8 | ![](\"test.php_files/aveskulov-large.jpg\")
");
7 | });
8 | });
--------------------------------------------------------------------------------
/docs/dev_doc/api_user_doc.rst:
--------------------------------------------------------------------------------
1 | .. _api-dev-guide:
2 |
3 | ==================
4 | API Dev user Guide
5 | ==================
6 |
7 |
8 | This documentation intends to help front end developers to integrate WAVES-core form api service.
9 |
10 | ...
--------------------------------------------------------------------------------
/docs/modules/source.rst:
--------------------------------------------------------------------------------
1 | Source Documentation
2 | ====================
3 |
4 | .. toctree::
5 | :maxdepth: 2
6 |
7 | models/services
8 | models/jobs
9 | models/runners
10 | models/base
11 | managers/managers
12 | adaptors/adaptors
13 |
14 |
15 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/_online_execution.html:
--------------------------------------------------------------------------------
1 | {% if available_for_submission %}
2 |
3 | {% if label %}{{ label }}{% else %}Online execution{% endif %}
4 | {% endif %}
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/materialize/inc.css.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_css.html' %}
2 | {% block css %}
3 |
4 | {{ block.super }}
5 | {% endblock %}
6 |
--------------------------------------------------------------------------------
/CONTRIBUTING.md:
--------------------------------------------------------------------------------
1 | Contributing
2 | ============
3 |
4 | You can contribute to WAVES project with following repositories:
5 |
6 | - Git source code: https://github.com/lirmm/waves-core
7 | - Issue tracker: https://github.com/lirmm/waves-core/issues
8 | - Mailing list: waves-webapp@googlegroups.com
9 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/bootstrap/inc.js.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_js.html' %}
2 | {% block js %}
3 |
4 |
5 | {{ block.super }}
6 | {% endblock %}
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/bootstrap3/inc.js.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_js.html' %}
2 | {% block js %}
3 |
4 | {{ block.super }}
5 | {% endblock %}
6 |
7 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/materialize/inc.js.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_js.html' %}
2 | {% block js %}
3 |
4 | {{ block.super }}
5 | {% endblock %}
6 |
7 |
--------------------------------------------------------------------------------
/tests/data/sample/services/hello_world.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | echo "Working dir: $(pwd)"
3 | dir=$(pwd)
4 | sleep 5
5 | echo "Hello world" > ${dir}/hello_world_output.txt
6 | sleep 5
7 | echo "Follow " $1 >> ${dir}/hello_world_output.txt
8 | sleep 5
9 | echo "Last" $2 >> ${dir}/hello_world_output.txt
10 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/bootstrap4/inc.css.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_css.html' %}
2 | {% block css %}
3 |
4 | {{ block.super }}
5 | {% endblock %}
6 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/bootstrap/inc.css.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_css.html' %}
2 | {% block css %}
3 |
4 | {{ block.super }}
5 | {% endblock %}
6 |
7 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/forms/bootstrap3/inc.css.html:
--------------------------------------------------------------------------------
1 | {% extends 'waves/services/forms/base_inc_css.html' %}
2 | {% block css %}
3 |
4 | {{ block.super }}
5 | {% endblock %}
6 |
7 |
--------------------------------------------------------------------------------
/MANIFEST.in:
--------------------------------------------------------------------------------
1 | include LICENSE.md
2 | include README.md
3 | include requirements.txt
4 | recursive-include waves/wcore/static *
5 | recursive-include waves/wcore/templates *
6 | recursive-include waves/front/templates *
7 | recursive-include docs *
8 | recursive-exclude waves_core *
9 | # recursive-exclude waves/wcore/migrations *.
