DATABASES/madrigal Commit - r2:98d277d09dd7

Add modules for interactive plots and upload data

jespinoza -

r2:98d277d09dd7

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r2:98d277d09dd7

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source/madpy/djangoMad/apps/login/__init__.py created 755 0 0

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source/madpy/djangoMad/apps/login/migrations/__init__.py created 755 0 0

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source/madpy/djangoMad/apps/login/templates/login/login.html created 755 +17 0

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	1	{% extends "base.html" %}
	2
	3	{% block title %}Login{% endblock %}
	4
	5	{% block content %}
	6	<center>
	7	<h4>Please login</h4>
	8
	9	<div style="margin-top: 30px;">
	10	<form method="POST">
	11	{{ form.as_p }}
	12	{% csrf_token %}
	13	<button type="submit">Login</button>
	14	</form>
	15	</div>
	16	</center>
	17	{% endblock %}

source/madpy/djangoMad/apps/login/urls.py created 755 +9 0

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	1	from django.conf.urls import url
	2	from . import views
	3
	4	urlpatterns = [
	5	url(r'^login/$', views.login_view, name='login'),
	6	url(r'^logout/$', views.logout_view, name='logout'),
	7	]
	8
	9	app_name = 'login' No newline at end of file

source/madpy/djangoMad/apps/login/views.py created 755 +38 0

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	1	from django.contrib.auth import authenticate
	2	from django.contrib.auth import login, logout
	3	from django.contrib.auth.forms import AuthenticationForm
	4	from django.shortcuts import render, redirect
	5
	6	''' Login to updata app for ROJ staff'''
	7
	8	def login_view(request):
	9
	10	form = AuthenticationForm()
	11	if request.method == "POST":
	12	form = AuthenticationForm(data=request.POST)
	13
	14	if form.is_valid():
	15
	16	username = form.cleaned_data['username']
	17	password = form.cleaned_data['password']
	18
	19	user = authenticate(username=username, password=password)
	20
	21	if user is not None:
	22
	23	if user.is_active:
	24	login(request, user)
	25
	26	return redirect('/updata')
	27	else:
	28	return render(request, "login/login.html" )
	29	else:
	30	context = {'error_login': "error"}
	31	return render(request, "login/login.html", context )
	32
	33	return render(request, "login/login.html", {'form': form})
	34
	35	def logout_view(request):
	36
	37	logout(request)
	38	return redirect('/') No newline at end of file

source/madpy/djangoMad/apps/updata/__init__.py created 755 0 0

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source/madpy/djangoMad/apps/updata/forms.py created 755 +108 0

