Swap deprecated method out. (#2566)

* Swap deprecated method out. * Remove solr_igv dependencies. (#2570) * Remove solr_igv dependencies. * Remove visualization_manager. * Upgrade django storage. (#2571) * Upgrade django storage. * Remove post-css library, unused. (#2574) * Update user/file facet/columns per user request. (#2577) * Remove post-css library, unused. * Update user/file facet/columns per user request. * Remove typo , * Fix typo, double quotes. * Remove space. * Add cell_type to facets. * Fix unit test. * Add missing facets. * Fix cypress test. * Revert to 1.6.0 due to django 1.9 support.
refinery-platform · Feb 9, 2018 · ca22e4c · ca22e4c
1 parent 6801aa0
commit ca22e4c
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Showing 19 changed files with 12 additions and 815 deletions.
diff --git a/.isort.cfg b/.isort.cfg
@@ -21,7 +21,6 @@ known_first_party =
     selenium_testing,
     tool_manager,
     user_files_manager,
-    visualization_manager,
     workflow_manager
 
 skip_glob = **/migrations/*
@@ -31,4 +30,4 @@ skip_glob = **/migrations/*
 #import_heading_django = 'django'
 #import_heading_thirdpary = 'thirdparty'
 #import_heading_firstparty = 'firstparty'
-#import_heading_localfolder = 'localfolder'
+#import_heading_localfolder = 'localfolder'
diff --git a/deployment/aws-config/config.yaml.template b/deployment/aws-config/config.yaml.template
@@ -64,7 +64,7 @@ REFINERY_GOOGLE_ANALYTICS_ID: ""
 
 REFINERY_URL_SCHEME: "http"
 
-USER_FILES_COLUMNS: "filename,organism,technology,antibody,date,genotype,experimenter"
+USER_FILES_COLUMNS: "sample_name,local_path,filetype,organism,technology,genotype,cell_type,antibody,experimenter,date_submitted"
 
 # == Rarely changed ==
 

diff --git a/refinery/analysis_manager/utils.py b/refinery/analysis_manager/utils.py
@@ -1,17 +1,13 @@
 import json
 import logging
 import os
-import re
 import uuid
 
 from django.conf import settings
 from django.contrib.auth.models import User
-from django.http import HttpResponseServerError
 from django.utils import timezone
 
 import jsonschema
-import requests
-from requests.packages.urllib3.exceptions import HTTPError
 
 from core.models import Analysis, Study, Workflow, WorkflowDataInputMap
 from core.utils import get_aware_local_time
@@ -102,84 +98,6 @@ def fetch_objects_required_for_analysis(validated_analysis_config):
     }
 
 
-def get_solr_results(query, facets=False, jsonp=False, annotation=False,
-                     only_uuids=False, selected_mode=True,
-                     selected_nodes=None):
-    """Helper function for taking solr request url.
-    Removes facet requests, converts to json, from input solr query
-    :param query: solr http query string
-    :type query: string
-    :param facets: Removes facet query from solr query string
-    :type facets: boolean
-    :param jsonp: Removes JSONP query from solr query string
-    :type jsonp: boolean
-    :param only_uuids: Returns list of file_uuids from all solr results
-    :type only_uuids: boolean
-    :param selected_mode: UI selection mode (blacklist or whitelist)
-    :type selected_mode: boolean
-    :param selected_nodes: List of UUIDS to remove from the solr query
-    :type selected_nodes: array
-    :returns: dictionary of current solr results
-    """
-    if not facets:
-        # replacing facets w/ false
-        query = query.replace('facet=true', 'facet=false')
-    if not jsonp:
-        # ensuring json not jsonp response
-        query = query.replace('&json.wrf=?', '')
-    if annotation:
-        # changing annotation
-        query = query.replace('is_annotation:false', 'is_annotation:true')
-    # Checks for limit on solr query
-    # replaces i.e. '&rows=20' to '&rows=10000'
-    m_obj = re.search(r"&rows=(\d+)", query)
-    if m_obj:
-        # TODO: replace 10000 with settings parameter for max solr results
-        replace_rows_str = '&rows=' + str(10000)
-        query = query.replace(m_obj.group(), replace_rows_str)
-
-    try:
-        # opening solr query results
-        results = requests.get(query, stream=True)
-        results.raise_for_status()
-    except HTTPError as e:
-        logger.error(e)
-        return HttpResponseServerError(e)
-
-    # converting results into json for python
-    results = json.loads(results.content)
-
-    # IF list of nodes to remove from query exists
-    if selected_nodes:
-        # need to iterate over list backwards to properly delete from a list
-        for i in xrange(len(results["response"]["docs"]) - 1, -1, -1):
-            node = results["response"]["docs"][i]
-
-            # blacklist mode (remove uuid's from solr query)
-            if selected_mode:
-                if 'uuid' in node:
-                    # if the current node should be removed from the results
-                    if node['uuid'] in selected_nodes:
-                        del results["response"]["docs"][i]
-                        # num_found -= 1
-            # whitelist mode (add's uuids from solr query)
-            else:
-                if 'uuid' in node:
-                    # if the current node should be removed from the results
-                    if node['uuid'] not in selected_nodes:
-                        del results["response"]["docs"][i]
-                        # num_found += 1
-    # Will return only list of file_uuids
-    if only_uuids:
-        ret_file_uuids = []
-        solr_results = results["response"]["docs"]
-        for res in solr_results:
-            ret_file_uuids.append(res["uuid"])
-        return ret_file_uuids
-
-    return results
-
-
 def validate_analysis_config(analysis_config):
     """
     Validate incoming Analysis Configurations

