Globus search integration

form_builder/templates/form_builder/CLIP_form.html

@@ -7,43 +7,20 @@
             <h1>eCLIP (CLIPper) Form Builder</h1>
             {{ form.as_p }} <!-- main form -->
         </div>
-
         <div class="container">
             <hr>
-            <h2>Add new sample (Full paths only)</h2>
+            <h2>Add multiple samples</h2>
             <div class="row">
-                <label for="experiment">Experiment name (alphanumeric or underscores only, no spaces)</label>
-                <div class="col"><input class="form-control" type="text" name="experiment" id="experiment" pattern="[a-zA-Z0-9_]+" list="experiment-select"></div>
-                <datalist name="experiment-select" id="experiment-select"> 
-                    {% for fastq in SEfastqs %}
-                    <option value="{{fastq.experiment}}">{{ fastq.experiment }}</option>
-                    {% endfor %}
-                </datalist>
-                <label for="sample">Sample name (alphanumeric or underscores only, no spaces)</label>
-                <div class="col"><input class="form-control" type="text" name="sample" id="sample" pattern="[a-zA-Z0-9_]+" list="sample-select"></div>
-                <datalist name="sample-select" id="sample-select"> 
-                    {% for fastq in SEfastqs %}
-                    <option value="{{fastq.sample}}">{{ fastq.sample }}</option>
-                    {% endfor %}
-                </datalist>
-                <label for="cells">Cells (alphanumeric or underscores only, no spaces)</label>
-                <div class="col"><input class="form-control" type="text" name="cells" id="cells" pattern="[a-zA-Z0-9_]+" list="cell-select"></div>
-                <datalist name="cell-select" id="cell-select"> 
-                    {% for fastq in SEfastqs %}
-                    <option value="{{fastq.cells}}">{{ fastq.cells }}</option>
-                    {% endfor %}
-                </datalist>
+                <label for="experiment">Use the Globus file browser to select one or more files.</label>
+                <button type="submit" name="experiment" class="info"><a href={{ globus_url }}>Globus</a></button>
             </div>
             <div class="row">
-                {% include 'form_builder/fastq_submit.html' %}
-            </div>
-            <div class="row my-4">
-                <div class="col-md">
-                    <button type="submit" name="newItem" value="newItem">Add sample</button>
-                </div>
+                <ul>Selected Fastqs:</ul>
+                {% for fi in files %}
+                    <li>{{fi}}</li>
+                {% endfor %}
             </div>
         </div>
-
         <div class="container my-4">
             <hr>
             {% include 'form_builder/fastq_display.html' %}

form_builder/templates/form_builder/index.html

@@ -17,11 +17,12 @@ <h2>Skipper</h2>
         <p><a class="btn btn-secondary" href="/skipper" role="button">Build forms &raquo;</a></p>
     </div>-->
     <div class="col-md-4">
-        <h2>eCLIP (CLIPper)</h2>
+        <h2>eCLIP (CLIPper)!</h2>
         <p>A pipeline designed to identify genomic locations (peaks) of RNA-bound proteins.</p>
         <p><a href="https://github.com/yeolab/eclip">Github</a></p>
         <p><a class="btn btn-secondary" href="/clipper" role="button">Build Form &raquo;</a></p>
     </div>
+
     <!--<div class="col-md-4">
         <h2>rnaseqSE form</h2>
         <p>Coming soon...</p>

form_builder/templates/form_builder/receive-data.html

@@ -0,0 +1,7 @@
+
+<div class="row">
+  <div class="col">
+    <h2 class="text-center mt-3 mb-5">wat</h2>
+  </div>
+</div>
+

form_builder/urls.py

@@ -15,4 +15,5 @@
     #path('skipper/', views.SKIPPER_form, name='SKIPPER_form'),
     #path('rnaseqSE/', views.rnaseqSE_form, name='rnaseqSE_form'),
     #path('rnaseqPE/', views.rnaseqPE_form, name='rnaseqPE_form'),
+    path('receive-data/', views.receive_data, name='receive_data'),
 ]

form_builder/views.py

@@ -1,28 +1,46 @@
 # imports
+from django.contrib.auth import login
 from django.contrib.auth.decorators import login_required
 from mysite import settings
 from .models import SingleEndFastq
 from django.shortcuts import render
 from .forms import CLIPManifestForm#, SkipperConfigManifestForm
 from .utils import *
-
+from django.views.decorators.csrf import csrf_exempt
 import yaml
 from django.http import HttpResponse
+import os
 
-
+@csrf_exempt
 @login_required
 def CLIP_form(request):
-    SEfastqs = SingleEndFastq.objects.filter(submitter=request.user)
+    files = []
+    try:
+        SEfastqs = SingleEndFastq.objects.filter(submitter=request.user)
+    except Exception as e:
+        print(e)
+        SEfastqs = []
+
     if request.method == 'POST':
         form = CLIPManifestForm(request.POST)
         data = make_CLIP_form(form, request)
         if data:
             return data
     else:
+        if request.GET.get('endpoint'):
+            base_url = '/projects/ps-yeolab5/seqdata' + request.GET.get('path')
+            for key in request.GET.keys():
+                if key.startswith('file'):
+                    files.append(os.path.join(base_url, request.GET.get(key)))
         form = CLIPManifestForm()
 