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	1	from django import forms
	2	import django.utils.html
	3	import django.utils.safestring
	4	import django.template.defaulttags
	5
	6	# third party imports
	7	import numpy
	8
	9	# Madrigal imports
	10	import madrigal.metadata
	11	import madrigal.ui.web
	12
	13	# madrigal imports
	14	import madrigal._derive
	15	import madrigal.metadata
	16	import madrigal.ui.web
	17	import madrigal.cedar
	18	import madrigal.isprint
	19	import madweb.forms
	20
	21	import datetime, time
	22
	23	def getSelection(keyword, args, kwargs):
	24	"""getSelection returns '0' if keyword not a key in either args[0] or kwargs,
	25	otherwise the value
	26
	27	args, kwargs - arguments as passed into SingleExpDefaultForm __init__
	28	"""
	29	if len(args) == 0 and len(list(kwargs.keys())) == 0:
	30	return('0') # default case when no data passed in
	31	elif len(args) > 0:
	32	# args[0] is data dict argument to bind data
	33	if keyword in args[0]:
	34	return(args[0][keyword])
	35	else:
	36	return('0')
	37	elif keyword in kwargs:
	38	return(kwargs[keyword])
	39	elif 'data' in kwargs:
	40	if keyword in kwargs['data']:
	41	return(kwargs['data'][keyword])
	42	else:
	43	return('0')
	44	else:
	45	return('0')
	46
	47	def getExperimentList(args, kwargs, madWeb, header='Select experiment: '):
	48
	49	instrumentsId= int(getSelection('instruments', args, kwargs))
	50
	51	kinstList = [int(instrumentsId)]
	52	startDate = datetime.datetime(1950,1,1)
	53	startDT = datetime.datetime(startDate.year, startDate.month, startDate.day, 0, 0, 0)
	54	now = datetime.datetime.now()
	55	endDate = datetime.datetime(now.year, 12, 31, 23, 59, 59)
	56	endDT = datetime.datetime(endDate.year, endDate.month, endDate.day, 23, 59, 59)
	57	experiments = madWeb.getExperimentList(kinstList,startDT, endDT, True)
	58	expListin = [('0', header),]
	59	for exp in experiments:
	60	expListin.append((exp[0], exp[2]))
	61
	62	# Using set
	63	seen = set()
	64
	65	# using list comprehension
	66	expList = [(a, b) for a, b in expListin
	67	if not (b in seen or seen.add(b))]
	68
	69	return(expList)
	70
	71	class UpdataForm(forms.Form):
	72	def __init__(self, args, *kwargs):
	73	super(UpdataForm, self).__init__(args, *kwargs)
	74	madDB = madrigal.metadata.MadrigalDB()
	75	madInstData = madrigal.metadata.MadrigalInstrumentData(madDB)
	76	instruments = madInstData.getInstruments(0, True)
	77	instList = [('0', "Select Instrument"), ]
	78	for kinst, instDesc, siteID in instruments:
	79	instList.append((str(kinst), instDesc))
	80
	81	instrumentSelection = getSelection('instruments', args, kwargs)
	82	self.fields['instruments'] = django.forms.ChoiceField(widget = django.forms.Select(attrs={"onChange":'populateExp(this)'}),
	83	choices=instList,
	84	initial=instrumentSelection,
	85	label='Instrument:')
	86
	87	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
	88	experimentSelection = getSelection('experiments', args, kwargs)
	89	self.fields['experiments'] = django.forms.ChoiceField(choices=getExperimentList(args, kwargs, madWebObj),
	90	initial=experimentSelection,
	91	required=False, label='Experiment:')
	92
	93	description = forms.CharField(widget=forms.Textarea(attrs={'cols': 40,'rows': 3, 'style': 'resize:none'}), label='Description')
	94	type = forms.ChoiceField(choices=[('0', 'Public'),('1', 'Private')], initial=0,widget=forms.RadioSelect(attrs={'class': 'custom-radio'}))
	95	file = forms.FileField(label='Select Files', widget=forms.ClearableFileInput(attrs={'multiple': True}))
	96
	97	class ExpForm(forms.Form):
	98	"""SingleExpInstForm is a Form class for the instrument select field in the Single Experiment interface.
	99	Use this because its faster to create than the full SingleExpDefaultForm
	100	"""
	101	def __init__(self, args, *kwargs):
	102	super(ExpForm, self).__init__(args, *kwargs)
	103	madDB = madrigal.metadata.MadrigalDB()
	104	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
	105	experimentSelection = getSelection('experiments', args, kwargs)
	106	self.fields['experiments'] = django.forms.ChoiceField(choices=getExperimentList(args, kwargs, madWebObj),
	107	initial=experimentSelection,
	108	required=False, label='Experiment')

source/madpy/djangoMad/apps/updata/migrations/__init__.py created 755 0 0

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source/madpy/djangoMad/apps/updata/templates/updata/experiments.html created 755 +9 0

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	1	<div class="row">
	2	{{ form.experiments.label }}
	3	</div>
	4	<!-- Instrument select is its own row in selections column -->
	5	<div class="row">
	6	<div class="col-md-12">
	7	{{ form.experiments }}
	8	</div> <!-- end span -->
	9	</div> <!-- end row --> No newline at end of file

source/madpy/djangoMad/apps/updata/templates/updata/index.html created 755 +102 0

