Merge pull request #571 from neuroscout/fix/bib

Fix bibliography + database backups, add scaling to DM plots
neuroscout · May 16, 2019 · 850c90b · 850c90b
2 parents 803ca18 + b3b17f2
commit 850c90b
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Showing 6 changed files with 172 additions and 7 deletions.
diff --git a/celery_worker/tasks.py b/celery_worker/tasks.py
@@ -44,7 +44,7 @@ def compile(analysis, predictor_events, resources, bids_dir, run_ids,
 
 @celery_app.task(name='workflow.generate_report')
 def generate_report(analysis, predictor_events, bids_dir, run_ids,
-                    sampling_rate, domain):
+                    sampling_rate, domain, scale):
     _, _, bids_analysis = build_analysis(
         analysis, predictor_events, bids_dir, run_ids)
     outdir = Path('/file-data/reports') / analysis['hash_id']
@@ -74,7 +74,7 @@ def generate_report(analysis, predictor_events, bids_dir, run_ids,
         results['design_matrix'].append(url)
         dense.to_csv(out, index=False)
 
-        dm_plot = plot_design_matrix(dense)
+        dm_plot = plot_design_matrix(dense, scale=scale)
         results['design_matrix_plot'].append(dm_plot)
 
         corr_plot = plot_corr_matrix(dense)

diff --git a/celery_worker/viz.py b/celery_worker/viz.py
@@ -17,7 +17,9 @@ def melt_dm(dm):
     return dm.melt('scan_number', var_name='regressor', value_name='value')
 
 
-def plot_design_matrix(dm_wide):
+def plot_design_matrix(dm_wide, scale=True):
+    if scale:
+        dm_wide = dm_wide.apply(lambda x: x / x.max())  # Scale for plotting
     dm = melt_dm(dm_wide)
 
     pts = alt.selection_multi(encodings=['x'])

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -42,6 +42,7 @@ services:
       - POSTGRES_PASSWORD=${POSTGRES_PASSWORD}
     env_file:
       - .env
+      - .pliersenv
 
