Add container apps as part of #739.

kive/container/ajax.py

@@ -9,8 +9,9 @@
 from rest_framework.decorators import action
 from rest_framework.response import Response
 
-from container.models import ContainerFamily, Container
-from container.serializers import ContainerFamilySerializer, ContainerSerializer
+from container.models import ContainerFamily, Container, ContainerApp
+from container.serializers import ContainerFamilySerializer, ContainerSerializer, \
+    ContainerAppSerializer
 from kive.ajax import CleanCreateModelMixin, RemovableModelViewSet, \
     SearchableModelMixin, IsDeveloperOrGrantedReadOnly, StandardPagination
 from metadata.models import AccessControl
@@ -141,3 +142,48 @@ def download(self, request, pk=None):
         finally:
             container.file.close()
         return response
+
+
+class ContainerAppViewSet(CleanCreateModelMixin,
+                          RemovableModelViewSet,
+                          SearchableModelMixin):
+    """ An app within a Singularity container.
+
+    Query parameters:
+
+    * is_granted - true For administrators, this limits the list to only include
+        records that the user has been explicitly granted access to, via their
+        parent containers. For other users, this has no effect.
+    * filters[n][key]=x&filters[n][val]=y - Apply different filters to the
+        search. n starts at 0 and increases by 1 for each added filter.
+        Some filters just have a key and ignore the val value. The possible
+        filters are listed below.
+    * filters[n][key]=container_id&filters[n][val]=match - parent container's
+        id equals the value
+    * filters[n][key]=smart&filters[n][val]=match - app name or description
+        contains the value (case insensitive)
+    * filters[n][key]=name&filters[n][val]=match - app name contains the
+        value (case insensitive)
+    * filters[n][key]=description&filters[n][val]=match - description contains
+        the value (case insensitive)
+    """
+    queryset = ContainerApp.objects.all()
+    serializer_class = ContainerAppSerializer
+    permission_classes = (permissions.IsAuthenticated, IsDeveloperOrGrantedReadOnly)
+    pagination_class = StandardPagination
+    filters = dict(
+        container_id=lambda queryset, value: queryset.filter(
+            container_id=value),
+        smart=lambda queryset, value: queryset.filter(
+            Q(name__icontains=value) |
+            Q(description__icontains=value)),
+        name=lambda queryset, value: queryset.filter(
+            name__icontains=value),
+        description=lambda queryset, value: queryset.filter(
+            description__icontains=value))
+
+    def filter_granted(self, queryset):
+        """ Apps don't have permissions, so filter by parent containers. """
+        granted_containers = Container.filter_by_user(self.request.user)
+
+        return queryset.filter(container_id__in=granted_containers)

kive/container/forms.py

@@ -1,6 +1,7 @@
 from django import forms
+from django.forms.widgets import TextInput
 
-from container.models import ContainerFamily, Container
+from container.models import ContainerFamily, Container, ContainerApp
 from metadata.forms import PermissionsForm
 
 
@@ -22,3 +23,23 @@ class ContainerUpdateForm(ContainerForm):
     def __init__(self, *args, **kwargs):
         super(ContainerUpdateForm, self).__init__(*args, **kwargs)
         self.fields.pop('file')
+
+
+class ContainerAppForm(forms.ModelForm):
+    inputs = forms.CharField(
+        widget=TextInput(attrs=dict(size=50)),
+        required=False,
+        help_text='A space-separated list of argument names. You can also use '
+                  'prefixes and suffixes for different kinds of arguments: '
+                  '--optional, multiple*, and --optional_multiple*.')
+    outputs = forms.CharField(
+        widget=TextInput(attrs=dict(size=50)),
+        required=False,
+        help_text='A space-separated list of argument names. You can also use '
+                  'prefixes and suffixes for different kinds of arguments: '
+                  '--optional, folder/, and --optional_folder/.')
+
+    class Meta(object):
+        model = ContainerApp
+        fields = ['name', 'description', 'inputs', 'outputs']
+        widgets = dict(description=forms.Textarea(attrs=dict(cols=50, rows=10)))

kive/container/migrations/0004_containerapp_containerargument.py

@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.15 on 2018-11-23 19:10
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('container', '0003_reverse_ordering'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='ContainerApp',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(blank=True, help_text=b'Leave blank for default', max_length=60)),
+                ('description', models.CharField(blank=True, max_length=1000, verbose_name=b'Description')),
+                ('container', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='apps', to='container.Container')),
+            ],
+            options={
+                'ordering': ('name',),
+            },
+        ),
+        migrations.CreateModel(
+            name='ContainerArgument',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=60)),
+                ('position', models.IntegerField(blank=True, help_text=b'Position in the arguments (gaps and duplicates are allowed). Leave position blank to pass as an option with --name.', null=True)),
+                ('type', models.CharField(choices=[(b'I', b'Input'), (b'O', b'Output')], max_length=1)),
+                ('allow_multiple', models.BooleanField(default=False, help_text=b'True for optional inputs that accept multiple datasets and outputs that just collect all files written to a directory')),
+                ('app', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='arguments', to='container.ContainerApp')),
+            ],
+        ),
+    ]

kive/container/models.py

@@ -161,6 +161,123 @@ def remove(self):
         remove_helper(removal_plan)
 