@@ -0,0 +1,102
	1	{% extends "base.html" %}
	2	{% block title %}Upload Data{% endblock %}
	3
	4	{% block extra_head %}
	5	<script type="text/javascript">
	6	function populateExp(select) {
	7
	8	var kinst = select.options[select.selectedIndex].value;
	9	var url = "{% url 'updata:get_experiments' %}" + '?instruments=' + kinst;
	10	// first delete all forms that are now out of date
	11	divIndex = $(".single_form").index($("#experiments"))
	12	$(".single_form").slice(divIndex).empty()
	13	// second populate the categories html
	14	$(".single_form").slice(divIndex, divIndex + 1).load(url);
	15	}
	16
	17	</script>
	18
	19	<style>
	20	.custom-radio {
	21	list-style: none;
	22	margin: 0;
	23	padding: 0;
	24	}
	25	</style>
	26	{% endblock %}
	27
	28	{% block content %}
	29
	30	<center><h4>Upload Data</h4></center>
	31	<form method="post" enctype="multipart/form-data">
	32
	33	{% csrf_token %}
	34
	35	{% block description %}
	36	<!-- subdivide selection column for instruments to be possibly filled in by ajax - single_form 0 -->
	37	<div class="col-md-12 single_form" id="description">
	38	<div class="row">
	39	{{ form.description.label }}
	40	</div>
	41	<!-- Instrument select is its own row in selections column -->
	42	<div class="row">
	43	<div class="col-md-12">
	44	{{ form.description }}
	45	</div> <!-- end span -->
	46	</div> <!-- end row -->
	47	</div> <!-- end subdivide -->
	48
	49	{% endblock %}
	50
	51	{% block file %}
	52	<div class="col-md-12 single_form" style="margin-top: 15px;" id="description">
	53	<div class="row">
	54	{{ form.file.label }}
	55	</div>
	56	<!-- Instrument select is its own row in selections column -->
	57	<div class="row">
	58	<div class="col-md-12">
	59	{{ form.file }}
	60	</div> <!-- end span -->
	61	</div> <!-- end row -->
	62	</div> <!-- end subdivide -->
	63
	64	{% endblock %}
	65
	66	{% block type %}
	67	<div class="col-md-12 single_form" style="margin-top: 15px;" id="description">
	68	<!-- Instrument select is its own row in selections column -->
	69	<div class="row">
	70	<div class="col-md-12">
	71	{{ form.type }}
	72	</div> <!-- end span -->
	73	</div> <!-- end row -->
	74	</div> <!-- end subdivide -->
	75
	76	{% endblock %}
	77
	78	{% block instruments %}
	79	<!-- subdivide selection column for instruments to be possibly filled in by ajax - single_form 0 -->
	80	<div class="col-md-12 single_form" style="margin-top: 15px;" id="instruments">
	81
	82	{% if form.instruments %}
	83	{% include "madweb/instruments.html" %}
	84	{% endif %}
	85
	86	</div> <!-- end subdivide -->
	87	{% endblock %}
	88
	89	{% block experiments %}
	90	<!-- subdivide selection column for experiments to be possibly filled in by ajax - single_form 0 -->
	91	<div class="col-md-12 single_form" style="margin-top: 15px;" id="experiments">
	92
	93	{% if form.experiments %}
	94	{% include "updata/experiments.html" %}
	95	{% endif %}
	96
	97	</div> <!-- end subdivide -->
	98	{% endblock %}
	99	<button style="margin-top: 15px;" type="submit">Load</button>
	100
	101	</form>
	102	{% endblock %} No newline at end of file

source/madpy/djangoMad/apps/updata/urls.py created 755 +9 0

@@ -0,0 +1,9
	1	from django.conf.urls import url
	2	from . import views
	3
	4	urlpatterns = [
	5	url(r'^$',views.index, name='updata_index'),
	6	url(r'^getExperiments/?$', views.get_experiments, name='get_experiments'),
	7	]
	8
	9	app_name = 'updata' No newline at end of file

source/madpy/djangoMad/apps/updata/views.py created 755 +83 0

@@ -0,0 +1,83
	1
	2	from django.contrib.auth.decorators import login_required
	3	from django.shortcuts import render
	4	from .forms import UpdataForm, ExpForm
	5	from django.core.files.storage import FileSystemStorage
	6	from django.contrib import messages
	7
	8	import os
	9
	10	# madrigal imports
	11	import madrigal.metadata
	12	import madrigal.ui.web
	13	import madrigal.admin
	14
	15	@login_required
	16	def index(request):
	17	'''
	18	Uploading experiments data view. Allows user to upload experiment files
	19
	20	'''
	21	dbAdminObj = madrigal.admin.MadrigalDBAdmin()
	22	madDB = madrigal.metadata.MadrigalDB()
	23	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
	24	siteName, siteList = madWebObj.getSiteInfo()
	25
	26	if request.method == 'POST':
	27	form = UpdataForm(request.POST, request.FILES)
	28	files = request.FILES.getlist('file')
	29
	30	if form.is_valid():
	31	try:
	32	description = form.cleaned_data['description']
	33	instCode = int(form.cleaned_data['instruments'])
	34	expId = form.cleaned_data['experiments']
	35	perm = int(form.cleaned_data['type'])
	36
	37	#saving file
	38	for f in files:
	39	fs = FileSystemStorage(location='/tmp')
	40	fs.save(f.name, f)
	41	madExp = madrigal.metadata.MadrigalExperiment()
	42	filepath = os.path.join('/tmp', f.name)
	43	expTitle = madExp.getExpNameByExpId(expId)
	44
	45	dbAdminObj.createMadrigalExperiment(filepath,expTitle, perm, description, instCode)
	46
	47
	48	madInstParams = madrigal.metadata.MadrigalInstrumentParameters()
	49	madInstKindats = madrigal.metadata.MadrigalInstrumentKindats()
	50
	51	print('* Updating local metadata *')
	52	dbAdminObj.__updateLocalMetadata__()
	53	print('* Rebuilding instParmTab.txt *')
	54	madInstParams.rebuildInstParmTable()
	55	print('* Rebuilding instKindatTab.txt *')
	56	madInstKindats.rebuildInstKindatTable()
	57	messages.success(
	58	request, 'Experimento(s) creado(s) exitosamente')
	59	form = UpdataForm()
	60
	61	except Exception as e:
	62	messages.error(
	63	request, str(e))
	64	else:
	65	form = UpdataForm()
	66
	67	return render(request, 'updata/index.html', {
	68	'form': form,
	69	'site_name': siteName,
	70	'site_list': siteList,
	71	})
	72
	73
	74	def get_experiments(request):
	75	"""get_experiments is a Ajax call that returns the experiments select html to support the
	76	updata UI. Called when a user modifies the intruments select field.
	77
	78	Inputs:
	79	request
	80	"""
	81	form = ExpForm(request.GET)
	82
	83	return render(request, 'updata/experiments.html', {'form': form})

source/madpy/djangoMad/madweb/static/loader.gif created 755 binary 0 0

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source/madpy/djangoMad/madweb/templates/madweb/parameter_selection.html created 755 +50 0

