--- /dev/null
+#!/usr/bin/env python
+
+from BeautifulSoup import BeautifulSoup
+from datetime import datetime
+import httplib2
+from operator import attrgetter
+from optparse import OptionParser
+# python keyring
+import keyring
+import logging
+import os
+import re
+# redland rdf lib
+import RDF
+import sys
+import urllib
+
+libraryNS = RDF.NS("http://jumpgate.caltech.edu/library/")
+submissionNS = RDF.NS("http://encodesubmit.ucsc.edu/pipeline/show/")
+submitNS = RDF.NS("http://jumpgate.caltech.edu/wiki/EncodeSubmit#")
+dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
+rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
+rdfsNS= RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
+
+LOGIN_URL = 'http://encodesubmit.ucsc.edu/account/login'
+USER_URL = 'http://encodesubmit.ucsc.edu/pipeline/show_user'
+DETAIL_URL = 'http://encodesubmit.ucsc.edu/pipeline/show/{0}'
+LIBRARY_URL = 'http://jumpgate.caltech.edu/library/{0}'
+USERNAME = 'detrout'
+
+def main(cmdline=None):
+ parser = make_parser()
+ opts, args = parser.parse_args(cmdline)
+
+ cookie = login()
+ if cookie is None:
+ print "Failed to login"
+
+ submissions = my_submissions(cookie)
+ for s in submissions:
+ for t in s.triples():
+ print t
+
+def make_parser():
+ parser = OptionParser()
+ return parser
+
+
+def login():
+ keys = keyring.get_keyring()
+ password = keys.get_password(LOGIN_URL, USERNAME)
+ credentials = {'login': USERNAME,
+ 'password': password}
+ headers = {'Content-type': 'application/x-www-form-urlencoded'}
+ http = httplib2.Http()
+ response, content = http.request(LOGIN_URL,
+ 'POST',
+ headers=headers,
+ body=urllib.urlencode(credentials))
+ logging.debug("Login to {0}, status {1}".format(LOGIN_URL,
+ response['status']))
+
+ cookie = response.get('set-cookie', None)
+ return cookie
+
+def my_submissions(cookie):
+ soup = get_url_as_soup(USER_URL, 'GET', cookie)
+ p = soup.find('table', attrs={'id':'projects'})
+ tr = p.findNext('tr')
+ # first record is header
+ tr = tr.findNext()
+ submissions = []
+ while tr is not None:
+ td = tr.findAll('td')
+ if td is not None and len(td) > 1:
+ subid = td[0].contents[0].contents[0]
+ species = get_contents(td[2])
+ name = get_contents(td[4])
+ status = get_contents(td[6]).strip()
+ date = get_date_contents(td[8])
+ age = get_contents(td[10])
+ submissions.append(
+ Submission(subid, species, name, status, date, age, cookie)
+ )
+ tr = tr.findNext('tr')
+ return submissions
+
+def get_contents(element):
+ """Return contents or none.
