available result types for a job.

  &print_result_types($job_id);

=cut

sub print_result_types {
    print_debug_message('result_types', 'Begin', 1);
    my $jobid = shift;
    print_debug_message('result_types', 'jobid: ' . $jobid, 1);
    if ($outputLevel > 0) {
        print STDERR 'Getting result types for job ', $jobid, "\n";
    }
    my $status = &rest_get_status($jobid);
    if ($status eq 'PENDING' || $status eq 'RUNNING') {
        print STDERR 'Error: Job status is ', $status,
            '. To get result types the job must be finished.', "\n";
    }
    else {
        my (@resultTypes) = &rest_get_result_types($jobid);
        if ($outputLevel > 0) {
            print STDOUT 'Available result types:', "\n";
        }
        foreach my $resultType (@resultTypes) {
            print STDOUT $resultType->{'identifier'}, "\n";
            if (defined($resultType->{'label'})) {
                print STDOUT "\t", $resultType->{'label'}, "\n";
            }
            if (defined($resultType->{'description'})) {
                print STDOUT "\t", $resultType->{'description'}, "\n";
            }
            if (defined($resultType->{'mediaType'})) {
                print STDOUT "\t", $resultType->{'mediaType'}, "\n";
            }
            if (defined($resultType->{'fileSuffix'})) {
                print STDOUT "\t", $resultType->{'fileSuffix'}, "\n";
            }
        }
        if ($status eq 'FINISHED' && $outputLevel > 0) {
            print STDERR "\n", 'To get results:', "\n",
                "  perl $scriptName --polljob --jobid " . $params{'jobid'} . "\n",
                "  perl $scriptName --polljob --outformat <type> --jobid "
                    . $params{'jobid'} . "\n";
        }
    }
    print_debug_message('result_types', 'End', 1);
}

=head2 submit_job()

Submit a job to the service.

  &submit_job($seq);

=cut

sub submit_job {
    print_debug_message('submit_job', 'Begin', 1);

    # Set input sequence
    $params{'sequence'} = shift;
    my $seq_id = shift;

    # Load parameters
    &load_params();

    # Submit the job
    my $jobid = &rest_run($params{'email'}, $params{'title'}, \%params);

    # Asynchronous submission.
    if (defined($params{'asyncjob'})) {
        print STDOUT $jobid, "\n";
        if ($outputLevel > 0) {
            print STDERR
                "To check status: perl $scriptName --status --jobid $jobid\n";
        }
    }

    # Simulate synchronous submission serial mode.
    else {
        if ($outputLevel > 0) {
            print STDERR "JobId: $jobid\n";
        } else {
            print STDERR "$jobid\n";
        }
        usleep($checkInterval);
        # Get results.
        &get_results($jobid, $seq_id);

    }
    print_debug_message('submit_job', 'End', 1);
    return $jobid;
}
=head2 multi_submit_job()

Submit multiple jobs assuming input is a collection of fasta formatted sequences.

  &multi_submit_job();

=cut

sub multi_submit_job {
    print_debug_message('multi_submit_job', 'Begin', 1);
    my (@filename_list) = ();

    # Query sequence
    if (defined($ARGV[0])) {                  # Bare option
        if (-f $ARGV[0] || $ARGV[0] eq '-') { # File
            push(@filename_list, $ARGV[0]);
        }
        else {
            warn 'Warning: Input file "' . $ARGV[0] . '" does not exist';
        }
    }
    if ($params{'sequence'}) {                                      # Via --sequence
        if (-f $params{'sequence'} || $params{'sequence'} eq '-') { # File
            push(@filename_list, $params{'sequence'});
        }
        else {
            warn 'Warning: Input file "'
                . $params{'sequence'}
                . '" does not exist';
        }
    }