--------------------------------------------------------------------------------
/waves/wcore/static/waves/css/forms.css:
--------------------------------------------------------------------------------
1 | .dis_dep_parameter {
2 | display:block;
3 | }
4 |
5 | .hid_dep_parameter {
6 | display: none;
7 | }
8 |
9 | #panel-form-service{
10 | padding-top: 2%;
11 | padding-left: 7%;
12 | }
13 |
14 | .copypaste > div.form-group > div.controls {
15 | width:100%;
16 | }
17 |
18 |
--------------------------------------------------------------------------------
/waves/wcore/api/v1/serializers/__init__.py:
--------------------------------------------------------------------------------
1 | """ WAVES API serializers package """
2 | from waves.wcore.api.v1.serializers.jobs import JobHistorySerializer, JobInputSerializer, JobSerializer, JobOutputSerializer
3 | from waves.wcore.api.v1.serializers.services import ServiceSubmissionSerializer, ServiceSerializer, ServiceFormSerializer
4 |
5 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/emails/job_admin_error.tpl:
--------------------------------------------------------------------------------
1 | -----------------------------------------------------------------
2 | [ADMIN-NOTIFICATION] - Job '{{ job.service }}' - job failed
3 | -----------------------------------------------------------------
4 |
5 | Sorry but job "{{ job.title }}" execution failed.
6 |
7 | {{ job.link }}
8 |
9 |
--------------------------------------------------------------------------------
/waves/wcore/templates/waves/services/_service_head.html:
--------------------------------------------------------------------------------
1 | Online since {{ service.created }} / last update {{ service.updated }}
5 |
8 | 
');
12 | $('#modal_alert').modal('toggle');
13 | $.getJSON($(this).attr('href'), function (data) {
14 | $('#modal_alert .modal-content .modal-body').html(data['connection_result'])
15 | })
16 | });
17 |
18 | var $loading = $('#loading').hide();
19 | $(document)
20 | .ajaxStart(function () {
21 | $loading.show();
22 | })
23 | .ajaxStop(function () {
24 | $loading.hide();
25 | });
26 | });
27 |
28 | })(jQuery || django.jQuery);
29 |
--------------------------------------------------------------------------------
/waves/authentication/views.py:
--------------------------------------------------------------------------------
1 | from __future__ import unicode_literals
2 |
3 | from rest_framework import parsers, renderers
4 | from rest_framework.response import Response
5 | from rest_framework.views import APIView
6 |
7 | from .models import WavesApiUser
8 | from .serializers import WavesApiUserSerializer
9 |
10 |
11 | class ObtainAuthToken(APIView):
12 | throttle_classes = ()
13 | permission_classes = ()
14 | parser_classes = (parsers.FormParser, parsers.MultiPartParser, parsers.JSONParser,)
15 | renderer_classes = (renderers.JSONRenderer,)
16 | serializer_class = WavesApiUserSerializer
17 |
18 | def post(self, request, *args, **kwargs):
19 | serializer = self.serializer_class(data=request.data)
20 | serializer.is_valid(raise_exception=True)
21 | user = serializer.validated_data['user']
22 | token, created = WavesApiUser.objects.get_or_create(user=user)
23 | return Response({'auth_api_key': token.key})
24 |
25 |
26 | obtain_auth_token = ObtainAuthToken.as_view()
27 |
--------------------------------------------------------------------------------
/waves/wcore/urls.py:
--------------------------------------------------------------------------------
1 | from __future__ import unicode_literals
2 |
3 | from django.conf.urls import url
4 | from django.contrib.auth.decorators import login_required
5 |
6 | from waves.wcore.views.jobs import JobInputView, JobOutputView, JobSubmissionView, JobView, JobListView
7 | from waves.wcore.views.services import ServiceListView, ServiceDetailView
8 |
9 |
10 | urlpatterns = [
11 | url(r'^services/$', ServiceListView.as_view(), name='services_list'),