   swagger-ui:
     image: swaggerapi/swagger-ui

diff --git a/neuroscout/config/bibliography.json b/neuroscout/config/bibliography.json
@@ -1621,6 +1621,166 @@
         ]
     },
     "PredefinedDictionaryExtractor": {
+      "concreteness.*": [
+        {
+        "id": "http://zotero.org/users/local/JXz6ijqB/items/Z8ZF6ICY",
+        "type": "article-journal",
+        "title": "Concreteness ratings for 40 thousand generally known English word lemmas",
+        "container-title": "Behavior Research Methods",
+        "page": "904-911",
+        "volume": "46",
+        "issue": "3",
+        "source": "DOI.org (Crossref)",
+        "URL": "http://link.springer.com/10.3758/s13428-013-0403-5",
+        "DOI": "10.3758/s13428-013-0403-5",
+        "ISSN": "1554-3528",
+        "journalAbbreviation": "Behav Res",
+        "language": "en",
+        "author": [
+        	{
+        		"family": "Brysbaert",
+        		"given": "Marc"
+        	},
+        	{
+        		"family": "Warriner",
+        		"given": "Amy Beth"
+        	},
+        	{
+        		"family": "Kuperman",
+        		"given": "Victor"
+        	}
+        ],
+        "issued": {
+        	"date-parts": [
+        		[
+        			"2014",
+        			9
+        		]
+        	]
+        },
+        "accessed": {
+        	"date-parts": [
+        		[
+        			"2019",
+        			5,
+        			15
+        		]
+        	]
+        }
+        }
+      ],
+      "calgarysemanticdecision.*" : [
+      	{
+      		"id": "http://zotero.org/users/local/JXz6ijqB/items/D5EM4SZP",
+      		"type": "article-journal",
+      		"title": "The Calgary semantic decision project: concrete/abstract decision data for 10,000 English words",
+      		"container-title": "Behavior Research Methods",
+      		"page": "407-417",
+      		"volume": "49",
+      		"issue": "2",
+      		"source": "Springer Link",
+      		"URL": "https://doi.org/10.3758/s13428-016-0720-6",
+      		"DOI": "10.3758/s13428-016-0720-6",
+      		"ISSN": "1554-3528",
+      		"shortTitle": "The Calgary semantic decision project",
+      		"journalAbbreviation": "Behav Res",
+      		"language": "en",
+      		"author": [
+      			{
+      				"family": "Pexman",
+      				"given": "Penny M."
+      			},
+      			{
+      				"family": "Heard",
+      				"given": "Alison"
+      			},
+      			{
+      				"family": "Lloyd",
+      				"given": "Ellen"
+      			},
+      			{
+      				"family": "Yap",
+      				"given": "Melvin J."
+      			}
+      		],
+      		"issued": {
+      			"date-parts": [
+      				[
+      					"2017",
+      					4,
+      					1
+      				]
+      			]
+      		},
+      		"accessed": {
+      			"date-parts": [
+      				[
+      					"2019",
+      					5,
+      					15
+      				]
+      			]
+      		}
+      	}
+      ],
+      "massiveauditorylexicaldecision.*": [
+      	{
+      		"id": "http://zotero.org/users/local/JXz6ijqB/items/KHYK769U",
+      		"type": "article-journal",
+      		"title": "The Massive Auditory Lexical Decision (MALD) database",
+      		"container-title": "Behavior Research Methods",
+      		"source": "Springer Link",
+      		"URL": "https://doi.org/10.3758/s13428-018-1056-1",
+      		"DOI": "10.3758/s13428-018-1056-1",
+      		"ISSN": "1554-3528",
+      		"journalAbbreviation": "Behav Res",
+      		"language": "en",
+      		"author": [
+      			{
+      				"family": "Tucker",
+      				"given": "Benjamin V."
+      			},
+      			{
+      				"family": "Brenner",
+      				"given": "Daniel"
+      			},
+      			{
+      				"family": "Danielson",
+      				"given": "D. Kyle"
+      			},
+      			{
+      				"family": "Kelley",
+      				"given": "Matthew C."
+      			},
+      			{
+      				"family": "Nenadić",
+      				"given": "Filip"
+      			},
+      			{
+      				"family": "Sims",
+      				"given": "Michelle"
+      			}
+      		],
+      		"issued": {
+      			"date-parts": [
+      				[
+      					"2018",
+      					6,
+      					18
+      				]
+      			]
+      		},
+      		"accessed": {
+      			"date-parts": [
+      				[
+      					"2019",
+      					5,
+      					15
+      				]
+      			]
+      		}
+      	}
+      ],
       "subtlexusfrequency.*":[
       	{
       		"id": "http://zotero.org/users/local/JXz6ijqB/items/HK7TT8RJ",

diff --git a/neuroscout/resources/analysis/endpoints.py b/neuroscout/resources/analysis/endpoints.py
@@ -220,7 +220,7 @@ def get(self, analysis):
 
         tools = [b['.*'] for k, b in bib.items()
                  if k in ['nipype', 'neuroscout', 'fitlins', 'nipype']]
-        all_csl_json = tools
+        all_csl_json = tools.copy()
 
         dataset_entry = bib.get(analysis.dataset.name, [])
         if dataset_entry:

diff --git a/neuroscout/resources/analysis/reports.py b/neuroscout/resources/analysis/reports.py
@@ -87,13 +87,14 @@ def get(self, analysis):
 @use_kwargs({
     'run_id': wa.fields.DelimitedList(fields.Int(),
                                       description='Run id(s).'),
-    'sampling_rate': wa.fields.Number(description='Sampling rate in Hz')
+    'sampling_rate': wa.fields.Number(description='Sampling rate in Hz'),
+    'scale': wa.fields.Boolean(description='Scale columns for plotting'),
 }, locations=['query'])
 @doc(tags=['analysis'])
 class ReportResource(MethodResource):
     @doc(summary='Generate analysis reports.')
     @fetch_analysis
-    def post(self, analysis, run_id=None, sampling_rate=None):
+    def post(self, analysis, run_id=None, sampling_rate=None, scale=True):
         # Submit report generation
         analysis_json, pes_json = jsonify_analysis(analysis, run_id=run_id)
 
@@ -102,7 +103,8 @@ def post(self, analysis, run_id=None, sampling_rate=None):
             args=[analysis_json, pes_json,
                   analysis.dataset.local_path, run_id,
                   sampling_rate,
-                  current_app.config['SERVER_NAME']])
+                  current_app.config['SERVER_NAME'],
+                  scale])
 
         # Create new Report
         report = Report(