    # Job identifier tracking for parallel execution.
    my @jobid_list = ();
    my $job_number = 0;
    $/ = '>';
    foreach my $filename (@filename_list) {
        my $INFILE;
        if ($filename eq '-') { # STDIN.
            open($INFILE, '<-')
                or die 'Error: unable to STDIN (' . $! . ')';
        }
        else { # File.
            open($INFILE, '<', $filename)
                or die 'Error: unable to open file '
                . $filename . ' ('
                . $! . ')';
        }
        while (<$INFILE>) {
            my $seq = $_;
            $seq =~ s/>$//;
            if ($seq =~ m/(\S+)/) {
                my $seq_id = $1;
                print STDERR "Submitting job for: $seq_id\n"
                    if ($outputLevel > 0);
                $seq = '>' . $seq;
                &print_debug_message('multi_submit_job', $seq, 11);
                $job_number++;
                my $job_id = &submit_job($seq, $seq_id);

                my $job_info_str = sprintf('%s %d %d', $job_id, 0, $job_number);

                push(@jobid_list, $job_info_str);
            }

            # Parallel mode, wait for job(s) to finish to free slots.
            while ($params{'maxJobs'} > 1
                && scalar(@jobid_list) >= $params{'maxJobs'}) {
                &_job_list_poll(\@jobid_list);
                print_debug_message('multi_submit_job',
                    'Remaining jobs: ' . scalar(@jobid_list), 1);
            }
        }
        close $INFILE;
    }

    # Parallel mode, wait for remaining jobs to finish.
    while ($params{'maxJobs'} > 1 && scalar(@jobid_list) > 0) {
        &_job_list_poll(\@jobid_list);
        print_debug_message('multi_submit_job',
            'Remaining jobs: ' . scalar(@jobid_list), 1);
    }
    print_debug_message('multi_submit_job', 'End', 1);
}


=head2 _job_list_poll()

Poll the status of a list of jobs and fetch results for finished jobs.

  while(scalar(@jobid_list) > 0) {
    &_job_list_poll(\@jobid_list);
  }

=cut

sub _job_list_poll {
    print_debug_message('_job_list_poll', 'Begin', 1);
    my $jobid_list = shift;
    print_debug_message('_job_list_poll', 'Num jobs: ' . scalar(@$jobid_list),
        11);

    # Loop though job Id list polling job status.
    for (my $jobNum = (scalar(@$jobid_list) - 1); $jobNum > -1; $jobNum--) {
        my ($jobid, $seq_id, $error_count, $job_number) =
            split(/\s+/, $jobid_list->[$jobNum]);
        print_debug_message('_job_list_poll', 'jobNum: ' . $jobNum, 12);
        print_debug_message('_job_list_poll',
            'Job info: ' . $jobid_list->[$jobNum], 12);

        # Get job status.
        my $job_status = &rest_get_status($jobid);
        print_debug_message('_job_list_poll', 'Status: ' . $job_status, 12);

        # Fetch results and remove finished/failed jobs from list.
        if (
            !(
                $job_status eq 'RUNNING'
                    || $job_status eq 'PENDING'
                    || ($job_status eq 'ERROR'
                    && $error_count < $maxErrorStatusCount)
            )
        ) {
            if ($job_status eq 'ERROR' || $job_status eq 'FAILED') {
                print STDERR
                    "Warning: job $jobid failed for sequence $job_number: $seq_id\n";
            }
            # Duplicated getting results.
            #&get_results($jobid, $seq_id);
            splice(@$jobid_list, $jobNum, 1);
        }
        else {

            # Update error count, increment for new error or clear old errors.
            if ($job_status eq 'ERROR') {
                $error_count++;
            }
            elsif ($error_count > 0) {
                $error_count--;
            }

            # Update job tracking info.
            my $job_info_str = sprintf('%s %s %d %d',
                $jobid, $seq_id, $error_count, $job_number);
            $jobid_list->[$jobNum] = $job_info_str;
        }
    }
    print_debug_message('_job_list_poll', 'Num jobs: ' . scalar(@$jobid_list),
        11);
    print_debug_message('_job_list_poll', 'End', 1);
}

=head2 list_file_submit_job()

Submit multiple jobs using a file containing a list of entry identifiers as
input.

