# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with libSigNetSim. If not, see <http://www.gnu.org/licenses/>.
""" ModelMiscView.py
This file ...
"""
from django.views.generic import TemplateView
from django import __version__
if int(__version__.split('.')[0]) < 2:
from django.core.urlresolvers import reverse
else:
from django.urls import reverse
from signetsim.views.HasWorkingModel import HasWorkingModel
from signetsim.views.HasErrorMessages import HasErrorMessages
from signetsim.views.edit.ModelMiscForm import ModelMiscForm
class ModelMiscView(TemplateView, HasWorkingModel, HasErrorMessages):
template_name = 'edit/misc.html'
def __init__(self, **kwargs):
# coding: utf-8
try:
from django import __version__ as django_version
# Django < 1.8
except ImportError:
from django import get_version
django_version = get_version()
from django.utils._os import safe_join
from django.template.base import TemplateDoesNotExist
from django.template.loaders.filesystem import Loader as BaseLoader
django_version = float('.'.join(django_version.split('.')[:2]))
is_django_18 = django_version == 1.8
if is_django_18:
from django.template.utils import get_app_template_dirs
from django.template.loaders.app_directories import (
Loader as AppsBaseLoader)
app_template_dirs = get_app_template_dirs('templates')
else:
from django.template.loaders.app_directories import (
Loader as AppsBaseLoader, app_template_dirs)
from django_vest.config import settings
__ALL__ = ('Loader', 'AppsLoader')
DJANGO_ORIGIN = 'DJANGO_ORIGIN/'
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with libSigNetSim. If not, see <http://www.gnu.org/licenses/>.
""" ModelAnnotationsView.py
This file ...
"""
from django.views.generic import TemplateView
from django import __version__
if int(__version__.split('.')[0]) < 2:
from django.core.urlresolvers import reverse
else:
from django.urls import reverse
from libsignetsim.uris.URI import URI
from signetsim.views.HasWorkingModel import HasWorkingModel
from signetsim.views.HasErrorMessages import HasErrorMessages
from .ModelAnnotationsForm import ModelAnnotationsForm
class ModelAnnotationsView(TemplateView, HasWorkingModel, HasErrorMessages):
template_name = 'edit/annotations.html'
def __init__(self, **kwargs):
def isUserLoggedIn(self, request):
if int(__version__.split('.')[0]) < 2:
return not request.user.is_anonymous()
else:
return not request.user.is_anonymous
def testBistable(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "tyson2.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
self.assertEqual(len(Continuation.objects.filter(project=project)), 0)
response_compute_curve = c.post(
'/analyse/bifurcations/', {
'action': 'compute_curve',
'parameter': 3,
'from_value': 0,
'to_value': 5000,
'max_steps': 500,
'ds': 5
})
self.assertEqual(response_compute_curve.status_code, 200)
self.assertEqual(
len(response_compute_curve.context['list_of_computations']), 1)
self.assertEqual(len(Continuation.objects.filter(project=project)), 1)
response_get_status = c.post('/json/get_continuation_status/',
{'continuation_id': 0})
self.assertEqual(response_get_status.status_code, 200)
json_response = loads(response_get_status.content.decode('utf-8'))
self.assertEqual(json_response['status'], 'Running')
sleep(60)
response_get_status = c.post('/json/get_continuation_status/',
{'continuation_id': 0})
self.assertEqual(response_get_status.status_code, 200)
json_response = loads(response_get_status.content.decode('utf-8'))