+ """
+ if len(element.contents) == 0:
+ return None
+
+ a = element.find('a')
+ if a is not None:
+ return a.contents[0]
+
+ return element.contents[0]
+
+def get_date_contents(element):
+ data = get_contents(element)
+ if data:
+ return datetime.strptime(data, "%Y-%m-%d %H:%M")
+ else:
+ return None
+
+SUBMISSIONS_LACKING_LIBID = [
+ ('1x75-Directional-HeLa-Rep1', '11208'),
+ ('1x75-Directional-HeLa-Rep2', '11207'),
+ ('1x75-Directional-HepG2-Rep1', '11210'),
+ ('1x75-Directional-HepG2-Rep2', '11209'),
+ ('1x75-Directional-H1-hESC-Rep1', '10947'),
+ ('1x75-Directional-H1-hESC-Rep2', '11009'),
+ ('1x75-Directional-HUVEC-Rep1', '11206'),
+ ('1x75-Directional-HUVEC-Rep2', '11205'),
+ ('1x75-Directional-K562-Rep1', '11008'),
+ ('1x75-Directional-K562-Rep2', '11007'),
+ ('1x75-Directional-NHEK-Rep1', '11204'),
+ ]
+
+class Submission(object):
+ def __init__(self, subid, species, name, status, date, age, cookie=None):
+ self.cookie = cookie
+ self.subid = subid
+ self.species = species
+ self.name = name
+ self.status = status
+ self.date = date
+ self.age = age
+ self._library_id = None
+ self._created_date = None
+
+ def triples(self):
+ subNode = submissionNS[self.subid.encode('utf-8')]
+ dateNode = self.date.strftime("%Y-%m-%d")
+ s = [RDF.Statement(subNode, submitNS['name'],
+ self.name.encode('utf-8')),
+ RDF.Statement(subNode, submitNS['status'],
+ self.status.encode('utf-8')),
+ RDF.Statement(subNode, submitNS['last_modify_date'], dateNode),
+ ]
+ if self.species is not None:
+ s.append(RDF.Statement(subNode, submitNS['species'],
+ self.species.encode('utf-8')))
+ if self.library_id is not None:
+ libId = libraryNS[self.library_id.encode('utf-8')]
+ s.append(RDF.Statement(subNode, rdfsNS['seeAlso'], libId))
+
+ return s
+
+
+ def _get_library_id(self):
+ if self._library_id is None:
+ match = re.search(r"[ -](?P<id>([\d]{5})|(SL[\d]{4}))", self.name)
+ if match is not None:
+ self._library_id = match.group('id')
+ else:
+ for dir_lib_name, lib_id in SUBMISSIONS_LACKING_LIBID:
+ if dir_lib_name in self.name:
+ self._library_id = lib_id
+ break
+
+ return self._library_id
+
+ library_id = property(_get_library_id)
+
+ def _get_detail(self):
+ detail = DETAIL_URL.format(self.subid)
+ soup = get_url_as_soup(detail, 'GET', self.cookie)
+
+ created_label = soup.find(text="Created: ")
+ if created_label:
+ self._created_date = get_date_contents(created_label.next)
+
+ def _get_created_date(self):
+ if self._created_date is None:
+ self._get_detail()
+ return self._created_date
+ created_date = property(_get_created_date)
+
+ def __unicode__(self):
+ return u"{0}\t{1}\t{2}".format(self.subid, self.library_id, self.name)
+
+ def __repr__(self):
+ return u"<Submission ({0}) '{1}'>".format(self.subid, self.name)
+
+
+def select_by_library_id(submission_list):
+ subl = [ (x.library_id, x) for x in submission_list if x.library_id ]
+ libraries = {}
+ for lib_id, subobj in subl:
+ libraries.setdefault(lib_id, []).append(subobj)
+
+ for submission in libraries.values():
+ submission.sort(key=attrgetter('date'), reverse=True)
+
+ return libraries
+
+def library_to_freeze(selected_libraries):
+ freezes = ['2010-Jan', '2010-Jul', '2011-Jan']
+ lib_ids = sorted(selected_libraries.keys())
+ report = ['<html><table border="1">']
+ report = ["""<html>
+<head>
+<style type="text/css">
+ td {border-width:0 0 1px 1px; border-style:solid;}
+</style>
+</head>
+<body>
+<table>
+"""]
+ report.append('<thead>')
+ report.append('<tr><td>Library ID</td><td>Name</td>')
+ for f in freezes:
+ report.append('<td>{0}</td>'.format(f))
+ report.append('</tr>')
+ report.append('</thead>')