  &list_file_submit_job($list_filename)

=cut

sub list_file_submit_job {
    print_debug_message('list_file_submit_job', 'Begin', 1);
    my $filename = shift;

    # Open the file of identifiers.
    my $LISTFILE;
    if ($filename eq '-') { # STDIN.
        open($LISTFILE, '<-')
            or die 'Error: unable to STDIN (' . $! . ')';
    }
    else { # File.
        open($LISTFILE, '<', $filename)
            or die 'Error: unable to open file ' . $filename . ' (' . $! . ')';
    }

    # Job identifier tracking for parallel execution.
    my @jobid_list = ();
    my $job_number = 0;

    # Iterate over identifiers, submitting each job
    while (<$LISTFILE>) {
        my $line = $_;
        chomp($line);
        if ($line ne '') {
            &print_debug_message('list_file_submit_job', 'line: ' . $line, 2);
            if ($line =~ m/\w:\w/) {
                # Check this is an identifier
                my $seq_id = $line;
                print STDERR "Submitting job for: $seq_id\n"
                    if ($outputLevel > 0);
                $job_number++;
                my $job_id = &submit_job($seq_id, $seq_id);
                my $job_info_str =
                    sprintf('%s %s %d %d', $job_id, $seq_id, 0, $job_number);
                push(@jobid_list, $job_info_str);
            }
            else {
                print STDERR
                    "Warning: line \"$line\" is not recognised as an identifier\n";
            }

            # Parallel mode, wait for job(s) to finish to free slots.
            while ($params{'maxJobs'} > 1
                && scalar(@jobid_list) >= $params{'maxJobs'}) {
                &_job_list_poll(\@jobid_list);
                print_debug_message('list_file_submit_job',
                    'Remaining jobs: ' . scalar(@jobid_list), 1);
            }
        }
    }
    close $LISTFILE;

    # Parallel mode, wait for remaining jobs to finish.
    while ($params{'maxJobs'} > 1 && scalar(@jobid_list) > 0) {
        &_job_list_poll(\@jobid_list);
        print_debug_message('list_file_submit_job',
            'Remaining jobs: ' . scalar(@jobid_list), 1);
    }
    print_debug_message('list_file_submit_job', 'End', 1);
}


=head2 load_data()

Load sequence data from file or option specified on the command-line.

  &load_data();

=cut

sub load_data {
    print_debug_message('load_data', 'Begin', 1);
    my $retSeq;

    # Query sequence
    if (defined($ARGV[0])) {                  # Bare option
        if (-f $ARGV[0] || $ARGV[0] eq '-') { # File
            $retSeq = &read_file($ARGV[0]);
        }
        else { # DB:ID or sequence
            $retSeq = $ARGV[0];
        }
    }
    if ($params{'sequence'}) {                                      # Via --sequence
        if (-f $params{'sequence'} || $params{'sequence'} eq '-') { # File
            $retSeq = &read_file($params{'sequence'});
        }
        else { # DB:ID or sequence
            $retSeq = $params{'sequence'};
        }
    }
    print_debug_message('load_data', 'End', 1);
    return $retSeq;
}

=head2 load_params()

Load job parameters from command-line options.

  &load_params();

=cut

sub load_params {
    print_debug_message('load_params', 'Begin', 1);

    # Pass default values and fix bools (without default value)
    if (!$params{'hsps'}) {
        $params{'hsps'} = 'false'
    }

    if (!$params{'explowlim'}) {
        $params{'explowlim'} = '0'
    }

    if (!$params{'hist'}) {
        $params{'hist'} = 'false'
    }

    if (!$params{'scores'}) {
        $params{'scores'} = 50
    }

    if (!$params{'alignments'}) {
        $params{'alignments'} = 50
    }

    if (!$params{'scoreformat'}) {
        $params{'scoreformat'} = 'default'
    }

    if (!$params{'stats'}) {
        $params{'stats'} = '1'
    }

    if (!$params{'annotfeats'}) {
        $params{'annotfeats'} = 'false'
    }

    if (!$params{'filter'}) {
        $params{'filter'} = 'none'
    }

    if (!$params{'transltable'}) {
        $params{'transltable'} = 1
    }

    print_debug_message('load_params', 'End', 1);
}

=head2 client_poll()

Client-side job polling.

