def __init__(self, opts=None):
"""
@type self: koala.ProtPredEDA.ProtPredEDA
@type opts: ArgsParse parameters
"""
assert opts is not None
self.opts = opts
self.time_execution = TimeJobExecution()
self.path_runs = PathRuns()
self.framework = Params('ProtPred-EDA', 'rboa')
def __init__(self, opts=None):
"""
@type self: koala.Mono2PG.Mono2PG
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.time_execution = TimeJobExecution()
self.path_runs = PathRuns()
self.framework = Params('2PG')
class Random2PG(object):
"""
Execute the 2PG Random evolutionary algorithm.
"""
progname = "2PG Random"
opts = None
sequence = None
initTime = 0
endTime = 0
ignoreoutfiles = ['.pdb']
os.environ["GMX_MAXBACKUP"] = "-1"
def __init__(self, opts=None):
"""
@type self: koala.Random2PG.Random2PG
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.time_execution = TimeJobExecution()
self.path_runs = PathRuns()
self.framework = Params('2PG')
def makeHtml(self):
""" Create an HTML file content to list all the artifacts found in the html_dir
@type self: koala.Random2PG.Random2PG
"""
try:
galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output" />
<title></title>
<link rel="stylesheet" href="/static/koala.css" type="text/css" />
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
<script type="text/javascript"
src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
<script src="http://code.highcharts.com/highcharts.js"></script>
<script src="http://code.highcharts.com/highcharts-more.js"></script>
<script src="http://code.highcharts.com/modules/exporting.js"></script>
</head>
<body>
<div class="toolFormBody">"""
galhtmlpostfix = """</div></body></html>\n"""
flist = os.listdir(self.opts.htmlfiledir)
flist.sort()
html = []
html.append(galhtmlprefix % self.progname)
html.append('<div class="sucessmessage">')
html.append('<br>')
html.append('<h1 align="center">2PG Random Ab Initio Algorithm results</h1><br></div>')
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Submitted Primary Sequence.<br><br></div>')
html.append('<div class="code">')
html.append('Length: %s<br>' % len(self.sequence))
html.append('%s<br></div>' % self.sequence)
fhtml = []
fitFiles = []
outputfiles = []
compressedFile = []
imageFiles = []
if len(flist) > 0:
for rownum, fname in enumerate(flist):
dname, e = os.path.splitext(fname)
sfsize = get_file_size(fname, self.opts.htmlfiledir)
if e.lower() == ".fit":
fitFiles.append(fname)
elif e.lower() == ".png":
imageFiles.append(fname)
elif e.lower() in ".zip, .gz":
compressedFile.append(fname)
elif not e.lower() in self.ignoreoutfiles:
outputfiles.append(fname)
# Arquivos fit
for fit in fitFiles:
sfsize = get_file_size(fit, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (fit, fit))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Download Calculated values of selected Objectives.<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
fhtml = []
# images (e depois models)
listaArquivosPdb = list_directory(
self.path_runs.get_path_execution(),
'randomSolution-M*.pdb')
if len(listaArquivosPdb) <= 20:
size = int(len(listaArquivosPdb) / 5)
rest = len(listaArquivosPdb) % 5
else:
size = 4 # vai mostrar no máximo 20 imagens
rest = 0
idx = 0 # controla indice das imagens e dos metodos
start = 0
end = 5 # limite de colunas para uma linha
if size < 1:
n = len(listaArquivosPdb)
fhtml.append('<tr>')
idx_linha = idx
for i in range(0, n):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="%s.png"><img src="%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (pdbName, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
fhtml.append(
'<td><a href="%s">%s</a></td>' % (
listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, n):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr>')
else:
for img in range(0, size):
fhtml.append('<tr>')
idx_linha = idx
for i in range(start, end):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="%s.png"><img src="%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (pdbName, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
fhtml.append(
'<td><a href="%s">%s</a></td>' % (
listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(start, end):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
fhtml.append('</tr>')
fhtml.append('<tr>')
idx_linha = idx
for i in range(0, rest):
pdbName, ext = os.path.splitext(listaArquivosPdb[idx])
fhtml.append(
'<td><a href="%s.png"><img src="%s.png" '
'title="Click to see %s.png bigger" width="130"/></a></td>'
% (pdbName, pdbName, pdbName))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
fhtml.append(
'<td><a href="%s">%s</a></td>' % (
listaArquivosPdb[idx], listaArquivosPdb[idx]))
idx += 1
idx = idx_linha
fhtml.append('</tr><tr>')
for i in range(0, rest):
sfsize = get_file_size(
listaArquivosPdb[idx],
self.opts.htmlfiledir)
fhtml.append('<td>%s</td>' % (sfsize))
idx += 1
idx = idx_linha
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Best Tertiary Structures<br>')
html.append('<br></div>')
if(self.opts.useJmol == 'true'):
html.append('<div class="active-jmol">')
html.append('<br>')
html.append(
'<a href=/datasets/%s/display/%s.htm>Activate JMol</a>' % (
self.opts.datasetID, self.opts.datasetID))
html.append('<br></div>')
model = ''
if size < 1:
for i in range(0, len(listaArquivosPdb)):
model += '<th>Model</th>'
else:
model = '<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'\
'<th>Model</th>'
fhtml.insert(
0,
'<div class="filetables"><table border="1">'
'<tr>' +
model +
'</tr>\n')
fhtml.append('</table></div><br/>')
html += fhtml
fhtml = []
# Outros arquivos de output
for output in outputfiles:
sfsize = get_file_size(output, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (output, output))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Download the output files:<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>Output File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
fhtml = []
# arquivo zipado
for output in compressedFile:
sfsize = get_file_size(output, self.opts.htmlfiledir)
fhtml.append('<tr>')
fhtml.append('<td><a href="%s">%s</a></td>' % (output, output))
fhtml.append('<td>%s</td>' % (sfsize))
fhtml.append('</tr>')
if len(fhtml) > 0:
html.append('<br>')
html.append('<div class="sectionmessage">')
html.append('<br>Compressed file with all the output files<br><br></div>')
fhtml.insert(
0,
'<div class="filetables"><table border="1"><tr><th>File</th>'
'<th>Size</th></tr>\n')
fhtml.append('</table></div><br>')
html += fhtml
self.time_execution.set_job_end(datetime.datetime.now())
self.endTime = datetime.datetime.now()
dif = self.time_execution.calculate_time_execution()
html.append('<div>Time execution:<br>')
html.append('Start: %s<br>' %
self.time_execution.get_job_start().strftime("%d/%m/%Y %H:%M:%S"))
html.append('End: %s<br>' %
self.time_execution.get_job_end().strftime("%d/%m/%Y %H:%M:%S"))
html.append('Total time: ~%dh:%dm:%ds' % (dif[0], dif[1], dif[2]))
html.append('</div>')
html.append('<hr>')
html.append('<div>Citation<br>')
html.append('Please, cite the used algorithm in this tool:<br><br>')
html.append('')
html.append('<br></div>')
html.append(galhtmlpostfix)
htmlf = file(self.opts.filehtml, 'w')
htmlf.write('\n'.join(html))
htmlf.write('\n')
htmlf.close()
except Exception, e:
show_error_message("Error on makeHtml:\n%s" % str(e))