def __init__(self, monthCalendar):
"""
monthCalendar : MonthCal -- an instance of MonthCal (or any other object that returns a
one-month HTML calendar table when its render(year, month) method is called)
"""
self._template = Template(self._renderTemplate, self._html)
self._monthCalendar = monthCalendar
def index():
try:
templates_path = str(
os.path.join(os.path.dirname(__file__), 'templates'))
file = open(templates_path + '/index.html')
db = MySQLdb.connect(host='localhost',
user='******',
passwd='asdqwe34',
db='of_site09')
template = Template(renderIndex, str(file.read()))
groups = docs_group.list_all(db, "core", 0)
html = str(template.render(groups))
except Exception as inst:
exc_type, exc_value, exc_traceback = sys.exc_info()
error = str(inst) # __str__ allows args to printed directly
error += "<br/>"
error += str(
traceback.format_exception(exc_type, exc_value, exc_traceback))
error.replace('\n', "<br/>")
return "Unexpected error:<br/>", error
return [html]
def class_detail():
try:
templates_path = str(
os.path.join(os.path.dirname(__file__), 'templates'))
file = open(templates_path + '/class.html')
db = MySQLdb.connect(host='localhost',
user='******',
passwd='asdqwe34',
db='of_site09')
template = Template(renderClassDetail, str(file.read()))
clazz = getClass(db, 1)
html = str(template.render(clazz))
except Exception as inst:
exc_type, exc_value, exc_traceback = sys.exc_info()
error = str(inst) # __str__ allows args to printed directly
error += "<br/>"
error += str(
traceback.format_exception(exc_type, exc_value, exc_traceback))
error.replace('\n', "<br/>")
return "Unexpected error:<br/>", error
return [html]
def main():
usage = "usage: %prog -f FASTA -p OUT_PAGE -o OUT_DIR -w PROG_WORK_DIR -d"
parser = OptionParser(usage=usage)
parser.add_option("-f", "--fasta", dest="fasta_file", help="File with FASTA sequences.")
parser.add_option("-p", "--out_page", dest="out_page", help="HTML output page with links to FASTA sequences.")
parser.add_option("-o", "--out", dest="out_dir", help="Output directory containing the FASTA sequences.")
(options, args) = parser.parse_args()
if not options.fasta_file:
print "Please specify the file with FASTA sequences (-f FASTA)"
return -1
if not options.out_page:
print "Please specify HTML output page (-p OUT_PAGE)"
return -2
if not options.out_dir:
print "Please specify the output directory (-o OUT_DIR)"
return -3
if (len(args) > 0):
print "Too many input arguments"
return -4
fasta_file = os.path.abspath(options.fasta_file)
out_page = os.path.abspath(options.out_page)
out_dir = os.path.abspath(options.out_dir)
if not os.path.isdir(out_dir):
os.system("mkdir " + out_dir)
else:
os.system("rm -rf " + out_dir)
os.system("mkdir " + out_dir)
split_fasta(fasta_file, out_dir)
os.chdir(out_dir)
files = os.listdir('.')
html_fastas = []
for file in files:
print file
html_fasta = HTMLFasta(file,file)
html_fastas.append(html_fasta)
# Generate output page
html_page_with_fastas = HTMLPageWithFastas("HTML FASTA report", html_fastas)
html_page_with_fastas_template_str = get_html_with_fastas_template()
html_page_with_fastas_template = Template(render_html_with_fastas_template, html_page_with_fastas_template_str)
html_page_with_fastas_html = html_page_with_fastas_template.render(html_page_with_fastas)
fd_out = open(out_page,"w")
fd_out.write(html_page_with_fastas_html)
fd_out.close()
# Done
print "Done."
return 0
def __init__(self, isSundayFirst=True):
"""
isSundayFirst : boolean -- if True, week begins on Sunday (the default); otherwise Monday
"""
self._template = Template(self._renderTemplate, self._html)
self._isSundayFirst = isSundayFirst
if isSundayFirst:
self._firstWeekday = 6
columnLabels = self._weekdaysFromSun
else:
self._firstWeekday = 0
columnLabels = self._weekdaysFromMon
self._template.labels.repeat(
self._renderLabels,
columnLabels) # pre-render column labels for efficiency
def renderdictionary(terms, style='py-appscript', options=[], template=None):
"""Render a Dictionary object's classes and commands as an XHTML string.