@@ -0,0 +1,50
	1	<div class="row" style="margin-bottom: 20px">
	2	Select parameter: <br>
	3	{{ form.param_list1d.label }}
	4	{{ form.param_list1d }}
	5	{% if form.param_list2d %}
	6	{{ form.param_list2d.label }}
	7	{{ form.param_list2d }}
	8	{% endif %}
	9
	10	</div>
	11
	12	<script>
	13	$('#id_param_list2d').bind('change', function (e) {
	14	var expID = '{{ expID }}';
	15	var param = $(this).val();
	16	var url = '{% url 'plot' %}' + '?expID=' + expID + '&param2d=' + param;
	17	console.log(url)
	18	// first delete all forms that are now out of date
	19	divIndex = $(".single_form").index($( "#file_plot" ))
	20	$(".single_form").slice(divIndex).empty()
	21	// second populate the file_plot html if '0' not selected
	22	if (param != '0') {
	23	$(".single_form").slice(divIndex,divIndex+1).html("<img src=\"static/loader.gif\" class=\"load_center\"/>").load(url);
	24	}
	25	})
	26	$('#id_param_list1d').bind('change', function (e) {
	27	var expID = '{{ expID }}';
	28	var param = $(this).val();
	29	var url = '{% url 'plot' %}' + '?expID=' + expID + '&param1d=' + param;
	30	console.log(url)
	31	// first delete all forms that are now out of date
	32	divIndex = $(".single_form").index($( "#file_plot" ))
	33	$(".single_form").slice(divIndex).empty()
	34	// second populate the file_plot html if '0' not selected
	35	if (param != '0') {
	36	$(".single_form").slice(divIndex,divIndex+1).html("<img src=\"static/loader.gif\" class =\"load_center\"/>").load(url);
	37	}
	38	})
	39	</script>
	40	<style>
	41	.load_center {
	42	display: block;
	43	margin-left: auto;
	44	margin-right: auto;
	45	margin-top: 100px;
	46	margin-bottom: 100px;
	47	width: 4%;
	48	align-items: center;
	49	}
	50	</style> No newline at end of file

source/madpy/djangoMad/djangoMad/settings.py +16 -10

             import os
             BASE_DIR = os.path.dirname(os.path.dirname(__file__))
             # Quick-start development settings - unsuitable for production
             # See https://docs.djangoproject.com/en/1.7/howto/deployment/checklist/
             # SECURITY WARNING: keep the secret key used in production secret!
-            SECRET_KEY = '!wa!749ow0!%7t7tr6fr^fvkqyd7yc#mmvpfedr+f2pb!4r)wd'
+            SECRET_KEY = '^c1l3d35+q28^66d2pc1qlu(k$wmw^*gg3rfitz^s)t=9eu1ui'
             # SECURITY WARNING: don't run with debug turned on in production!
             DEBUG = True
             # Application definition
             INSTALLED_APPS = (
-                #'django.contrib.admin',
+                'django.contrib.admin',
                 'django.contrib.auth',
                 'django.contrib.contenttypes',
                 'django.contrib.sessions',
                 'django.contrib.staticfiles',
                 'madweb',
                 'django_bootstrap_calendar',
-                'bootstrap3'
+                'bootstrap3',
+                'apps.login',
+                'apps.updata',
             )
-            MIDDLEWARE_CLASSES = (
+            MIDDLEWARE = [
-                'django.contrib.auth.middleware.AuthenticationMiddleware',
+                'django.middleware.security.SecurityMiddleware',
-                'django.contrib.messages.middleware.MessageMiddleware',
                 'django.contrib.sessions.middleware.SessionMiddleware',
                 'django.middleware.common.CommonMiddleware',
                 'django.middleware.csrf.CsrfViewMiddleware',
-                'django.contrib.auth.middleware.SessionAuthenticationMiddleware',
+                'django.contrib.auth.middleware.AuthenticationMiddleware',
+                'django.contrib.messages.middleware.MessageMiddleware',
                 'django.middleware.clickjacking.XFrameOptionsMiddleware',
+            ]
             ROOT_URLCONF = 'djangoMad.urls'
                             'django.template.context_processors.static',
                             'django.template.context_processors.tz',
                             'django.contrib.messages.context_processors.messages',
+                            'django.template.context_processors.request',
                         ],
                     },
                 },
             # https://docs.djangoproject.com/en/1.7/ref/settings/#databases
             DATABASES = {
+                'default': {
+                    'ENGINE': 'django.db.backends.sqlite3',
+                    'NAME': 'madrigal.sqlite',
+                }
             }
             # Internationalization
             # https://docs.djangoproject.com/en/1.7/topics/i18n/