diff --git a/refinery/annotation_server/management/commands/create_taxonomy.py b/refinery/annotation_server/management/commands/create_taxonomy.py
@@ -116,5 +116,5 @@ def handle(self, *args, **options):
                     taxon.save()
                     sys.stdout.write("%s created." % taxon)
                 except IntegrityError:
-                    transaction.rollback_unless_managed()
+                    transaction.rollback()
                     sys.stdout.write("Duplicate Value %s" % taxon)
diff --git a/refinery/config/config.json.erb b/refinery/config/config.json.erb
@@ -130,6 +130,6 @@
   "TOKEN_DURATION": 3,
   "USE_I18N": true,
   "USE_L10N": true,
-  "USER_FILES_COLUMNS": "filename,organism,technology,antibody,date,genotype,experimenter",
-  "USER_FILES_FACETS": "organism,technology,antibody,genotype,experimenter"
+  "USER_FILES_COLUMNS": "sample_name,local_path,filetype,organism,technology,genotype,cell_type,antibody,experimenter,date_submitted",
+  "USER_FILES_FACETS": "filetype,organism,technology,genotype,cell_type,antibody,experimenter"
 }
diff --git a/refinery/config/settings/base.py b/refinery/config/settings/base.py
@@ -207,7 +207,6 @@ def get_setting(name, settings=local_settings, default=None):
     'workflow_manager',
     'file_store',
     'file_server',
-    'visualization_manager',
     'annotation_server',
     'selenium_testing',
     'tool_manager',

diff --git a/refinery/config/urls.py b/refinery/config/urls.py
@@ -65,7 +65,6 @@
     url(r'^workflow_manager/', include('workflow_manager.urls')),
     url(r'^analysis_manager/', include('analysis_manager.urls')),
     url(r'^data_set_manager/', include('data_set_manager.urls')),
-    url(r'^visualization_manager/', include('visualization_manager.urls')),
     url(r'^file_server/', include('file_server.urls')),
     url(r'^tasks/', include('djcelery.urls')),
     url(r'^docs/', include('rest_framework_swagger.urls')),

diff --git a/refinery/core/urls.py b/refinery/core/urls.py
@@ -55,7 +55,6 @@
         'workflow_engine', name="workflow_engine"),
     url(r'^visualize/genome/$', 'visualize_genome', name='visualize_genome'),
 
-    url(r'^solr/igv/$', 'solr_igv'),
     url(r'^solr/core/select/$', 'solr_core_search', name="solr_core_search"),
     url(r'^solr/(?P<core>.+)/select/$', 'solr_select', name="solr_select"),
 

diff --git a/refinery/core/views.py b/refinery/core/views.py
@@ -35,12 +35,8 @@
 from rest_framework.views import APIView
 import xmltodict
 
-from analysis_manager.utils import get_solr_results
-from annotation_server.models import GenomeBuild
 from data_set_manager.models import Node
-from data_set_manager.utils import generate_solr_params_for_assay
 from file_store.models import FileStoreItem
-from visualization_manager.views import igv_multi_species
 
 from .forms import ProjectForm, UserForm, UserProfileForm, WorkflowForm
 from .models import (Analysis, CustomRegistrationProfile, DataSet,
@@ -580,62 +576,6 @@ def solr_select(request, core):
         return JsonResponse(response_dict)
 
 
-def solr_igv(request):
-    """Function for taking solr request url.
-    Removes pagination, facets from input query to create multiple
-    :param request: Django HttpRequest object including solr query
-    :type source: HttpRequest object.
-    :returns:
-    """
-
-    # copy querydict to make it editable
-    if request.is_ajax():
-        igv_config = json.loads(request.body)
-
-        logger.debug(json.dumps(igv_config, indent=4))
-
-        logger.debug('IGV data query: ' + str(igv_config['query']))
-        logger.debug('IGV annotation query: ' + str(igv_config['annotation']))
-
-        if igv_config['query'] is None:
-            # generate solr_query method
-            # assay uuid
-            solr_query = generate_solr_params_for_assay(
-                {},
-                igv_config['assay_uuid']
-            )
-            url_path = '/'.join(["data_set_manager", "select"])
-            url = urljoin(settings.REFINERY_SOLR_BASE_URL, url_path)
-            igv_config['query'] = ''.join([url, '/?', solr_query])
-
-        # attributes associated with node selection from interface
-        node_selection_blacklist_mode = igv_config[
-            'node_selection_blacklist_mode']
-        node_selection = igv_config['node_selection']
-
-        solr_results = get_solr_results(
-            igv_config['query'], selected_mode=node_selection_blacklist_mode,
-            selected_nodes=node_selection)
-
-        if igv_config['annotation'] is not None:
-            solr_annot = get_solr_results(igv_config['annotation'])
-        else:
-            solr_annot = None
-        # if solr query returns results
-        if solr_results:
-            try:
-                session_urls = igv_multi_species(solr_results, solr_annot)
-            except GenomeBuild.DoesNotExist:
-                logger.error(
-                    "Provided genome build cannot be found in the database.")
-                session_urls = "Couldn't find the provided genome build."
-
-        logger.debug("session_urls")
-        logger.debug(json.dumps(session_urls, indent=4))
-
-        return JsonResponse(session_urls)
-
-
 def samples_solr(request, ds_uuid, study_uuid, assay_uuid):
     logger.debug("core.views.samples_solr called")
     data_set = get_object_or_404(DataSet, uuid=ds_uuid)