+ report.append('<tbody>')
+ for lib_id in lib_ids:
+ report.append('<tr>')
+ lib_url = LIBRARY_URL.format(lib_id)
+ report.append('<td><a href="{0}">{1}</a></td>'.format(lib_url, lib_id))
+ submissions = selected_libraries[lib_id]
+ report.append('<td>{0}</td>'.format(submissions[0].name))
+ batched = {}
+ for sub in submissions:
+ date = date_to_freeze(sub.date)
+ batched.setdefault(date, []).append(sub)
+ print lib_id, batched
+ for d in freezes:
+ report.append('<td>')
+ for s in batched.get(d, []):
+ subid = '<a href="http://encodesubmit.ucsc.edu/pipeline/show/{0}">{0}</a>'.format(s.subid)
+ report.append("{0}:{1}".format(subid, s.status))
+ report.append('</td>')
+ else:
+ report.append('<td></td>')
+ report.append("</tr>")
+ report.append('</tbody>')
+ report.append("</table></html>")
+ return "\n".join(report)
+
+
+def date_to_freeze(d):
+ freezes = [ (datetime(2010, 1, 30), '2010-Jan'),
+ (datetime(2010, 7, 30), '2010-Jul'),
+ (datetime(2011, 1, 30), '2011-Jan'),
+ ]
+ for end, name in freezes:
+ if d < end:
+ return name
+ else:
+ return None
+
+
+def get_url_as_soup(url, method, cookie=None):
+ http = httplib2.Http()
+ headers = {}
+ if cookie is not None:
+ headers['Cookie'] = cookie
+ response, content = http.request(url, method, headers=headers)
+ if response['status'] == '200':
+ soup = BeautifulSoup(content,
+ fromEncoding="utf-8", # should read from header
+ convertEntities=BeautifulSoup.HTML_ENTITIES
+ )
+ return soup
+ else:
+ msg = "error accessing {0}, status {1}"
+ msg = msg.format(url, response['status'])
+ e = httplib2.HttpLib2ErrorWithResponse(msg, response, content)
+
+if __name__ == "__main__":
+ main()
+
+import logging
import urlparse
from django.db import models
from django.contrib.auth.models import User, UserManager
from htsworkflow.frontend import settings
from htsworkflow.frontend.reports.libinfopar import *
+
# Create your models here.
+logger = logging.getLogger(__name__)
class Antibody(models.Model):
antigene = models.CharField(max_length=500, db_index=True)
('2A', 'Ligation, PCR, gel, PCR'),
('Done', 'Completed'),
)
+ PROTOCOL_END_POINTS_DICT = dict(PROTOCOL_END_POINTS)
+
stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
amplified_from_sample = models.ForeignKey('self', blank=True, null=True, related_name='amplified_into_sample')
return u'#%s: %s' % (self.id, self.library_name)
class Meta:
- verbose_name_plural = "libraries"
- #ordering = ["-creation_date"]
- ordering = ["-id"]
+ verbose_name_plural = "libraries"
+ #ordering = ["-creation_date"]
+ ordering = ["-id"]
def antibody_name(self):
str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.nickname+'</a>'
else:
return False
+ def stopping_point_name(self):
+ end_points = Library.PROTOCOL_END_POINTS_DICT
+ name = end_points.get(self.stopping_point, None)
+ if name is None:
+ name = "Lookup Error"
+ logger.error("protocol stopping point in database didn't match names in library model")
+ return name
+
+
def libtags(self):
affs = self.tags.all().order_by('tag_name')
ar = []
summary['lanes_run'] = lanes_run
summary['is_archived'] = lib.is_archived()
records.append(summary)
- cl.result_count = unicode(cl.paginator._count) + u" libraries"
+ cl.result_count = unicode(cl.paginator._count)
return {'library_list': records }
def library(request):
context.update(create_library_context(fcl))
t = get_template('samples/library_index.html')
c = RequestContext(request, context)
+ return HttpResponse( t.render(c) )
- app_context = {
- 'page_name': 'Library Index',
- 'body': t.render(c)
- }
- app_context.update(SAMPLES_CONTEXT_DEFAULTS)
-
- app_t = get_template('flowcell_libraries_app.html')