# we cannot really test, because the test database doesn't like threads.
# Maybe we could find a trick for that, but for now i will give up
# Actually, it works with the django2 version, maybe earlier
if int(__version__.split('.')[0]) >= 2:
self.assertEquals(json_response['status'], 'Finished')
response_get_curve = c.post('/json/get_equilibrium_curve/', {'id': 0})
self.assertEqual(response_get_curve.status_code, 200)
json_response = loads(response_get_curve.content.decode('utf-8'))
results_x = [
86.21626556089748, 86.93136694242513, 86.94136664253448,
86.95636588693405, 86.97886476364202, 87.01261309970393,
87.0632356457539, 87.13916954386701, 87.25307052670914,
87.42392219789149, 87.68019988610622, 87.93647750061857,
88.19275478462879, 88.44903150259645, 88.70530739977113,
88.96158217168826, 89.21785542721256, 89.47412663532754,
89.73039504055562, 89.98665951951536, 90.24291832449998,
90.49916860217002, 90.75540544872487, 91.0116199967866,
91.2677956036832, 91.52390157555016, 91.77989210265201,
92.03575224504068, 92.2916069887797, 92.54761930179735,
92.8037697036536, 93.0599857623939, 93.31623220069396,
93.57249438783006, 93.8287654431462, 94.08504180486419,
94.34132150954666, 94.59760341765312, 94.85388683671873,
95.11017132823656, 95.36645660412772, 95.62274246886504,
95.87902878586507, 96.26345891675822, 96.64788962815832,
97.03232075827674, 97.41675220826578, 97.99339984566075,
98.57004789353306, 99.14669623978276, 99.72334481626827,
100.58831801810842, 101.45329152519751, 102.31826526008953,
103.183239175166, 104.04821323655267, 105.34567455379258,
106.64313608729213, 107.94059779260975, 109.23805964068934,
111.18425263761446, 113.13044585614014, 115.07663925538233,
117.02283280770853, 119.94212338125946, 122.8614142000694,
125.78070522116666, 128.69999641449544, 131.61928775634857,
135.99822500984263, 140.37716250627656, 144.75610020357604,
149.13503807138557, 153.51397608534575, 157.89291422561152,
164.46132164049422, 171.02972926072346, 177.59813704915535,
184.16654497886415, 190.73495302827374, 197.3033611798905,
203.87176941938367, 210.44017773490575, 217.00858611658194,
223.57699455612052, 233.4296073100613, 243.2822201600283,
253.1348330893996, 262.9874460858843, 272.84005913950733,
282.6926722420998, 292.54528538691727, 302.3978985683488,
312.2505117816942, 322.1031250229907, 336.8820449306969,
351.66096488488546, 366.4398848775416, 381.2188049027232,
395.9977249556008, 410.77664503221536, 425.5555651292957,
440.3344852441193, 455.11340537440503, 469.89232551822937,
492.06070575612307, 514.2290860165135, 536.3974662955129,
558.5658465902391, 580.7342268983501, 602.9026072179273,
625.0709875473859, 647.2393678854078, 669.4077482308886,
691.5761285828979, 724.8286991215903, 758.0812696711193,
791.3338402296085, 824.5864107956661, 857.8389813681619,
891.0915519461701, 924.3441225289263, 957.5966931157949,
990.8492637062436, 1024.1018342998236, 1073.980690195309,
1123.8595460959802, 1173.738402000934, 1223.6172579094982,
1273.4961138211258, 1323.3749697353683, 1373.2538256518537,
1423.1326815702719, 1473.0115374903617, 1522.8903934119012,
1572.7692493347008, 1647.58753322093, 1722.405817109175,
1797.2241009990273, 1872.0423848901576, 1946.860668782274,
2021.6789526751081, 2096.4972365683993, 2171.31552046188,
2246.1338043552564, 2320.952088248184, 2395.7703721402336,
2470.588656030846, 2545.4069399192604, 2620.2252238044252,
2695.043507684898, 2769.8617915587974, 2844.6800754239853,
2919.4983592787917, 2994.3166431234426, 3069.13492696142,
3143.953210798908, 3218.7714946418932, 3293.589778493592,
3368.408062354334, 3443.2263462228975, 3518.044630097655,
3592.862913977101, 3667.681197859983, 3742.49948174527,
3817.3177656320604, 3892.1360495194563, 3966.9543334063414,
4041.7726172908388, 4116.590901168191, 4154.000043098162,
4172.704614055171, 4191.409184990714, 4196.085327703541,
4197.254363366462, 4197.838881181483, 4198.423398947319,
4198.715657915437
]
results_y_min = [
0.015, 0.01779248945502492, 0.01781466715442101,
0.01784814446747936, 0.017897610027032624, 0.017970902620809023,
0.018079271045145166, 0.018238208415341954, 0.01847126939258336,
0.01881051666378573, 0.019305356919514405, 0.019794467664002596,
0.020285748283462638, 0.02078748660799787, 0.02130700451266831,
0.02185242686262597, 0.022433682717773365, 0.023062677206187803,