12 | url(r'^service/(?P{{ file_content }}
15 | Availability : {{ sub.submission.get_availability_display }}22 | {% endif %} 23 |
Availability : {{ sub.submission.get_availability_display }}22 | {% endif %} 23 |
Availability : {{ sub.submission.get_availability_display }}22 | {% endif %} 23 |
Availability : {{ sub.submission.get_availability_display }}23 | {% endif %} 24 |
 }})
14 |  }})
20 |  }})
26 |  }})
32 | Availability : {{ sub.submission.get_availability_display }}25 | {% endif %} 26 |
');
31 | $('#popup_modal_content').load($(this).attr('href'), function () {
32 | console.log('loaded')
33 | });
34 | });
35 | $('#popup_modal').on('toggle', function () {
36 | console.log('show raised');
37 | $(this).find('.modal-body').css({
38 | 'max-height': '100%'
39 | });
40 | });
41 | })
42 | })(jQuery || django.jQuery);
--------------------------------------------------------------------------------
/tests/data/sample/fast_me/fastme_matrix.txt:
--------------------------------------------------------------------------------
1 | 9
2 | Aurora 0.0 0.1 0.13 0.12 0.57 0.22 0.86 0.89 0.97
3 | Boylii 0.1 0.0 0.7 0.7 0.5 0.9 0.65 0.67 0.72
4 | Cascadae 0.13 0.7 0.0 0.7 0.4 0.11 0.54 0.66 0.79
5 | Muscosa 0.12 0.7 0.7 0.0 0.45 0.15 0.48 0.49 0.67
6 | Temporaria 0.57 0.5 0.4 0.45 0.0 0.48 0.85 0.83 1.07
7 | Pretiosa 0.22 0.9 0.11 0.15 0.48 0.0 0.54 0.55 0.6
8 | Catesbaiana 0.86 0.65 0.54 0.48 0.85 0.54 0.0 0.54 0.59
9 | Pipiens 0.89 0.67 0.66 0.49 0.83 0.55 0.54 0.0 0.48
10 | Tarahumarae 0.97 0.72 0.79 0.67 1.07 0.60 0.59 0.48 0.0
11 |
12 |
13 | 9
14 | Aurora 0.0 0.11 0.13 0.1 0.57 0.25 0.86 0.89 0.9
15 | Boylii 0.11 0.0 0.8 0.7 0.52 0.6 0.65 0.67 0.77
16 | Cascadae 0.13 0.8 0.0 0.7 0.42 0.11 0.52 0.66 0.80
17 | Muscosa 0.1 0.7 0.7 0.0 0.45 0.15 0.48 0.49 0.67
18 | Temporaria 0.57 0.52 0.42 0.45 0.0 0.45 0.85 0.83 1.07
19 | Pretiosa 0.25 0.6 0.11 0.15 0.45 0.0 0.54 0.57 0.6
20 | Catesbaiana 0.86 0.65 0.52 0.48 0.85 0.54 0.0 0.54 0.53
21 | Pipiens 0.89 0.67 0.66 0.49 0.83 0.57 0.54 0.0 0.46
22 | Tarahumarae 0.9 0.77 0.8 0.67 1.07 0.6 0.53 0.46 0.0
23 |
24 | 9
25 | Aurora 0.0 0.10 0.15 0.12 0.59 0.22 0.86 0.9 0.97
26 | Boylii 0.1 0.0 0.7 0.6 0.5 0.9 0.65 0.67 0.72
27 | Cascadae 0.15 0.7 0.0 0.7 0.4 0.11 0.54 0.66 0.79
28 | Muscosa 0.12 0.6 0.7 0.0 0.45 0.15 0.48 0.46 0.67
29 | Temporaria 0.59 0.5 0.4 0.45 0.0 0.47 0.85 0.83 1.03
30 | Pretiosa 0.22 0.9 0.11 0.15 0.47 0.0 0.54 0.55 0.6
31 | Catesbaiana 0.86 0.65 0.54 0.48 0.85 0.54 0.0 0.54 0.59
32 | Pipiens 0.90 0.67 0.66 0.46 0.83 0.55 0.54 0.0 0.48
33 | Tarahumarae 0.97 0.72 0.79 0.67 1.03 0.6 0.59 0.48 0.0
34 |
--------------------------------------------------------------------------------
/waves/wcore/admin/views/job_tool.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | """ Job tool WAVES admin dedicated views """
3 | from __future__ import unicode_literals
4 |
5 | from django.views.generic import View
6 | from django.shortcuts import get_object_or_404
7 | from django.shortcuts import redirect
8 | from django.core.urlresolvers import reverse
9 | from django.contrib import messages
10 | from waves.wcore.exceptions import WavesException
11 | from waves.wcore.models import Job
12 | from waves.wcore.adaptors.const import JobStatus
13 |
14 |
15 | class JobCancelView(View):
16 | """ View after cancel a job, if possible """
17 |
18 | def get(self, request):
19 | """ Try to cancel specified job (in kwargs), redirect to current job page """
20 | try:
21 | job = get_object_or_404(Job, id=self.kwargs['job_id'])
22 | runner = job.adaptor
23 | if runner is not None:
24 | runner.cancel_job(job)
25 | else:
26 | job.status = JobStatus.JOB_CANCELLED
27 | job.save()
28 | messages.add_message(request, level=messages.SUCCESS, message="Job cancelled")
29 | except WavesException as e:
30 | messages.add_message(request, level=messages.ERROR, message=e.message)
31 | return redirect(reverse('admin:wcore_job_change', args=[self.kwargs['job_id']]))