source/madpy/djangoMad/djangoMad/urls.py +3 0

             urlpatterns = [
                 url(r'^', include('madweb.urls')),
                 url(r'^$', madweb.views.index),
+                url(r'^updata/', include('apps.updata.urls', namespace="updata")),
+                url(r'^accounts/', include('apps.login.urls', namespace="login")),
+                url(r'^admin/', admin.site.urls),
             ]

source/madpy/djangoMad/djangoMad/wsgi.py +1 -1

             madDB = madrigal.metadata.MadrigalDB()
             os.environ['PYTHON_EGG_CACHE'] = os.path.join(madDB.getMadroot(), 'eggs')
-            os.environ.setdefault("DJANGO_SETTINGS_MODULE", "djangoMad.settings_production")
+            os.environ.setdefault("DJANGO_SETTINGS_MODULE", "djangoMad.settings")
             from django.core.wsgi import get_wsgi_application
             application = get_wsgi_application()

source/madpy/djangoMad/madweb/forms.py +134 0

@@ -16,6 +16,7 import django.template.defaulttags
16		16
17	# third party imports	17	# third party imports
18	import numpy	18	import numpy
		19	import h5py
19		20
20	# Madrigal imports	21	# Madrigal imports
21	import madrigal.metadata	22	import madrigal.metadata
@@ -637,6 +638,139 class SingleExpPlotsForm(django.forms.Form):
637	choices=plotList,	638	choices=plotList,
638	required=False)	639	required=False)
639		640
		641	'''get_params2 retrieves a list of 1d and 2d parameters of type 1 hdf5 files'''
		642	def get_params1(args, kwargs, madExpObj, madWebObj):
		643
		644	expID = getSelection('experiment_list', args, kwargs)
		645	expDir = madExpObj.getExpDirByExpId(expID)
		646	fileList = madWebObj.getFileFromExpID(expID, False)
		647
		648	firsttuple = [a_tuple[0] for a_tuple in fileList]
		649	basename = firsttuple[0]
		650	fullFilename = os.path.join(expDir, basename)
		651	f = h5py.File(fullFilename, "r")
		652	data = f[list(f.keys())[0]]
		653	array = data[list(data.keys())[0]]
		654
		655	param1d = array[list(array.keys())[0]]
		656	param2d = array[list(array.keys())[1]]
		657	paramch1d = list(param1d.keys())
		658	paramch2d = list(param2d.keys())
		659
		660	dataparameters = param1d[list(param1d.keys())[0]]
		661	paramch_mn_bin = list(dataparameters['mnemonic'])
		662	paramch_bin = list(dataparameters['description'])
		663	paramch_mn = list()
		664	paramch = list()
		665
		666	for i in range(len(paramch_bin)):
		667	paramch_mn.append(paramch_mn_bin[i].decode("utf-8"))
		668	paramch.append(paramch_bin[i].decode("utf-8"))
		669
		670	choices1d = ['Select parameter']
		671	for ch in paramch1d[1:]:
		672	aux = paramch[paramch_mn.index(ch.upper())]
		673	choices1d.append(aux)
		674
		675
		676	dataparameters = param2d[list(param2d.keys())[0]]
		677	paramch_mn_bin = list(dataparameters['mnemonic'])
		678	paramch_mn = list()
		679	paramch_bin = list(dataparameters['description'])
		680	paramch = list()
		681
		682	for i in range(len(paramch_bin)):
		683	paramch_mn.append(paramch_mn_bin[i].decode("utf-8"))
		684	paramch.append(paramch_bin[i].decode("utf-8"))
		685
		686	choices2d = ['Select parameter']
		687	for ch in paramch2d[1:]:
		688	aux = paramch[paramch_mn.index(ch.upper())]
		689	choices2d.append(aux)
		690
		691
		692	choices = [choices1d,choices2d]
		693	return choices
		694
		695
		696	'''get params2 retrieves a list of 1d parameters of type 2 of hdf5 files'''
		697	def get_params2(args, kwargs, madExpObj, madWebObj):
		698
		699	expID = getSelection('experiment_list', args, kwargs)
		700	expDir = madExpObj.getExpDirByExpId(expID)
		701	fileList = madWebObj.getFileFromExpID(expID, False)
		702
		703	firsttuple = [a_tuple[0] for a_tuple in fileList]
		704	basename = firsttuple[0]
		705	fullFilename = os.path.join(expDir, basename)
		706	f = h5py.File(fullFilename, "r")
		707
		708	metadata = f[list(f.keys())[1]]
		709	table = metadata[list(metadata.keys())[0]]
		710	param_mn_bin = list(table['mnemonic'])
		711	param_mn = list()
		712	for p in param_mn_bin:
		713	param_mn.append(p.decode("utf"))
		714
		715	index = param_mn.index('UT2_UNIX')
		716	params = list(table['description'])
		717	choices = ['Select parameter']
		718	for p in params[index+1:]:
		719	choices.append(p.decode("utf-8"))
		720
		721	return choices
		722
		723
		724	class SingleExpPlotsSelectionForm(django.forms.Form):
		725	"""SingleExpPlotsSselectionForm is a Form class for the parameters selection for plotting in the Single Experiment interface.
		726	Use this because its faster to create than the full SingleExpDefaultForm
		727	"""
		728
		729	def __init__(self, args, *kwargs):
		730	super(SingleExpPlotsSelectionForm, self).__init__(args, *kwargs)
		731	madDB = madrigal.metadata.MadrigalDB()
		732	madExpObj = madrigal.metadata.MadrigalExperiment(madDB)
		733	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
		734	expID = getSelection('experiment_list', args, kwargs)
		735	try:
		736	expID = int(expID)
		737	except ValueError:
		738	# convert expPath to expID
		739	expID = madWebObj.getExpIDFromExpPath(expID, True)
		740	expDir = madExpObj.getExpDirByExpId(expID)
		741	fileList = madWebObj.getFileFromExpID(expID, False)
		742
		743	firsttuple = [a_tuple[0] for a_tuple in fileList]
		744	basename = firsttuple[0]
		745	fullFilename = os.path.join(expDir, basename)
		746	f = h5py.File(fullFilename, "r")
		747	data = f[list(f.keys())[0]]
		748
		749	if 'Array Layout' in list(data.keys()):
		750	choices = get_params1(args, kwargs, madExpObj, madWebObj)
		751	params1d = choices[0]
		752	params2d = choices[1]
		753
		754	index = list(range(len(params1d)))
		755	paramchoices1d = list(zip(index, params1d))
		756
		757
		758	index = list(range(len(params2d)))
		759	paramchoices2d = list(zip(index, params2d))
		760
		761
		762	self.fields['param_list2d'] = django.forms.ChoiceField(widget = django.forms.Select(), choices=paramchoices2d, label="2D Parameters", required=False)
		763
		764	else:
		765	params1d = get_params2(args, kwargs, madExpObj, madWebObj)
		766	#if params1d[0] == 'ut2_unix':
		767	# params1d[0] = 'Select parameter'
		768	index = list(range(len(params1d)))
		769	paramchoices1d = list(zip(index, params1d))
		770
		771	self.fields['param_list1d'] = django.forms.ChoiceField(widget = django.forms.Select(), choices=paramchoices1d, label="1D Parameters", required=False)
		772
		773
640		774
641	class SingleExpDownloadAsIsForm(django.forms.Form):	775	class SingleExpDownloadAsIsForm(django.forms.Form):
642	"""SingleExpDownloadAsIsForm is a Form class for the download as is field in the Single Experiment interface.	776	"""SingleExpDownloadAsIsForm is a Form class for the download as is field in the Single Experiment interface.