terms : osaterminology.dom.osadictionary.Dictionary -- pre-parsed dictionary object
style : str -- keyword formatting style ('appscript' or 'applescript')
options : list of str -- formatting options (zero or more of: 'collapse', 'showall')
template : str -- custom HTML template to use
Result : str -- HTML data, or empty string if no terminology was found
"""
if 'showall' in options:
oldvis = terms.setvisibility(osadictionary.kAll)
if terms.suites():
if template:
tpl = Template(renderTemplate, template)
else:
tpl = _template
html = encodeNonASCII(
tpl.render(terms, gettyperenderer(style), options))
else:
html = ''
if 'showall' in options:
terms.setvisibility(oldvis)
return html
def doc(path, file, style='appscript', options=[], template=None):
"""Render an XHTML file listing a scriptable application's classes and commands.
path : str -- name or path to application
file : str -- HTML file's destination.
style : str -- keyword formatting style ('appscript' or 'applescript')
options : list of str -- formatting options ([] or ['collapse'])
template : str -- custom HTML template to use
"""
if path.endswith('.sdef'):
terms = sdefparser.parsefile(path, style)
elif path.endswith('.aete'):
terms = aeteparser.parsefile(path, style)
else:
terms = aeteparser.parseapp(findapp.byname(path), style)
if terms.suites():
if template:
tpl = Template(renderTemplate, template)
else:
tpl = _template
result = encodeNonASCII(
tpl.render(terms, typerenderers[style](), options))
f = open(expanduser(file), 'w')
f.write(str(result))
f.close()
f.write(txt.encode('utf8'))
f.close()
######################################################################
# PRIVATE - Template Controllers
######################################################################
# Frame
def render_frame(node, terms, info):
node.title.content = '%s terminology for %s' % (stripappsuffix(
terms.name), terms.style)
frametpl = Template(render_frame, framehtml)
######################################################################
# Index
def render_index(node, terms, info):
now = datetime.now()
generated = now.strftime("%a %b %d %Y %H:%M:%S")
node.title.content = node.title2.content = stripappsuffix(terms.name)
node.location.content = "Generated on %s for %s" % (generated, terms.path)
generatorname = info.get('generator-name', "")
generatorversion = info.get('generator-version', "")
if (generatorname != ""):
node.build.content = "by %s %s" % (generatorname, generatorversion)
else:
node.row.repeat(render_row, people, [False])
def render_row(node, person, isEvenRow):
if isEvenRow[0]:
node.atts['bgcolor'] = '#CCF'
isEvenRow[0] = not isEvenRow[0]
node.name.content = person[0]
node.phone.repeat(render_phone, person[1])
def render_phone(node, tel):
node.content = node.content % tel
template = Template(render_template, html)
#######
def write(path, txt):
f = open(path, 'w')
f.write(txt)
f.close()
def listPeopleWithPhones():
p = app('Address Book').people[its.phones != []]
people = zip(p.last_name.get(), p.first_name.get(), p.phones.label.get(),
p.phones.value.get())
result = []
def renderSideCommand(node, (name, suiteName)):
node.link.atts['href'] = '#command_' + stripNonChars(name + '__' +
suiteName)
node.link.content = name
def renderSideClass(node, (name, suiteName)):
node.link.atts['href'] = '#class_' + stripNonChars(name + '__' + suiteName)
node.link.content = name
######################################################################
# PRIVATE - Compiled Template
######################################################################
_template = Template(renderTemplate, _html)
######################################################################
# PUBLIC
######################################################################
def renderdictionary(terms, style='py-appscript', options=[], template=None):
"""Render a Dictionary object's classes and commands as an XHTML string.
terms : osaterminology.dom.osadictionary.Dictionary -- pre-parsed dictionary object
style : str -- keyword formatting style ('appscript' or 'applescript')
options : list of str -- formatting options (zero or more of: 'collapse', 'showall')
template : str -- custom HTML template to use
Result : str -- HTML data, or empty string if no terminology was found
"""
if 'showall' in options:
def main():
usage = "usage: %prog -z ZIP_ARCHIVE -p OUT_PAGE -o OUT_DIR -w PROG_WORK_DIR -d"
parser = OptionParser(usage=usage)
parser.add_option("-z",
"--zip_archive",
dest="zip_archive",
help="Zip archive consisting of images.")
parser.add_option("-p",
"--out_page",
dest="out_page",
help="HTML output page with images.")
parser.add_option("-o",
"--out",
dest="out_dir",
help="Output directory with images.")
parser.add_option(
"-w",
"--prog_work",
dest="prog_work_dir",
help="Program working directory, contains all processed files.")
parser.add_option(
"-d",
"--delete_program_work",
action="store_true",
dest="delete_program_work",
default=False,
help="Delete program working directory after program has completed.")