32 |
33 |
34 | class JobRerunView(View):
35 | def get(self, request):
36 | job = get_object_or_404(Job, id=self.kwargs['job_id'])
37 | if job.allow_rerun:
38 | try:
39 | job.re_run()
40 | messages.success(request, message="Job '%s' successfully marked for re-run" % job.title)
41 | except WavesException as exc:
42 | messages.error(request, message="Error occured %s " % exc.message)
43 | else:
44 | messages.error(request, message="You can't rerun this job")
45 | return redirect(reverse('admin:wcore_job_changelist'))
46 |
--------------------------------------------------------------------------------
/tests/data/sample/mafft/aln.fasta:
--------------------------------------------------------------------------------
1 | >TestSequence1
2 | ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY
3 | YVKQ--YKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER
4 | AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYV---QD
5 | SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL
6 | GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQ--
7 | KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR
8 | >TestSequence2
9 | ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY
10 | YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER
11 | AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD
12 | SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYAEAKDVFL
13 | GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPQ--
14 | NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGTKCCSLAEGER
15 | >TestSequence3
16 | ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY
17 | YANK--YNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER
18 | ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD
19 | TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQEAKDAFL
20 | GSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQ--
21 | NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER
22 | >TestSequence4
23 | ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
24 | FAKR--YKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER
25 | AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD
26 | SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYAEAKDVFL
27 | GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL
28 | NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR
29 | >TestSequence5
30 | ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY
31 | YAEE--YKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER
32 | AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD
33 | SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQEAKDVFL
34 | GTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPH--
35 | NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER
--------------------------------------------------------------------------------
/waves/wcore/static/waves/admin/js/admin.js:
--------------------------------------------------------------------------------
1 | /**
2 | * Created by Marc Chakiachvili on 23/09/16.
3 | * Standard JQuery library to attache events to Django BO
4 | */
5 | (function ($) {
6 | $(document).ready(function () {
7 | $('#popup_modal').on('shown.bs.modal', function () {
8 | $(this).find('.modal-dialog').css({
9 | width: 'auto',
10 | height: 'auto',
11 | 'max-height': '80%'
12 | });
13 | });
14 |
15 | $('.js-popup-link').click(function (e) {
16 | e.preventDefault();
17 | // language=JQuery-CSS
18 | var modalContent = $('#popup_modal_content');
19 | console.log('Js-pop-up-modal called ' + $('#popup_modal'));
20 | if ($(this).attr('js-modal-title') !== null) {
21 | modalContent.find('.modal-header').html("
28 | Created
29 | by: {{ service.created_by }}
30 | Current Status: {{ service.get_status_display }}
31 |
33 | {{ service.short_description|default:service.description|truncatechars:200 }}
34 |
35 | Released {{ service.created }}
36 | Last update {{ service.updated }}
37 |