diff --git a/refinery/ui/Gruntfile.js b/refinery/ui/Gruntfile.js
@@ -129,35 +129,6 @@ module.exports = function (grunt) {
   };
 
   grunt.initConfig({
-    /*
-     * Add vendor prefixes to out CSS to ensure better browser support.
-     */
-    postcss: {
-      options: {
-        processors: [
-          require('autoprefixer')({ browsers: [
-            '> 5%',
-            'last 2 versions',
-            'Firefox ESR',
-            'Explorer >= 10',
-            'iOS >= 6',
-            'Opera >= 12',
-            'Safari >= 6'
-          ] })
-        ]
-      },
-      styles: {
-        files: [
-          {
-            expand: true,
-            cwd: '<%= cfg.basePath.ui.src %>/styles',
-            src: ['**/*.css'],
-            dest: '<%= cfg.basePath.ui.tmp %>/styles'
-          }
-        ]
-      }
-    },
-
     /*
      * Read configs from `config.json`. Separating scripts and configs help
      * to keep things readable.
@@ -851,7 +822,6 @@ module.exports = function (grunt) {
     'clean:uiCompile',
     'clean:staticCompile',
     'less:compile',
-    'postcss',
     // IMPORTANT:
     // `concat-by-feature:compile` has to be called before `ngAnnotate` because
     // it adds features to the `ngAnnotate` task.

diff --git a/refinery/ui/cypress/integration/anonymous/not_logged_in_spec.js b/refinery/ui/cypress/integration/anonymous/not_logged_in_spec.js
@@ -56,7 +56,6 @@ describe('Not logged in', function() {
     cy.visit('/');
     cy.visible_btn('List').click();
 
-    cy.visible('Filename');
     cy.visible('Organism');
     cy.visible('Technology');
     cy.visible('Antibody');

diff --git a/refinery/ui/package.json b/refinery/ui/package.json
@@ -38,7 +38,6 @@
     "grunt-karma": "1.0.0",
     "grunt-newer": "1.2.0",
     "grunt-ng-annotate": "2.0.1",
-    "grunt-postcss": "0.8.0",
     "hasbin": "1.1.1",
     "isbinaryfile": "3.0.0",
     "jasmine-core": "2.3.4",

diff --git a/refinery/user_files_manager/tests.py b/refinery/user_files_manager/tests.py
@@ -112,14 +112,18 @@ def test_generate_solr_params_for_user(self):
         query = generate_solr_params_for_user(QueryDict({}), user.id)
         self.assertEqual(str(query).split('&'), [
                          'fq=assay_uuid%3A%28{}%29'.format(assay_uuid),
+                         'facet.field=filetype_Characteristics_generic_s',
+                         'facet.field=filetype_Factor_Value_generic_s',
                          'facet.field=organism_Characteristics_generic_s',
                          'facet.field=organism_Factor_Value_generic_s',
                          'facet.field=technology_Characteristics_generic_s',
                          'facet.field=technology_Factor_Value_generic_s',
-                         'facet.field=antibody_Characteristics_generic_s',
-                         'facet.field=antibody_Factor_Value_generic_s',
                          'facet.field=genotype_Characteristics_generic_s',
                          'facet.field=genotype_Factor_Value_generic_s',
+                         'facet.field=cell_type_Characteristics_generic_s',
+                         'facet.field=cell_type_Factor_Value_generic_s',
+                         'facet.field=antibody_Characteristics_generic_s',
+                         'facet.field=antibody_Factor_Value_generic_s',
                          'facet.field=experimenter_Characteristics_generic_s',
                          'facet.field=experimenter_Factor_Value_generic_s',
                          'fl=%2A_generic_s'

diff --git a/refinery/visualization_manager/__init__.py b/refinery/visualization_manager/__init__.py
diff --git a/refinery/visualization_manager/models.py b/refinery/visualization_manager/models.py
diff --git a/refinery/visualization_manager/tests.py b/refinery/visualization_manager/tests.py
diff --git a/refinery/visualization_manager/urls.py b/refinery/visualization_manager/urls.py