source/madpy/djangoMad/madweb/templates/madweb/show_experiment.html +9 -1

@@ -56,4 +56,12
56	{% include "madweb/show_plots.html" %}	56	{% include "madweb/show_plots.html" %}
57	{% endif %}	57	{% endif %}
58	</div> <!-- end subdivide -->	58	</div> <!-- end subdivide -->
59	{% endblock %} No newline at end of file	59
		60	<!-- file select div -->
		61	<div class="col-md-12 single_form" id="file_plot">
		62	{% if form.show_plots %}
		63	{% include "madweb/parameter_selection.html" %}
		64	{% endif %}
		65	</div> <!-- end subdivide -->
		66
		67	{% endblock %} No newline at end of file

source/madpy/djangoMad/madweb/templates/madweb/single.html +9 0

@@ -257,3 +257,12
257	</div> <!-- end subdivide -->	257	</div> <!-- end subdivide -->
258	{% endblock %}	258	{% endblock %}
259		259
		260	{% block file_plot %}
		261	<!-- file select div -->
		262	<div class="col-md-12 single_form" id="file_plot">
		263	{% if form.show_plots %}
		264	{% include "madweb/parameter_selection.html" %}
		265	{% endif %}
		266	</div> <!-- end subdivide -->
		267	{% endblock %}
		268

source/madpy/djangoMad/madweb/urls.py +3 0

                                    url(r'^showPlots/?$',
                                        views.show_plots,
                                        name='show_plots'),
+                                   url(r'^view_plot/?$',
+                                       views.view_plot,
+                                       name='plot'),
                                    url(r'^downloadAsIs/?$',
                                        views.download_as_is,
                                        name='download_as_is'),