  &client_poll($job_id);

=cut

sub client_poll {
    print_debug_message('client_poll', 'Begin', 1);
    my $jobid = shift;
    my $status = 'PENDING';

    # Check status and wait if not finished. Terminate if three attempts get "ERROR".
    my $errorCount = 0;
    while ($status eq 'RUNNING'
        || $status eq 'PENDING'
        || ($status eq 'ERROR' && $errorCount < 2)) {
        $status = rest_get_status($jobid);
        print STDERR "$status\n" if ($outputLevel > 0);
        if ($status eq 'ERROR') {
            $errorCount++;
        }
        elsif ($errorCount > 0) {
            $errorCount--;
        }
        if ($status eq 'RUNNING'
            || $status eq 'PENDING'
            || $status eq 'ERROR') {

            # Wait before polling again.
            usleep($checkInterval);
        }
    }
    print_debug_message('client_poll', 'End', 1);
    return $status;
}

=head2 get_results()

Get the results for a job identifier.

  &get_results($job_id);

=cut

sub get_results {
    print_debug_message('get_results', 'Begin', 1);
    my $jobid = shift;
    print_debug_message('get_results', 'jobid: ' . $jobid, 1);
    my $seq_id = shift;
    print_debug_message('get_results', 'seq_id: ' . $seq_id, 1) if ($seq_id);

    my $output_basename = $jobid;

    # Verbose
    if ($outputLevel > 1) {
        print 'Getting results for job ', $jobid, "\n";
    }

    # Check status, and wait if not finished
    client_poll($jobid);

    # Default output file names use JobId, however the name can be specified...
    if (defined($params{'outfile'})) {
        $output_basename = $params{'outfile'};
    }
    # Or use sequence identifer.
    elsif (defined($params{'useSeqId'} && defined($seq_id) && $seq_id ne '')) {
        $output_basename = $seq_id;

        # Make safe to use as a file name.
        $output_basename =~ s/\W/_/g;
    }

    # Use JobId if output file name is not defined
    else {
        unless (defined($params{'outfile'})) {
            #$params{'outfile'} = $jobid;
            $output_basename = $jobid;
        }
    }

    # Get list of data types
    my (@resultTypes) = rest_get_result_types($jobid);


    # Get the data and write it to a file
    if (defined($params{'outformat'})) {
        # Specified data type
        # check to see if there are multiple formats (comma separated)
        my $sep = ",";
        my (@multResultTypes);
        if ($params{'outformat'} =~ /$sep/) {
            @multResultTypes = split(',', $params{'outformat'});
        }
        else {
            $multResultTypes[0] = $params{'outformat'};
        }
        # check if the provided formats are recognised
        foreach my $inputType (@multResultTypes) {
            my $expectation = 0;
            foreach my $resultType (@resultTypes) {
                if ($resultType->{'identifier'} eq $inputType && $expectation eq 0) {
                    $expectation = 1;
                }
            }
            if ($expectation ne 1) {
                die 'Error: unknown result format "' . $inputType . '"';
            }
        }
        # if so get the files
        my $selResultType;
        foreach my $resultType (@resultTypes) {
            if (grep {$_ eq $resultType->{'identifier'}} @multResultTypes) {
                $selResultType = $resultType;
                my $result = rest_get_result($jobid, $selResultType->{'identifier'});
                if (defined($params{'outfile'}) && $params{'outfile'} eq '-') {
                    write_file($params{'outfile'}, $result);
                }
                else {
                    write_file(
                        $output_basename . '.'
                            . $selResultType->{'identifier'} . '.'
                            . $selResultType->{'fileSuffix'},
                        $result
                    );
                }
            }
        }
    }
    else { # Data types available
        # Write a file for each output type
        for my $resultType (@resultTypes) {
            if ($outputLevel > 1) {
                print STDERR 'Getting ', $resultType->{'identifier'}, "\n";
            }
            my $result = rest_get_result($jobid, $resultType->{'identifier'});
            if (defined($params{'outfile'}) && $params{'outfile'} eq '-') {
                write_file($params{'outfile'}, $result);
            }
            else {
                write_file(
                    $output_basename . '.'
                        . $resultType->{'identifier'} . '.'
                        . $resultType->{'fileSuffix'},
                    $result
                );
            }
        }
    }
    print_debug_message('get_results', 'End', 1);
}