0.02375511389830091, 0.02453260758714392, 0.025425674049219825,
0.02647963781620497, 0.02776856978970085, 0.029410680319980738,
0.031610024337097704, 0.034726897799411995, 0.03932877014518192,
0.04601587394134079, 0.05460644763550759, 0.06381677453817167,
0.07247671841679726, 0.08011427017070318, 0.0867397606728453,
0.0925263319586254, 0.0975933691845283, 0.10205930864509616,
0.1061053256316217, 0.10972482938513746, 0.11301831932468002,
0.11604845017702685, 0.11879049581093279, 0.12139823905473571,
0.12378244752249859, 0.12709474349049438, 0.130069504557534,
0.1328199904208261, 0.13537348222690082, 0.13879542245006585,
0.14192438994822912, 0.1447268702157785, 0.14730853344717082,
0.1507760615453077, 0.15383733398545604, 0.15662042049667121,
0.1591028854040179, 0.1613893673874808, 0.1644281832486283,
0.16712444656553793, 0.16949268085111988, 0.1716523111017552,
0.17444447883598924, 0.1768938853138476, 0.1789720368151608,
0.1808269116402629, 0.1831954477245585, 0.18512199516638175,
0.18676795249280798, 0.18812306196208597, 0.1892753972195709,
0.1906418274919116, 0.19167933810647023, 0.19245560775782786,
0.1930321734576467, 0.19341461746110294, 0.19365924509497814,
0.1938143752188859, 0.1937797004176894, 0.19357370566612236,
0.19324493971482118, 0.1928089620150613, 0.1922915559879814,
0.19172804217675363, 0.1911305185579582, 0.19048571362559427,
0.18978214312974617, 0.18873144545371104, 0.1876629199978579,
0.18656124308248598, 0.18545076312894732, 0.18433148486020326,
0.18320441652755481, 0.18211719501875914, 0.18103519102990565,
0.17993037943853663, 0.17888328607369688, 0.17733747750093387,
0.17579400386362903, 0.17433156576257358, 0.17290352076659338,
0.17149960790637864, 0.17013239876242758, 0.16882052805184136,
0.16755196934041847, 0.166302199537738, 0.1650857871542732,
0.16335709190488507, 0.1616733263236863, 0.16005400122141833,
0.158535032690282, 0.15704698674293444, 0.15561213573594232,
0.15424106780403124, 0.15290774495805673, 0.1516199169576196,
0.15040371660207963, 0.1486284223502365, 0.14693315403049792,
0.14530496216184446, 0.14376870455592214, 0.14229393289706316,
0.14087594000737147, 0.13951030972566653, 0.1381939194089944,
0.13692725360905944, 0.1357134001130735, 0.13396430021146344,
0.1322810309057875, 0.13068408923881478, 0.12916360659552625,
0.1276948173757566, 0.12627366641084253, 0.12490836748142213,
0.12359069510333424, 0.12231145231445813, 0.12106450391647534,
0.11983452066712103, 0.11806061709708432, 0.11632958474173705,
0.11461806339488086, 0.1129419109211148, 0.11127070930167597,
0.10958230592861472, 0.10787666027808301, 0.10612519164120864,
0.10431205380552988, 0.10240290412490836, 0.10036160434644706,
0.09814220338721417, 0.09568146752056707, 0.09294118584463974,
0.08980748445267493, 0.08620366745941492, 0.08204818040400452,
0.07733958898818614, 0.07213794952360476, 0.06666614519144401,
0.06120243510843881, 0.05601161975336735, 0.051258065564562166,
0.04698389607330316, 0.043173865538347664, 0.03976962029537009,
0.03670102016416955, 0.03390735045586199, 0.03133300523283533,
0.028922727381242734, 0.026631118719707938, 0.02439937293180102,
0.02214964074296716, 0.019718390664111976, 0.018282620834660743,
0.017406476849576424, 0.0161818624043725, 0.015647591255827396,
0.015432508900836119, 0.015271569258573625, 0.015000160118060336,
0.01500007079793588
]
results_y_max = [
0.015, 0.012534264754228688, 0.012517014368486849,
0.012491369869760845, 0.012453392783801583, 0.012397497486646702,
0.012315675345077461, 0.012196312017180203, 0.012025663526074164,
0.011783772507285883, 0.011444616052897413, 0.011126465172851532,
0.01082236245979298, 0.010526877904158736, 0.010236562869673274,
0.009948218012102732, 0.009659050156982383, 0.00936393327936833,
0.009061222769991207, 0.008744229480719548, 0.008408376956995285,
0.0080459763457337, 0.007647120848241773, 0.007195741837286061,
0.006674292500042547, 0.0060595011663057835, 0.0053426402523300215,
0.004572538254385119, 0.0038749584618548464, 0.0033479924375637814,
0.002986502366284256, 0.0027384532238182778, 0.0025622055057415603,
0.002435865904728113, 0.002336736399966977, 0.002258861983013471,
0.0021970368066777037, 0.002145826715008738, 0.0021030695516715938,
0.002067469553634481, 0.002036049646205007, 0.002008727527684407,
0.001984382272711667, 0.0019533609711444863, 0.0019270621747126341,