 
+class ContainerApp(models.Model):
+    container = models.ForeignKey(Container, related_name="apps")
+    name = models.CharField(max_length=maxlengths.MAX_NAME_LENGTH,
+                            help_text="Leave blank for default",
+                            blank=True)
+    description = models.CharField('Description',
+                                   blank=True,
+                                   max_length=maxlengths.MAX_DESCRIPTION_LENGTH)
+    arguments = None  # Filled in later from child table.
+    objects = None  # Filled in later by Django.
+
+    class Meta:
+        ordering = ('name',)
+
+    @property
+    def inputs(self):
+        return self._format_arguments(ContainerArgument.INPUT)
+
+    @property
+    def outputs(self):
+        return self._format_arguments(ContainerArgument.OUTPUT)
+
+    def _format_arguments(self, argument_type):
+        arguments = self.arguments.filter(type=argument_type)
+        optionals = [argument
+                     for argument in arguments
+                     if argument.position is None]
+        positionals = [argument
+                       for argument in arguments
+                       if argument.position is not None]
+        terms = [argument.formatted for argument in optionals]
+        if (argument_type == ContainerArgument.INPUT and
+                any(argument.allow_multiple for argument in optionals)):
+            terms.append('--')
+        terms.extend(argument.formatted for argument in positionals)
+        return ' '.join(terms)
+
+    def write_inputs(self, formatted):
+        self._write_arguments(ContainerArgument.INPUT, formatted)
+
+    def write_outputs(self, formatted):
+        self._write_arguments(ContainerArgument.OUTPUT, formatted)
+
+    def _write_arguments(self, argument_type, formatted):
+        self.arguments.filter(type=argument_type).delete()
+        expected_multiples = {ContainerArgument.INPUT: '*',
+                              ContainerArgument.OUTPUT: '/'}
+        for position, term in enumerate(formatted.split(), 1):
+            if term == '--':
+                continue
+            match = re.match(r'(--)?(\w+)([*/])?$', term)
+            if match is None:
+                raise ValueError('Invalid argument name: {}'.format(term))
+            if match.group(1):
+                position = None
+            if not match.group(3):
+                allow_multiple = False
+            elif match.group(3) == expected_multiples[argument_type]:
+                allow_multiple = True
+            else:
+                raise ValueError('Invalid argument name: {}'.format(term))
+            self.arguments.create(name=match.group(2),
+                                  position=position,
+                                  allow_multiple=allow_multiple,
+                                  type=argument_type)
+
+    def get_absolute_url(self):
+        return reverse('container_app_update', kwargs=dict(pk=self.pk))
+
+    @transaction.atomic
+    def build_removal_plan(self, removal_accumulator=None):
+        """ Make a manifest of objects to remove when removing this. """
+        removal_plan = removal_accumulator or empty_removal_plan()
+        assert self not in removal_plan["ContainerApps"]
+        removal_plan["ContainerApps"].add(self)
+
+        return removal_plan
+
+    @transaction.atomic
+    def remove(self):
+        removal_plan = self.build_removal_plan()
+        remove_helper(removal_plan)
+
+
+class ContainerArgument(models.Model):
+    INPUT = 'I'
+    OUTPUT = 'O'
+    TYPES = ((INPUT, 'Input'),
+             (OUTPUT, 'Output'))
+
+    app = models.ForeignKey(ContainerApp, related_name="arguments")
+    name = models.CharField(max_length=maxlengths.MAX_NAME_LENGTH)
+    position = models.IntegerField(
+        null=True,
+        blank=True,
+        help_text="Position in the arguments (gaps and duplicates are allowed). "
+                  "Leave position blank to pass as an option with --name.")
+    type = models.CharField(max_length=1, choices=TYPES)
+    allow_multiple = models.BooleanField(
+        default=False,
+        help_text="True for optional inputs that accept multiple datasets and "
+                  "outputs that just collect all files written to a directory")
+
+    def __repr__(self):
+        return 'ContainerArgument(name={!r})'.format(self.name)
+
+    @property
+    def formatted(self):
+        text = self.name
+        if self.position is None:
+            # noinspection PyTypeChecker
+            text = '--' + text
+        if self.allow_multiple:
+            text += '*' if self.type == ContainerArgument.INPUT else '/'
+        return text
+
+
 @receiver(models.signals.post_delete, sender=Container)
 def delete_container_file(instance, **_kwargs):
     if instance.file:

kive/container/serializers.py

@@ -1,7 +1,7 @@
 from rest_framework import serializers
 from rest_framework.fields import URLField
 