(options, args) = parser.parse_args()
if not options.zip_archive:
print "Please specify the zip archive consisting of images (-z ZIP_ARCHIVE)"
return -1
if not options.out_page:
print "Please specify HTML output page (-p OUT_PAGE)"
return -2
if not options.out_dir:
print "Please specify the output directory (-o OUT_DIR)"
return -4
if not options.prog_work_dir:
print "Please specify the program working directory (-w PROG_WORK_DIR)"
return -4
if (len(args) > 0):
print "Too many input arguments"
return -5
zip_archive = os.path.abspath(options.zip_archive)
out_page = os.path.abspath(options.out_page)
out_dir = os.path.abspath(options.out_dir)
prog_work_dir = os.path.abspath(options.prog_work_dir)
timestamp = commands.getoutput("date +%Y-%m-%d_%H_%M_%S_%N")
base_dir = prog_work_dir + "/generate_html_with_images_report_" + timestamp
if not os.path.isdir(prog_work_dir):
os.system("mkdir " + prog_work_dir)
if os.path.isdir(prog_work_dir):
if os.path.isdir(base_dir):
os.system("rm -rf " + base_dir)
os.system("mkdir " + base_dir)
else:
os.system("mkdir " + base_dir)
else:
print "Program working directory does not exist."
return -5
if not os.path.isdir(out_dir):
os.system("mkdir " + out_dir)
else:
os.system("rm -rf " + out_dir)
os.system("mkdir " + out_dir)
os.chdir(base_dir)
os.system("unzip " + zip_archive)
# Simple test to check if the files are images. Add only the images to the HTML page to be rendered.
files = os.listdir('.')
html_images = []
for file in files:
if (imghdr.what(file)):
print file
html_image = HTMLImage(file, file)
html_images.append(html_image)
os.system("cp " + file + " " + out_dir)
else:
print file + " is not an image file!"
# Generate output page
html_page_with_images = HTMLPageWithImages("HTML with images report",
html_images)
html_page_with_images_template_str = get_html_with_images_template()
html_page_with_images_template = Template(
render_html_with_images_template, html_page_with_images_template_str)
html_page_with_images_html = html_page_with_images_template.render(
html_page_with_images)
fd_out = open(out_page, "w")
fd_out.write(html_page_with_images_html)
fd_out.close()
# Delete program working directory if indicated
if (options.delete_program_work):
print "Delete working directory"
os.system("rm -rf " + base_dir)
# Done
print "Done."
return 0
def main():
usage = "usage: %prog -j JOB_ID -p JOB_HTML_PAGE -o OUT_DIR -w PROG_WORK_DIR -d"
parser = OptionParser(usage=usage)
parser.add_option("-j", "--job_id", dest="job_id", help="JobId of the InterProScan run.")
parser.add_option("-p", "--job_html_page", dest="job_html_page", help="InterProScan job html output page.")
parser.add_option("-o", "--out", dest="out_dir", help="Output directory with single html IterProScan result.")
parser.add_option("-w", "--prog_work", dest="prog_work_dir", help="Program working directory, contains all processed files.")
parser.add_option("-d", "--delete_program_work", action="store_true", dest="delete_program_work", default=False, help="Delete program working directory after program has completed.")
(options, args) = parser.parse_args()
if not options.job_id:
print "Please specify the InterProScan JobId (-j JOB_ID)"
return -1
if not options.job_html_page:
print "Please specify InterProScan job html output page (-p JOB_HTML_PAGE)"
return -2
if not options.out_dir:
print "Please specify the output directory (-o OUT_DIR)"
return -4
if not options.prog_work_dir:
print "Please specify the program working directory (-w PROG_WORK_DIR)"
return -4
if (len(args) > 0):
print "Too many input arguments"
return -5
iprscan_output_dir = os.environ.get("IPRSCAN_OUTPUT_DIR")
iprscan_images_dir = os.environ.get("IPRSCAN_IMAGES_DIR")
out_dir = os.path.abspath(options.out_dir)
job_html_page = os.path.abspath(options.job_html_page)
date = options.job_id.split("-")[1]
iprscan_output_dir = iprscan_output_dir + "/" + date + "/" + options.job_id
nr_chunks = len(glob.glob(iprscan_output_dir + "/chunk*"))
prog_work_dir = os.path.abspath(options.prog_work_dir)
timestamp = commands.getoutput("date +%Y-%m-%d_%H_%M_%S_%N")
base_dir = prog_work_dir + "/generate_interproscan_html_report_" + timestamp
if not os.path.isdir(prog_work_dir):
os.system("mkdir " + prog_work_dir)
if os.path.isdir(prog_work_dir):
if os.path.isdir(base_dir):
os.system("rm -rf " + base_dir)
os.system("mkdir " + base_dir)
else:
os.system("mkdir " + base_dir);
else:
print "Program working directory does not exist."