source/madpy/djangoMad/madweb/views.py +208 -4

@@ -38,6 +38,9 from wsgiref.util import FileWrapper
38		38
39	# third party imports	39	# third party imports
40	import numpy	40	import numpy
		41	import plotly.offline as py
		42	import plotly.graph_objs as go
		43	import h5py
41		44
42		45
43	# madrigal imports	46	# madrigal imports
@@ -336,16 +339,217 def show_plots(request):
336	Inputs:	339	Inputs:
337	request	340	request
338	"""	341	"""
		342	madDB = madrigal.metadata.MadrigalDB()
		343	madExpObj = madrigal.metadata.MadrigalExperiment(madDB)
		344	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
		345
339	try:	346	try:
340	expID = int(request.GET['experiment_list'])	347	expID = int(request.GET['experiment_list'])
341	except ValueError:	348	except ValueError:
342	# convert expPath to expID	349	# convert expPath to expID
343	madDB = madrigal.metadata.MadrigalDB()
344	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
345	expID = madWebObj.getExpIDFromExpPath(request.GET['experiment_list'], True)	350	expID = madWebObj.getExpIDFromExpPath(request.GET['experiment_list'], True)
346	form = madweb.forms.SingleExpPlotsForm(request.GET)	351	plotList = madExpObj.getExpLinksByExpId(expID)
		352	if len(plotList) != 0:
		353	form = madweb.forms.SingleExpPlotsForm(request.GET)
		354	template = 'madweb/show_plots.html'
		355	context = {'form': form}
		356	else:
		357	template = 'madweb/parameter_selection.html'
		358	form = madweb.forms.SingleExpPlotsSelectionForm(request.GET)
		359	context = {'form': form, 'expID': expID}
		360
		361	return render(request, template, context)
		362
		363
		364	def view_plot(request):
		365
		366	param1d = int(request.GET.get('param1d','0'))
		367	param2d = int(request.GET.get('param2d','0'))
		368
		369	madDB = madrigal.metadata.MadrigalDB()
		370	madWebObj = madrigal.ui.web.MadrigalWeb(madDB)
		371	madExpObj = madrigal.metadata.MadrigalExperiment(madDB)
		372
		373	expID =int(request.GET['expID'])
		374	expDir = madExpObj.getExpDirByExpId(expID)
		375	if expDir is None:
		376	raise ValueError('No expDir found for exp_id %i' % (int(expID)))
347		377
348	return render(request, 'madweb/show_plots.html', {'form': form})	378	fileList = madWebObj.getFileFromExpID(expID, False)
		379	firsttuple = [a_tuple[0] for a_tuple in fileList]
		380	basename = firsttuple[0]
		381	fullFilename = os.path.join(expDir, basename)
		382
		383	with h5py.File(fullFilename, "r") as f:
		384
		385	# Get the data
		386
		387	data = f[list(f.keys())[0]]
		388
		389	if 'Array Layout' in list(data.keys()):
		390	array = data[list(data.keys())[0]]
		391	timestamps = array[list(array.keys())[4]]
		392	datatime = [datetime.datetime.fromtimestamp(t) for t in list(timestamps)]
		393
		394	range = array[list(array.keys())[3]]
		395	datarange = list(range)
		396
		397
		398	if param1d==0:
		399	parameters_2d = array[list(array.keys())[1]]
		400	paramname = list(parameters_2d.keys())[param2d]
		401	param = parameters_2d[list(parameters_2d.keys())[param2d]]
		402	dataparam = list(param)
		403	plot = plot_heatmap(datatime,datarange,dataparam,paramname)
		404
		405	else:
		406	parameters_1d = array[list(array.keys())[0]]
		407	paramname = list(parameters_1d.keys())[param1d]
		408	param = parameters_1d[list(parameters_1d.keys())[param1d]]
		409	dataparam = list(param)
		410	plot = plot_scatter(datatime,dataparam,paramname)
		411
		412	else:
		413	table = data[list(data.keys())[0]]
		414	a = list(table.dtype.fields.keys())
		415	index = a.index('ut2_unix')
		416	v = a[index:]
		417	paramname = v[param1d]
		418	dataparam = list(table[paramname])
		419	datatime = [datetime.datetime.fromtimestamp(t) for t in list(table['ut2_unix'])]
		420	plot = plot_scatter(datatime,dataparam,paramname)
		421
		422	return HttpResponse(plot)
		423
		424	def plot_scatter(datatime,dataparam,paramname):
		425	if (numpy.isnan(dataparam).all()):
		426	plot = "There is no valid data available for this plot"
		427
		428	else:
		429	fig = go.Figure()
		430	fig.add_trace(go.Scatter(x=datatime, y=dataparam))
		431	fig.update_yaxes(title_text=paramname)
		432
		433	delta = datatime[-1] - datatime[1]
		434
		435	if (delta>datetime.timedelta(days=30)):
		436	# Add range slider
		437	fig.update_layout(
		438	xaxis=dict(
		439	rangeselector=dict(
		440	buttons=list([
		441	dict(count=1,
		442	label="1m",
		443	step="month",
		444	stepmode="backward"),
		445	dict(count=6,
		446	label="6m",
		447	step="month",
		448	stepmode="backward"),
		449	dict(count=1,
		450	label="1y",
		451	step="year",
		452	stepmode="backward"),
		453	dict(step="all")
		454	])
		455	),
		456	rangeslider=dict(
		457	visible=True
		458	),
		459	type="date"
		460	)
		461	)
		462
		463
		464	plot = py.plot(fig, include_plotlyjs=False, output_type='div')
		465
		466
		467	return plot
		468
		469
		470	def plot_heatmap(datatime,datarange,dataparam,paramname):
		471	if (numpy.isnan(dataparam).all()):
		472	plot = "There is no valid data available for this plot"
		473	else:
		474	fig = go.Figure()
		475	fig.add_trace(go.Heatmap(x=datatime,y=datarange,z= dataparam,colorscale='Jet',colorbar={"title":paramname}))
		476	fig.update_yaxes(title_text="range")
		477	fig.update_layout(
		478	updatemenus=[
		479	dict(
		480	buttons=list([
		481	dict(
		482	args=["colorscale", "Jet"],
		483	label="Jet",
		484	method="restyle"
		485	),
		486	dict(
		487	args=["colorscale", "RdBu"],
		488	label="Red-Blue",
		489	method="restyle"
		490	),
		491	dict(
		492	args=["colorscale", "Viridis"],
		493	label="Viridis",
		494	method="restyle"
		495	),
		496	dict(
		497	args=["colorscale", "Cividis"],
		498	label="Cividis",
		499	method="restyle"
		500	),
		501	dict(
		502	args=["colorscale", "Greens"],
		503	label="Greens",
		504	method="restyle"
		505	),
		506	]),
		507	type = "dropdown",
		508	direction="down",
		509	pad={"r": 10, "t": 10},
		510	showactive=True,
		511	x=0.1,
		512	xanchor="left",
		513	y=1.05,
		514	yanchor="top"
		515	),
		516	dict(
		517	buttons=list([
		518	dict(
		519	args=[{"contours.showlines": False, "type": "contour"}],
		520	label="Hide lines",
		521	method="restyle"
		522	),
		523	dict(
		524	args=[{"contours.showlines": True, "type": "contour"}],
		525	label="Show lines",
		526	method="restyle"
		527	),
		528	]),
		529	direction="down",
		530	pad={"r": 10, "t": 10},
		531	showactive=True,
		532	x=0.32,
		533	xanchor="left",
		534	y=1.05,
		535	yanchor="top"
		536	),
		537	]
		538	)
		539
		540	fig.update_layout(
		541	annotations=[
		542	dict(text="Colorscale", showarrow=False,
		543	x=0, xref="paper", y=1.03, yref="paper", align="left"),
		544	dict(text="Lines", x=0.25, xref="paper", y=1.03, yref="paper",
		545	showarrow=False)
		546	]
		547	)
		548
		549
		550	plot = py.plot(fig, include_plotlyjs=False, output_type='div')
		551
		552	return plot
349		553
350		554
351	def download_as_is(request):	555	def download_as_is(request):