=head2 read_file()

Read a file into a scalar. The special filename '-' can be used to read from
standard input (STDIN).

  my $data = &read_file($filename);

=cut

sub read_file {
    print_debug_message('read_file', 'Begin', 1);
    my $filename = shift;
    print_debug_message('read_file', 'filename: ' . $filename, 2);
    my ($content, $buffer);
    if ($filename eq '-') {
        while (sysread(STDIN, $buffer, 1024)) {
            $content .= $buffer;
        }
    }
    else {
        # File
        open(my $FILE, '<', $filename)
            or die "Error: unable to open input file $filename ($!)";
        while (sysread($FILE, $buffer, 1024)) {
            $content .= $buffer;
        }
        close($FILE);
    }
    print_debug_message('read_file', 'End', 1);
    return $content;
}

=head2 write_file()

Write data to a file. The special filename '-' can be used to write to
standard output (STDOUT).

  &write_file($filename, $data);

=cut

sub write_file {
    print_debug_message('write_file', 'Begin', 1);
    my ($filename, $data) = @_;
    print_debug_message('write_file', 'filename: ' . $filename, 2);
    if ($outputLevel > 0) {
        print STDERR 'Creating result file: ' . $filename . "\n";
    }
    if ($filename eq '-') {
        print STDOUT $data;
    }
    else {
        open(my $FILE, '>', $filename)
            or die "Error: unable to open output file $filename ($!)";
        syswrite($FILE, $data);
        close($FILE);
    }
    print_debug_message('write_file', 'End', 1);
}

=head2 usage()

Print program usage message.

  &usage();

=cut

sub usage {
    print STDERR <<EOF
EMBL-EBI FASTA Perl Client:

Sequence similarity search with FASTA.

[Required (for job submission)]
  --email               E-mail address.
  --program             The FASTA program to be used for the Sequence Similarity
                        Search.
  --stype               Indicates if the query sequence is protein, DNA or RNA. Used
                        to force FASTA to interpret the input sequence as specified
                        type of sequence (via. the '-p', '-n' or '-U' options), this
                        prevents issues when using nucleotide sequences that contain
                        many ambiguous residues.
  --sequence            The query sequence can be entered directly into this form.
                        The sequence can be in GCG, FASTA, EMBL (Nucleotide only),
                        GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein
                        only) format. A partially formatted sequence is not
                        accepted. Adding a return to the end of the sequence may
                        help certain applications understand the input. Note that
                        directly using data from word processors may yield
                        unpredictable results as hidden/control characters may be
                        present.
  --database            The databases to run the sequence similarity search against.
                        Multiple databases can be used at the same time.