return -5
if not os.path.isdir(out_dir):
os.system("mkdir " + out_dir)
else:
os.system("rm -rf " + out_dir)
os.system("mkdir " + out_dir)
iprscan_raw_html_file = os.path.abspath(base_dir + "/iprscan_raw.html")
for i in range(1,int(nr_chunks) + 1):
# create picture output
os.system("iprscan tool=iprscan jobid=" + options.job_id + " cnk=" + str(i) + " view=picture >> " + iprscan_raw_html_file)
# create table output
os.system("iprscan tool=iprscan jobid=" + options.job_id + " cnk=" + str(i) + " view=Table >> " + iprscan_raw_html_file)
fd_in = open(iprscan_raw_html_file, "r")
ips_report_start = False
ips_report = ""
ips_report_start_string = "<table width=\"100%\" cellSpacing=\"0\" cellPadding=\"3\" border=\"1\" bordercolor=\"#999999\" bgcolor=\"#eeeeee\" class=\"tabletop\">"
ips_report_end_string = "</tr>\n</table>\n</td></tr>\n</table>\n<br>"
ips_report_header = "<html><head><title>InterProScan Results - [email protected]</title></head><link rel=\"SHORTCUT ICON\" href=\"https://foobar.com/images/bookmark.gif\">\n<br>\n<span class=\"text\">"
ips_report_footer = "</span>"
ips_reports = {}
ips_report_id = "";
for line in fd_in:
if (line.find(ips_report_start_string) > -1):
if(ips_report_start): # Do not save results for first round. ips_report_start = False initially
if (ips_report_id in ips_reports):
report = ips_reports[ips_report_id]
report = report + ips_report
ips_reports[ips_report_id] = report
else:
ips_reports[ips_report_id] = ips_report
ips_report_start = True
ips_report = ""
if(ips_report_start):
ips_report = ips_report + line
if (line.find("SEQUENCE") > -1):
ips_report_id = get_ips_id(line)
# Get last report
if (ips_report_id in ips_reports):
report = ips_reports[ips_report_id]
report = report + ips_report
ips_reports[ips_report_id] = report
else:
ips_reports[ips_report_id] = ips_report
# Add html header and footer
for ips_report_id in ips_reports:
report = ips_reports[ips_report_id]
report = ips_report_header + report + ips_report_footer
ips_reports[ips_report_id] = report
# Clean html
for ips_report_id in ips_reports:
report = ips_reports[ips_report_id]
report = clean_html(report, ips_report_id)
ips_reports[ips_report_id] = report
interproscan_reports = []
report_ids = ips_reports.keys()
sorted_report_ids = sorted(report_ids)
# Print all reports
for ips_report_id in sorted_report_ids:
fd_out = open(out_dir + "/" + ips_report_id + "_interproscan.html", "w")
fd_out.write(ips_reports[ips_report_id])
fd_out.close()
interproscan_report = InterProScanReport(ips_report_id, ips_report_id + "_interproscan.html")
interproscan_reports.append(interproscan_report)
fd_in.close()
# Cannot access html pages or links in galaxy output data subfolders. Need to put all file and images in root directory. Messy! find better way.
# Need to do for now!
# os.system("mkdir " + out_dir + "/images")
# os.system("cp " + iprscan_images_dir + "/*.gif " + out_dir + "/images")
os.system("cp " + iprscan_images_dir + "/*.gif " + out_dir )
# Generate InterProScan job index page
interproscan_job = InterProScanJob(options.job_id, interproscan_reports)
intproscan_job_html_template_str = get_intproscan_job_html_template()
intproscan_job_html_template = Template(render_interproscan_job_template, intproscan_job_html_template_str)
intproscan_job_html = intproscan_job_html_template.render(interproscan_job)
fd_out = open(job_html_page,"w")
fd_out.write(intproscan_job_html)
fd_out.close()
# Delete program working directory if indicated
if(options.delete_program_work):
print "Delete working directory"
os.system("rm -rf " + base_dir)
return 0