source/madpy/djangoMad/templates/base_single.html +2 0

             	<meta charset="UTF-8">
             	<meta name="viewport" content="width=device-width, initial-scale=1.0">
             	<link rel="shortcut icon" type="image/png" href="/static/favicon.ico"/>
+            	<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
             	<title>{% block title %}Madrigal Database{% endblock %}</title>
                 <style type="text/css">
             		html body {
             			{% block file_select %}{% endblock %}
             			{% block file_buttons %}{% endblock %}
             			{% block file_data %}{% endblock %}
+            			{% block file_plot %}{% endblock %}
             			</div>
             		</div>

source/madpy/djangoMad/templates/navbar.html +2 -1

                                     {% endfor %}
                                     </ul>
                                 </li>
                                 <li><a href="http://cedar.openmadrigal.org/openmadrigal" data-toggle="tooltip" data-original-title="Click here to go to OpenMadrigal, where you can download API&#39;s in python, Matlab, and IDL to run Madrigal scripts, and access Madrigal&#39;s source code." data-placement="bottom">OpenMadrigal</a></li>
+            					<li><a href="{% url 'updata:updata_index' %}" data-toggle="tooltip" data-original-title="Click here to upload data to Madrigal database." data-placement="bottom">Upload Madrigal Data</a></li>
                             </ul>
                         </div>
                      </nav>

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