-from container.models import ContainerFamily, Container
+from container.models import ContainerFamily, Container, ContainerApp
 from kive.serializers import AccessControlSerializer
 
 
@@ -64,3 +64,31 @@ class Meta:
                   'users_allowed',
                   'groups_allowed',
                   'removal_plan')
+
+
+class ContainerAppSerializer(serializers.ModelSerializer):
+    absolute_url = URLField(source='get_absolute_url', read_only=True)
+    container = serializers.HyperlinkedRelatedField(
+        view_name='container-detail',
+        lookup_field='pk',
+        queryset=Container.objects.all())
+    removal_plan = serializers.HyperlinkedIdentityField(
+        view_name='containerapp-removal-plan')
+
+    class Meta:
+        model = ContainerApp
+        fields = ('id',
+                  'url',
+                  'absolute_url',
+                  'container',
+                  'name',
+                  'description',
+                  'inputs',
+                  'outputs',
+                  'removal_plan')
+
+    def save(self, **kwargs):
+        app = super(ContainerAppSerializer, self).save(**kwargs)
+        app.write_inputs(self.initial_data.get('inputs', ''))
+        app.write_outputs(self.initial_data.get('outputs', ''))
+        return app

kive/container/static/container/ContainerAppTable.js

@@ -0,0 +1,21 @@
+(function(permissions) {//dependent on PermissionsTable class
+    "use strict";
+    permissions.ContainerAppTable = function($table, is_user_admin, $navigation_links) {
+        permissions.PermissionsTable.call(this, $table, is_user_admin, $navigation_links);
+        this.list_url = "/api/containerapps/";
+        this.registerLinkColumn("Name", "", "name", "absolute_url");
+        this.registerColumn("Description", "description");
+        this.registerColumn("Inputs", "inputs");
+        this.registerColumn("Outputs", "outputs");
+    };
+    permissions.ContainerAppTable.prototype = Object.create(permissions.PermissionsTable.prototype);
+    permissions.ContainerAppTable.prototype.extractRows = function(response) {
+        var rows = response.results;
+        for(var i in rows) {
+            if (rows[i].name === '') {
+                rows[i].name = '[default]';
+            }
+        }
+        return rows;
+    };
+})(permissions);

kive/container/templates/container/container_form.html

@@ -8,7 +8,30 @@
     <script src="/static/portal/jquery-2.0.3.min.js"></script>
     <script src="/static/portal/noxss.js"></script>
     <script src="/static/portal/permissions.js"></script>
+    <script src="/static/portal/ajaxsearchfilter.js"></script>
     <script src="/static/portal/helptext.js"></script>
+    <script src="/static/container/ContainerAppTable.js"></script>
+    <script type="text/javascript">
+
+    $(function(){
+        var table = new permissions.ContainerAppTable(
+            $("#container_apps"),
+            {{ is_user_admin|lower }},
+            $(".navigation_links")
+        );
+        var asf = new AjaxSearchFilter(table, $("#asf"));
+
+        // This adds a filter for the current object.
+        table.filterSet.add("container_id", {{container.id}}, true).hide();
+
+        asf.reloadTable();
+    });
+    </script>
+{% endblock %}
+
+{% block stylesheets %}
+    <link rel="stylesheet" href="/static/portal/permissions.css"/>
+    <link rel="stylesheet" href="/static/portal/search.css"/>
 {% endblock %}
 
 {% block widget_media %}
@@ -58,4 +81,45 @@ <h2>Container</h2>
     <input type="submit" value="Submit" />
 </form>
 
+{% if object %}
+    <h3>Apps in the Container:</h3>
+    <a class="button" href="app_add">+&ensp;<span class="button-lbl">Create
+        a new app</span></a>
+
+    <div id="asf">
+        <form class="asf-form">
+            <div class="asf-main-search">
+                <div class="asf-active-filters"></div>
+                <input type="text" name="smart" class="asf-search-field">
+                <input type="button" class="advanced ctrl" value="Advanced">
+                <input type="submit" value="Filter" class="asf-search-button">
+            </div>
+        </form>
+        <form class="asf-advanced-form">
+            <input type="button" class="advanced ctrl" value="Advanced">
+            <h4>Advanced search</h4>
+            <div class="asf-field-container">
+                <label for="search-name">Name</label><input
+                    name="name"
+                    id="search-name"
+                    type="text"
+                    class="asf-search-fixed-field">
+            </div>
+            <div class="asf-field-container">
+                <label for="search-description">Description</label><input
+                    name="description"
+                    id="search-description"
+                    type="text"
+                    class="asf-search-fixed-field">
+            </div>
+            <input type="submit" value="Filter" class="asf-search-button">
+        </form>
+    </div>
+
+    <div class="navigation_links"></div>
+
+    <div class="dev_results">
+        <table id="container_apps"></table>
+    </div>
+{% endif %}
 {% endblock %}