0.0019065929979655111, 0.0018863816627336417, 0.001860369148790495,
0.0018393111696830566, 0.0018219877660465632, 0.001807368451209874,
0.0017835886551585511, 0.0017668411379635279,
0.0017531473091314004, 0.0017414081978817046,
0.0017297501035202808, 0.0017155672108435925,
0.0017068748538581612, 0.0016948027641555522, 0.00168514391131058,
0.0016776081767589143, 0.0016736825641594827,
0.0016606799514123772, 0.0016501670706449783,
0.0016460494275206373, 0.0016358766528365668,
0.0016272837551583527, 0.0016257931394156849,
0.0016199949967516036, 0.0016125740897525937,
0.0016039086635181153, 0.0016013208967950786, 0.001594712594446004,
0.0015931300306848799, 0.001591158329712106, 0.001588134400998554,
0.0015789195067751022, 0.0015765197728761302,
0.0015717680150328572, 0.0015725725754542096, 0.001566547475955274,
0.0015645215825848787, 0.0015611708327354194, 0.001561780769238155,
0.0015589122862886208, 0.00156059096485287, 0.0015524393897311916,
0.0015495851836002472, 0.0015498293117081816, 0.001550346119081149,
0.0015445577615843592, 0.0015465327417541674,
0.0015433947279573882, 0.0015405941581496867,
0.0015397947379674065, 0.0015419169592059926, 0.001540254486710611,
0.001535952871074679, 0.001536547403524718, 0.001534571852451974,
0.0015365666945997623, 0.001535142590259309, 0.0015366105582365174,
0.001534040084211, 0.0015344248217052656, 0.0015365508313836887,
0.0015387826253372204, 0.001536200324072751, 0.001537285866249574,
0.0015396692350562258, 0.0015445286508095242,
0.0015457388381933264, 0.001544325846526447, 0.0015459833519596824,
0.0015488154843095031, 0.0015538134039891993,
0.0015556471640707627, 0.0015607861979179335, 0.001566303653610892,
0.0015693855496971248, 0.0015751484053101441,
0.0015843352272207948, 0.0015869431855743106,
0.0015919428915231923, 0.0015989507978459868,
0.0016105032632677213, 0.0016189635379107073,
0.0016324607435556108, 0.0016431843495952189,
0.0016553306829635817, 0.0016718384898788666,
0.0016830994402972793, 0.0016987388615838, 0.001717236574454972,
0.001731073454768622, 0.001749113799547458, 0.0017787785354525323,
0.0018086891005735237, 0.0018444064226043094, 0.001880209883636673,
0.0019241655795429133, 0.0019672636477568012,
0.0020192145100548604, 0.0020749229276047854, 0.002139138291241035,
0.002212801356330611, 0.0022957572283281687, 0.0023931778861117506,
0.002506072326216011, 0.0026408834554555553, 0.0028006515739885164,
0.0029943149979535506, 0.0032271096719927814,
0.0035059594262233343, 0.0038323186988080352,
0.0042023881580846535, 0.0046051201740328505, 0.005025483295606982,
0.00545355200514633, 0.00588065609085823, 0.0063064723792300905,
0.0067338980769049905, 0.007166783842958959, 0.00761204250310208,
0.008080547064544044, 0.00858483863348207, 0.009143407280710112,
0.009786924055892257, 0.010574186868621695, 0.01165059887012554,
0.012446014162856046, 0.013010359544461425, 0.013928527030370294,
0.014387119488881016, 0.014583232496931468, 0.014734718105243402,
0.01499983829289777, 0.014999928013256687
]
results_y = [
[
0.8333333333333334, 0.7843159339200015, 0.7326044445035558,
0.6788911899587932, 0.6239908892510664, 0.5687941386232487,
0.5142108486903624, 0.4611110588320116, 0.41027114816011584
], [0.4010838917701569],
[
0.3471948943768529, 0.29898884639695344, 0.25628787636022327,
0.21879111116443942, 0.18611512357614748, 0.1578293478118742,
0.13348490439314156, 0.1126365134135259, 0.09485799450183797,
0.07975229568782109, 0.06695715359259546, 0.05614746214037572,
0.04703529928793173, 0.03936839121806458, 0.03292761927501417,
0.027524017606943972, 0.022995578073929674,
0.019612988083479492, 0.017097927256941214
], [0.015582774896335588], [0.013952173100764704]
]
if int(__version__.split('.')[0]) >= 2:
self.assertEquals(json_response['stability'],
['S', 'N', 'U', 'N', 'S'])
for i, x_i in enumerate(json_response['curve_lc_x']):
self.assertAlmostEquals(x_i, results_x[i], delta=1e-6 * x_i)
for i, y_i in enumerate(
json_response['curve_lc_ys']['cyclin_cdk_p']['min']):
self.assertAlmostEquals(y_i,
results_y_min[i],
delta=1e-6 * y_i)
for i, y_i in enumerate(
json_response['curve_lc_ys']['cyclin_cdk_p']['max']):
self.assertAlmostEquals(y_i,
results_y_max[i],
delta=1e-6 * y_i)
for i, ys_i in enumerate(json_response['curve_ys']['cyclin_cdk']):
for ii, y_i in enumerate(ys_i):
self.assertAlmostEquals(y_i,
results_y[i][ii],
delta=1e-6 * y_i)