- app_c = RequestContext(request, app_context)
- return HttpResponse( app_t.render(app_c) )
def library_to_flowcells(request, lib_id):
"""
#UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
#UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
#UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
+# Where "results_dir" means directory with all the flowcells
if options.has_option('frontend', 'results_dir'):
RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
else:
--- /dev/null
+<!--overrride pagination-->
+{% load admin_list %}
+{% load i18n %}
+<p class="paginator">
+{% if pagination_required %}
+{% for i in page_range %}
+ {% paginator_number cl i %}
+{% endfor %}
+{% endif %}
+{{ cl.result_count }} {% ifequal cl.result_count 1 %}{{ cl.opts.verbose_name }}{% else %}{{ cl.opts.verbose_name_plural }}{% endifequal %}
+{% if show_all_url %}  <a href="{{ show_all_url }}" class="showall">{% trans 'Show all' %}</a>{% endif %}
+{% if cl.formset and cl.result_count %}<input type="submit" name="_save" class="default" value="{% trans 'Save' %}"/>{% endif %}
+</p>
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html lang="en">
-<head>
- <title>{% block title %}{{ app_name }} - {{ page_name }}{% endblock %}</title>
-
- <!-- ADMIN STYLE INTERFACE STUFF -->
- {% block additional_css %}
- {% endblock %}
-
- <!-- App Stuff -->
- <link type="text/css" rel="stylesheet" href="/static/css/app.css" />
- <script type="text/javascript" src="/static/js/jquery.min.js"></script>
-
- {% block additional_javascript %}
- {% endblock %}
-
- <script type="text/javascript" src="/static/js/htsw.js"></script>
-</head>
-<body class="{% block bodyclass %}{% endblock %}">
- <!-- Content -->
- <div id="content" class="{% block coltype %}colM{% endblock %}">
- {% block pretitle %}{% endblock %}
- {% block content_title %}{% if title %}<h1>{{ title }}</h1>{% endif %}{% endblock %}
- {% block content %}
- {% block object-tools %}{% endblock %}
- {{ body }}
- {% endblock %}
- {% block sidebar %}{% endblock %}
- <br class="clear" />
- </div>
- <!-- END Content -->
-
- {% block footer %}<div id="footer"></div>{% endblock %}
-</body>
-</html>
-{% load i18n %}
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html lang="en">
+{% load i18n %}<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML+RDFa 1.0//EN"
+ "http://www.w3.org/MarkUp/DTD/xhtml-rdfa-1.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+ version="XHTML+RDFa 1.0"
+ xmlns:xml="http://www.w3.org/1999/xhtml"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:xmls="http://www.w3.org/2001/XMLSchema#"
+ xmlns:libns="http://jumpgate.caltech.edu/wiki/LibraryOntology#"
+ xml:lang="en"
+>
+<!--base.html-->
<head>
<title>{% block title %}{{ app_name }} - {{ page_name }}{% endblock %}</title>
{% block branding %}{% endblock %}
</div>
{% if user.is_authenticated and user.is_staff %}
- <div id="user-tools">{% trans 'Welcome,' %} <strong>{% firstof user.first_name user.username %}</strong>. {% block userlinks %}{% url django-admindocs-docroot as docsroot %}{% if docsroot %}<a href="{{ docsroot }}">{% trans 'Documentation' %}</a> / {% endif %}<a href="{{ root_path }}password_change/">{% trans 'Change password' %}</a> / <a href="{{ root_path }}logout/">{% trans 'Log out' %}</a>{% endblock %}
+ <div id="user-tools">{% trans 'Welcome,' %} <strong>{% firstof user.first_name user.username %}</strong>. {% block userlinks %}{% url django-admindocs-docroot as docsroot %}{% if docsroot %}<a href="{{ docsroot }}">{% trans 'Documentation' %}</a> / {% endif %}<a href="/admin/password_change/">{% trans 'Change password' %}</a> / <a href="/admin/logout/">{% trans 'Log out' %}</a>{% endblock %}
