docs(updates): update precommit and fix whitespace, comments/updates/…

.gitignore

@@ -2,4 +2,4 @@ themes_used
 *.DS_Store
 ./resources/
 */_gen/
-.idea
+.idea

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
         -   id: detect-secrets
             args: ['--baseline', '.secrets.baseline']
     -   repo: https://github.com/pre-commit/pre-commit-hooks
-        rev: v2.5.0
+        rev: v5.0.0
         hooks:
         -   id: trailing-whitespace
         -   id: end-of-file-fixer

.secrets.baseline

@@ -368,7 +368,7 @@
         "filename": "gen3/docs/gen3-resources/user-guide/analyze-data.md",
         "hashed_secret": "98fd178574fc77b708149e559bf75052cc3c81a6",
         "is_verified": false,
-        "line_number": 215
+        "line_number": 227
       }
     ],
     "gen3/docs/gen3-resources/user-guide/notebooks/notebook2_canine.ipynb": [
@@ -500,16 +500,16 @@
         "filename": "gen3/docs/gen3-resources/user-guide/search.md",
         "hashed_secret": "13333fbf17a0b71d02dda8e6e5c195263bfe03d6",
         "is_verified": false,
-        "line_number": 138
+        "line_number": 146
       },
       {
         "type": "Hex High Entropy String",
         "filename": "gen3/docs/gen3-resources/user-guide/search.md",
         "hashed_secret": "8595e69444146fbf187e8c512b6fdc66f8da1d23",
         "is_verified": false,
-        "line_number": 162
+        "line_number": 170
       }
     ]
   },
-  "generated_at": "2024-12-12T11:53:58Z"
+  "generated_at": "2024-12-09T16:54:41Z"
 }

archetypes/default.md

@@ -3,4 +3,3 @@ title: "{{ replace .Name "-" " " | title }}"
 date: {{ .Date }}
 draft: true
 ---
-

config.yaml

@@ -334,8 +334,8 @@ params:
                 link: /resources/user/analyze-data/#1-launch-workspace
               - name: Getting Files into the Gen3 Workspace
                 link: /resources/user/analyze-data/#2-getting-files-into-the-gen3-workspace
-              - name: Working with the proxy and whitelists
-                link: /resources/user/analyze-data/#3-working-with-the-proxy-and-whitelists
+              - name: Working with the proxy and allow lists
+                link: /resources/user/analyze-data/#3-working-with-the-proxy-and-allow-lists
               - name: Using the Gen3 Python SDK
                 link: /resources/user/analyze-data/#4-using-the-gen3-python-sdk
               - name: Jupyter Notebook Demos

content/community/events.md

@@ -56,7 +56,7 @@ g3past:
   Slides:  Gen3 Forum September 6 2023 - Security and Compliance.pdf
 - Title: Data Modeling in Gen3 Data Commons
   Date: July 6, 2023, 3:30-5:00 pm CDT; July 7, 2023, 6:30-8:00 am AEST
-  Description: Gen3 supports a flexible graph-based data model, which can be customized for a wide variety of projects and use cases.  At this community event we will hear from several data commons operators on how they have created their dictionaries and about any tools or processes they use for updating and configuring them.  
+  Description: Gen3 supports a flexible graph-based data model, which can be customized for a wide variety of projects and use cases.  At this community event we will hear from several data commons operators on how they have created their dictionaries and about any tools or processes they use for updating and configuring them.
   Agenda2: /community/events/gen3forum_20230706
   Youtube: xjFUYa4C_hw
   Slides:  Gen3 Forum July 6 2023 - Data Models.pdf

content/community/medium.md

@@ -5,4 +5,3 @@ linktitle: /community/medium
 date: 2018-09-04T22:16:21-05:00
 draft: true
 ---
-

content/ga4gh.md

@@ -49,9 +49,9 @@ g3Feature:
           Driver Projects
         </h1>
         <p class="g3-space__margin-sm-bottom introduction g3-space__margin-sm-right">
-        Gen3 technology is used by four different driver projects:  
+        Gen3 technology is used by four different driver projects:
         <ul>
-          <li>The Biomedical Research Hub, which as a data fabric, enables access to multiple independent data commons containing biomedical data.</li>  
+          <li>The Biomedical Research Hub, which as a data fabric, enables access to multiple independent data commons containing biomedical data.</li>
           <li>The Data Commons Framework Services, which underpins interoperability within the Cancer Research Data Commons.</li>
           <li>The NHLBI BioData Catalyst (BDC) is a cloud-based ecosystem that offers researchers data, analytic tools, applications, and workflows in secure workspaces. It is a community where researchers can find, access, share, store, and analyze heart, lung, blood, and sleep data resources.</li>
           <li>The NIH Cloud Platform Interoperability (NCPI) program seeks to create a federated genomic data ecosystem and is a collaborative project between NIH and external partners comprising three working groups.</li>