[Optional]
  --matrix              (Protein searches) The substitution matrix used for scoring
                        alignments when searching the database. Target identity is
                        the average alignment identity the matrix would produce in
                        the absence of homology and can be used to compare different
                        matrix types. Alignment boundaries are more accurate when
                        the alignment identity matches the target identity
                        percentage.
  --match_scores        (Nucleotide searches) The match score is the bonus to the
                        alignment score when matching the same base. The mismatch is
                        the penalty when failing to match.
  --gapopen             Score for the first residue in a gap.
  --gapext              Score for each additional residue in a gap.
  --hsps                Turn on/off the display of all significant alignments
                        between query and library sequence.
  --expupperlim         Limits the number of scores and alignments reported based on
                        the expectation value. This is the maximum number of times
                        the match is expected to occur by chance.
  --explowlim           Limit the number of scores and alignments reported based on
                        the expectation value. This is the minimum number of times
                        the match is expected to occur by chance. This allows
                        closely related matches to be excluded from the result in
                        favor of more distant relationships.
  --strand              For nucleotide sequences specify the sequence strand to be
                        used for the search. By default both upper (provided) and
                        lower (reverse complement of provided) strands are used, for
                        single stranded sequences searching with only the upper or
                        lower strand may provide better results.
  --hist                Turn on/off the histogram in the FASTA result. The histogram
                        gives a qualitative view of how well the statistical theory
                        fits the similarity scores calculated by the program.
  --scores              Maximum number of match score summaries reported in the
                        result output.
  --alignments          Maximum number of match alignments reported in the result
                        output.
  --scoreformat         Different score report formats.
  --stats               The statistical routines assume that the library contains a
                        large sample of unrelated sequences. Options to select what
                        method to use include regression, maximum likelihood
                        estimates, shuffles, or combinations of these.
  --annotfeats          Turn on/off annotation features. Annotation features shows
                        features from UniProtKB, such as variants, active sites,
                        phospho-sites and binding sites that have been found in the
                        aligned region of the database hit. To see the annotation
                        features in the results after this has been enabled, select
                        sequences of interest and click to 'Show' Alignments. This
                        option also enables a new result tab (Domain Diagrams) that
                        highlights domain regions.
  --annotsym            Specify the annotation symbols.
  --dbrange             Specify the sizes of the sequences in a database to search
                        against. For example: 100-250 will search all sequences in a
                        database with length between 100 and 250 residues,
                        inclusive.
  --seqrange            Specify a range or section of the input sequence to use in
                        the search. Example: Specifying '34-89' in an input sequence
                        of total length 100, will tell FASTA to only use residues 34
                        to 89, inclusive.
  --filter              Filter regions of low sequence complexity. This can avoid
                        issues with low complexity sequences where matches are found
                        due to composition rather then meaningful sequence
                        similarity. However in some cases filtering also masks
                        regions of interest and so should be used with caution.
  --transltable         Query Genetic code to use in translation.
  --ktup                FASTA uses a rapid word-based lookup strategy to speed the
                        initial phase of the similarity search. The KTUP is used to
                        control the sensitivity of the search. Lower values lead to
                        more sensitive, but slower searches.

[General]
  -h, --help            Show this help message and exit.
  --asyncjob            Forces to make an asynchronous query.
  --title               Title for job.
  --status              Get job status.
  --resultTypes         Get available result types for job.
  --polljob             Poll for the status of a job.
  --pollFreq            Poll frequency in seconds (default 3s).
  --jobid               JobId that was returned when an asynchronous job was submitted.
  --outfile             File name for results (default is JobId; for STDOUT).
  --multifasta          Treat input as a set of fasta formatted sequences.
  --useSeqId            Use sequence identifiers for output filenames.
                        Only available in multi-fasta and multi-identifier modes.
  --maxJobs             Maximum number of concurrent jobs. Only
                        available in multifasta or list file modes.
  --outformat           Result format(s) to retrieve. It accepts comma-separated values.
  --params              List input parameters.
  --paramDetail         Display details for input parameter.
  --quiet               Decrease output.
  --verbose             Increase output.
  --version             Prints out the version of the Client and exit.
  --baseUrl             Base URL. Defaults to:
                        https://www.ebi.ac.uk/Tools/services/rest/fasta

Synchronous job:
  The results/errors are returned as soon as the job is finished.
  Usage: perl $scriptName --email <your\@email.com> [options...] <SeqFile|SeqID(s)>
  Returns: results as an attachment

Asynchronous job:
  Use this if you want to retrieve the results at a later time. The results
  are stored for up to 24 hours.
  Usage: perl $scriptName --asyncjob --email <your\@email.com> [options...] <SeqFile|SeqID(s)>
  Returns: jobid

Check status of Asynchronous job:
  Usage: perl $scriptName --status --jobid <jobId>

Retrieve job data:
  Use the jobid to query for the status of the job. If the job is finished,
  it also returns the results/errors.
  Usage: perl $scriptName --polljob --jobid <jobId> [--outfile string]
  Returns: string indicating the status of the job and if applicable, results
  as an attachment.

Further information:
  https://www.ebi.ac.uk/Tools/webservices and
    https://github.com/ebi-wp/webservice-clients

Support/Feedback:
  https://www.ebi.ac.uk/support/
EOF
}

=head1 FEEDBACK/SUPPORT

Please contact us at L<https://www.ebi.ac.uk/support/> if you have any
feedback, suggestions or issues with the service or this client.

=cut