-    return render(request, 'form_builder/CLIP_form.html', {'form': form,
-                                                           'SEfastqs': SEfastqs})
+    context = {
+        'form': form,
+        'SEfastqs': SEfastqs,
+        'files': files,
+        'globus_url': "https://app.globus.org/file-manager?method=GET&origin_id=d9358457-3f23-4b35-bbae-68d2f4190545&origin_path=%2F&action=http://localhost:8000/clipper/"
+    }
+    return render(request, 'form_builder/CLIP_form.html', context=context)
 
 '''
 @login_required
@@ -142,3 +160,11 @@ def index_view(request):
     context = {'LOGIN_URL': settings.LOGIN_URL}
     template = 'form_builder/index.html'
     return render(request, template, context)
+
+
+@csrf_exempt
+def receive_data(request):
+    print('post', request.POST)
+
+    context = {}
+    return render(request, 'form_builder/receive-data.html', context)

globus_portal_framework/__init__.py

@@ -47,5 +47,3 @@
     'get_helper_page_url', 'is_file',
 
 ]
-
-default_app_config = 'globus_portal_framework.apps.GlobusPortalFrameworkConfig'

globus_portal_framework/auth.py

@@ -3,35 +3,41 @@
     https://docs.globus.org/api/auth
 """
 import logging
+import urllib
 from social_core.backends.globus import (
     GlobusOpenIdConnect as GlobusOpenIdConnectBase
 )
 from social_core.exceptions import AuthForbidden
-from globus_portal_framework.gclients import (
-    get_service_url, GROUPS_SCOPE, GLOBUS_GROUPS_V2_MY_GROUPS
-)
+import globus_sdk
+from globus_sdk.scopes import GroupsScopes
+from globus_sdk import config as globus_sdk_config
 
 log = logging.getLogger(__name__)
 
 
 class GlobusOpenIdConnect(GlobusOpenIdConnectBase):
-    OIDC_ENDPOINT = get_service_url('auth')
+
+    OIDC_ENDPOINT = globus_sdk_config.get_service_url('auth')
     GLOBUS_APP_URL = 'https://app.globus.org'
     # Fixed by https://github.com/python-social-auth/social-core/pull/577
     JWT_ALGORITHMS = ['RS512']
 
     def introspect_token(self, auth_token):
+        url = urllib.parse.urljoin(self.OIDC_ENDPOINT,
+                                   'v2/oauth2/token/introspect')
         return self.get_json(
-            self.OIDC_ENDPOINT + '/v2/oauth2/token/introspect',
+            url,
             method='POST',
             data={"token": auth_token,
                   "include": "session_info,identities_set"},
             auth=self.get_key_and_secret()
         )
 
     def get_globus_identities(self, auth_token, identities_set):
+        url = urllib.parse.urljoin(self.OIDC_ENDPOINT,
+                                   '/v2/api/identities')
         return self.get_json(
-            self.OIDC_ENDPOINT + '/v2/api/identities',
+            url,
             method='GET',
             headers={'Authorization': 'Bearer ' + auth_token},
             params={'ids': ','.join(identities_set),
@@ -128,25 +134,22 @@ def get_user_globus_groups(self, other_tokens):
         groups a user belongs. The API is PUBLIC, and no special allowlists
         are needed to use it.
         """
+        groups_scopes = (GroupsScopes.all,
+                         GroupsScopes.view_my_groups_and_memberships)
         groups_token = None
         for item in other_tokens:
-            if item.get('scope') == GROUPS_SCOPE:
+            if item.get('scope') in groups_scopes:
                 groups_token = item.get('access_token')
 
         if groups_token is None:
             raise ValueError(
-                'You must set the {} scope on {} in order to set an allowed '
-                'group'.format(GROUPS_SCOPE,
-                               'settings.SOCIAL_AUTH_GLOBUS_SCOPE')
+                f'You must set one of {groups_scopes} scopes on '
+                'settings.SOCIAL_AUTH_GLOBUS_SCOPE in order to set an allowed'
             )
 
-        # Get the allowed group
-        return self.get_json(
-            '{}{}'.format(get_service_url('groups'),
-                          GLOBUS_GROUPS_V2_MY_GROUPS),
-            method='GET',
-            headers={'Authorization': 'Bearer ' + groups_token}
-        )
+        authorizer = globus_sdk.AccessTokenAuthorizer(groups_token)
+        groups_client = globus_sdk.GroupsClient(authorizer=authorizer)
+        return groups_client.get_user_groups()
 
     def auth_params(self, state=None):
         params = super(GlobusOpenIdConnect, self).auth_params(state)

globus_portal_framework/checks.py

@@ -1,58 +1,17 @@
 import logging
-from django.core.checks import Error, Warning, register
+import os
+from django.core.checks import Error, Warning, Info, register
 from django.conf import settings
 import globus_sdk
 
-from globus_portal_framework.constants import FILTER_TYPES
-from globus_portal_framework.gclients import get_globus_environment
+from globus_portal_framework.constants import (
+    FILTER_TYPES, DEFAULT_RESULT_FORMAT_VERSION
+)
 
 log = logging.getLogger(__name__)
 log.debug('Debugging is active.')
 