</div>
{% endif %}
{% block nav-global %}{% endblock %}
</div>
-
- {% block breadcrumbs %}<div class="breadcrumbs"><a href="/">{% trans 'Home' %}</a>{% if title %} › {{ title }}{% endif %}</div>{% endblock %}
{% endif %}
{% if messages %}
<ul class="messagelist">{% for message in messages %}<li>{{ message }}</li>{% endfor %}</ul>
+++ /dev/null
-{% extends "app_base.html" %}
-
-{% block additional_css %}
- {% load adminmedia %}
- {% if LANGUAGE_BIDI %}<link rel="stylesheet" type="text/css" href="{% block stylesheet_rtl %}{% admin_media_prefix %}css/rtl.css{% endblock %}" />{% endif %}
- {% block extrastyle %}{% endblock %}
- {% block extrahead %}{% endblock %}
- {% block blockbots %}<meta name="robots" content="NONE,NOARCHIVE" />{% endblock %}
- <link rel="stylesheet" type="text/css" href="{{ MEDIA_URL }}css/data-browse-index.css" />
-{% endblock %}
-
-{% block dynamic_panels %}
- <ul id="Libraries" class="x-hidden">
- <li>
- <img src="/static/img/s.gif" class="icon-show-all" />
- <a href="{% url htsworkflow.frontend.samples.views.library %}">Index</a><br />
- </li>
- </ul>
- <ul id="Flowcells" class="x-hidden">
- <li>
- <img src="/static/img/s.gif" class="icon-show-all" />
- <a href="/runfolders/">Run Folders</a><br />
- </li>
- </ul>
-{% endblock %}
-
-{% block app_toolbar_west %}
- <div id="Library Index" href="{% url htsworkflow.frontend.samples.views.library %}"></div>
- <div id="Run Folders" href="/runfolders/"></div>
-{% endblock %}
-
-{% block app_toolbar_east %}
- <!--<div id="Admin" href="/admin/"></div>-->
-{% endblock %}
+++ /dev/null
-{% extends "app_base.html" %}
-
-{% block additional_css %}
-{% endblock %}
-
-{% block dynamic_panels %}
- <ul id="Libraries" class="x-hidden">
- <li>
- <img src="/static/img/s.gif" class="icon-show-all" />
- <a href="{% url htsworkflow.frontend.samples.views.library %}">Index</a><br />
- </li>
- </ul>
-{% endblock %}
-
-{% block app_toolbar_west %}
- <div id="Inventory Index" href="{% url htsworkflow.frontend.inventory.views.index %}"></div>
-{% endblock %}
-
-{% block app_toolbar_east %}
- <!--<div id="Admin" href="/admin/"></div>-->
-{% endblock %}
-{% extends "app_base.html" %}
+{% extends "base_site.html" %}
{% load i18n %}
{% block additional_css %}{% load adminmedia %}{{ block.super }}
<link rel="stylesheet" type="text/css" href="{% admin_media_prefix %}css/base.css" />
<link rel="stylesheet" type="text/css" href="{% admin_media_prefix %}css/login.css" />
{% endblock %}
+
{% block title %}Login{% endblock %}
{% block bodyclass %}login{% endblock %}
<p class="errornote">{{ error_message }}</p>
{% endif %}
<div id="container">
- <div id="header">
<h1>Login</h1>
- </div>
<form action="{{ app_path }}" method="post" id="login-form">
<div class="form-row">
<label for="id_username">{% trans 'Username:' %}</label> <input type="text" name="username" id="id_username" />
-{% extends "flowcell_libraries_app.html" %}
+{% extends "base_site.html" %}
{% block content %}
<table>
{% extends "base_site.html" %}
-{# extends "app_base.html" #}
{% load adminmedia admin_list i18n %}
{% block bodyclass %}change-list{% endblock %}
-{% extends "flowcell_libraries_app.html" %}
-{% load humanize %}
+{% extends "base_site.html" %}
+{% load adminmedia humanize i18n %}
+{% block extrahead %}
+ <!-- App Stuff -->
+ <link type="text/css" rel="stylesheet" href="/static/css/app.css" />
+ <script type="text/javascript" src="/static/js/jquery.min.js"></script>
+
+ {% block additional_javascript %}
+ {% endblock %}
-{% block additional_css %}
<style type="text/css">
/* <
projects / htsworkflow.git / commitdiff