 
-@register()
-def check_old_v2_config(app_configs, **kwargs):
-    warnings = []
-    title_template = 'Version 0.3.x Update: "{}" is no longer used'
-    OLD_SETTINGS = {
-        'ENTRY_SERVICE_VARS':
-            {'hint': 'These are now defined in SEARCH_INDEXES under "fields"'},
-        'SEARCH_INDEX':
-            {'hint': 'This is now defined in SEARCH_INDEXES as "uuid"'},
-        'SEARCH_SCHEMA':
-            {'hint': 'The JSON in the search schema file have been moved to '
-                     'SEARCH_INDEXES, see "fields" and "facets"'},
-        'SEARCH_MAPPER':
-            {'hint': 'Please replace this with a function in SEARCH_INDEXES '
-                     '"fields" for your index. See the README for examples'},
-        'SEARCH_ENTRY_FIELD_PATH':
-            {'hint': 'The framework no longer assumes all data resides under '
-                     'this field, and it has now been removed.'}
-    }
-    for name, warn_opts in OLD_SETTINGS.items():
-        if getattr(settings, name, None):
-            warnings.append(Warning(title_template.format(name),
-                            hint=warn_opts.get('hint'),
-                            obj=settings)
-                            )
-    return warnings
-
-
-@register()
-def check_old_apps(app_configs, **kwargs):
-    installed_apps = getattr(settings, 'INSTALLED_APPS', [])
-    old_apps = ['globus_portal_framework.search',
-                'globus_portal_framework.transfer']
-    if not installed_apps:
-        return []
-    warn = '{} is now built in, and no longer needs to be explicitly added'
-    hint = 'Remove {} from settings.INSTALLED_APPS'
-    return [Warning(warn.format(oa),
-                    hint=hint.format(oa),
-                    obj=settings)
-            for oa in old_apps if oa in installed_apps]
-
-
 @register()
 def check_search_indexes(app_configs, **kwargs):
     errors = []
@@ -66,23 +25,23 @@ def check_search_indexes(app_configs, **kwargs):
                 id = r.data['id']
             except globus_sdk.SearchAPIError:
                 pass
+            hint = f'Search UUID for "{index_name}" is "{id}".' if id else None
             errors.append(Error(
-                'Could not find "uuid" for settings.SEARCH_INDEXES.{}'
-                ''.format(index_name),
+                'Could not find "uuid" for '
+                f'settings.SEARCH_INDEXES.{index_name}',
                 obj=settings,
-                hint=('Search UUID for "{}" is "{}".'.format(index_name, id)
-                      if id else None),
+                hint=hint,
                 id='globus_portal_framework.settings.E001'
                 )
             )
-        if idata.get('result_format_version') == '2019-08-27':
+        rf_version = idata.get('result_format_version')
+        if rf_version and rf_version != DEFAULT_RESULT_FORMAT_VERSION:
             errors.append(Warning(
                 'Globus Portal Framework does not support '
-                'result_format_version=="2019-08-27"',
+                f'result_format_version=="{rf_version}"',
                 obj=settings,
-                hint=('Suggested you unset '
-                      'settings.SEARCH_INDEXES.{}.result_format_version'
-                      ''.format(index_name)),
+                hint=('Suggested you unset settings.SEARCH_INDEXES.'
+                      f'{index_name}.result_format_version'),
                 id='globus_portal_framework.settings.E002'
                 )
             )
@@ -92,17 +51,16 @@ def check_search_indexes(app_configs, **kwargs):
                 Warning('SEARCH_INDEXES.{}.filter_match is invalid.'
                         ''.format(index_name),
                         obj=settings,
-                        hint='Must be one of {}'.format(
-                            tuple(FILTER_TYPES.keys()))
+                        hint=f'Must be one of {tuple(FILTER_TYPES.keys())}'
                         ))
     return errors
 
 
 @register()
 def check_globus_env(app_configs, **kwargs):
-    env = get_globus_environment()
-    # 'default' is used in Globus SDK v2, 'production' in v3
-    if env not in ['default', 'production']:
-        return [Warning('Environment set to "{}", unset with '
-                        '"unset GLOBUS_SDK_ENVIRONMENT"'.format(env))]
+    env = os.getenv('GLOBUS_SDK_ENVIRONMENT')
+    if env and env != 'production':
+        return [Info(f'GLOBUS_SDK_ENVIRONMENT set to "{env}".',
+                     hint='Non-production services may contain experimental '
+                          'features.')]
     return []

globus_portal_framework/constants.py

@@ -62,7 +62,7 @@
     'missing'
 ]
 # https://docs.globus.org/api/search/search/#request_documents
-DEFAULT_RESULT_FORMAT_VERSION = '2017-09-01'
+DEFAULT_RESULT_FORMAT_VERSION = '2019-08-27'
 
 BASE_TEMPLATES = 'globus-portal-framework/v2/'