content/gen3-tools.md

@@ -18,21 +18,21 @@ g3Starts:
   s2:
     name: gen3utils
     fig: /figs/UChicago_CTDS_Vertical_Color RGB.svg
-    detail: Utilities for Gen3 management including validation tools. Created by the Center for Translational Data Science at the University of Chicago.                                                       
+    detail: Utilities for Gen3 management including validation tools. Created by the Center for Translational Data Science at the University of Chicago.
     button:
       caption: GitHub
       link: https://github.com/uc-cdis/gen3utils
   s3:
     name: g3t
     fig: /figs/OHSU-logo.png
-    detail: Gen3 Tracker (g3t) includes utilities to manage Gen3 schemas, projects and submissions.  Tools include those to create and manage metadata, manipulate file manifests, status checks, metadata validation, user access, and others.                                                       
+    detail: Gen3 Tracker (g3t) includes utilities to manage Gen3 schemas, projects and submissions.  Tools include those to create and manage metadata, manipulate file manifests, status checks, metadata validation, user access, and others.
     button:
       caption: GitHub
       link: https://github.com/ACED-IDP/gen3_util
   s4:
     name: g3t_etl
     fig: /figs/OHSU-logo.png
-    detail: g3t_etl is a command-line tool and library designed to manage Gen3 metadata including transformations to and from FHIR formatted data. The tool provides various commands, each serving a specific purpose.                                   
+    detail: g3t_etl is a command-line tool and library designed to manage Gen3 metadata including transformations to and from FHIR formatted data. The tool provides various commands, each serving a specific purpose.
     button:
       caption: GitHub
       link: https://github.com/ACED-IDP/g3t_etl
@@ -99,7 +99,7 @@ g3Starts:
           {{< param "g3Starts.s2.name" >}}
         </h3>
         <p class="g3-space__margin-sm-bottom g3-text__desktop-left">
-          {{< param "g3Starts.s2.detail" >}} <br>       <br> <br>               
+          {{< param "g3Starts.s2.detail" >}} <br>       <br> <br>
         </p>
         <a class="g3-button g3-button--primary g3-align__bottom" href="{{< param "g3Starts.s2.button.link" >}}">
           {{< param "g3Starts.s2.button.caption" >}}
@@ -111,7 +111,7 @@ g3Starts:
           {{< param "g3Starts.s3.name" >}}
         </h3>
         <p class="g3-space__margin-sm-bottom g3-text__desktop-left">
-          {{< param "g3Starts.s3.detail" >}} <br>       <br> <br>               
+          {{< param "g3Starts.s3.detail" >}} <br>       <br> <br>
         </p>
         <a class="g3-button g3-button--primary g3-align__bottom" href="{{< param "g3Starts.s3.button.link" >}}">
           {{< param "g3Starts.s3.button.caption" >}}
@@ -155,7 +155,7 @@ g3Starts:
         {{< param "g3Starts.s6.name" >}}
       </h3>
       <p class="g3-space__margin-sm-bottom g3-text__desktop-left">
-        {{< param "g3Starts.s6.detail" >}} <br>       <br> <br>               
+        {{< param "g3Starts.s6.detail" >}} <br>       <br> <br>
       </p>
       <a class="g3-button g3-button--primary g3-align__bottom" href="{{< param "g3Starts.s6.button.link" >}}">
         {{< param "g3Starts.s6.button.caption" >}}

content/gen3refs.md

@@ -49,7 +49,7 @@ The Gen3 data platform is used as the basis for many data repositories and enabl
       <a href="https://arxiv.org/abs/2404.15475">View Article</a>
     </p>
     <p class="g3-space__margin-sm-bottom">
-    Kim, Erika, et al. "NCI cancer research data commons: lessons learned and future state." Cancer Research 84.9 (2024): 1404-1409.      
+    Kim, Erika, et al. "NCI cancer research data commons: lessons learned and future state." Cancer Research 84.9 (2024): 1404-1409.
       <a href="https://aacrjournals.org/cancerres/article/84/9/1404/745076">View Article</a>
     </p>
     <p class="g3-space__margin-sm-bottom">
@@ -92,7 +92,7 @@ The Gen3 data platform is used as the basis for many data repositories and enabl
     Wyatt, Kirk D., et al. "An open-source platform for pediatric cancer data exploration: a report from Data for the Common Good." JAMIA open 7.1 (2024): ooae004.
       <a href="https://academic.oup.com/jamiaopen/article/7/1/ooae004/7595632">View Article</a>
     </p>
-  </div>  
+  </div>
 </section>
 
 

content/powered-by-gen3.md

@@ -283,7 +283,7 @@ g3Commons:
          </a>
       </div>
    </div>
-</section>         
+</section>
 <section class="g3-bg__white">
    <h3 class="g3-text__center g3-space__padding-md-left g3-space__padding-md-top-bottom">
       {{< param "g3Teaser.detail" >}}

content/resources/developer/build-app.md

@@ -35,7 +35,7 @@ The standard GraphQL endpoint for a Gen3 commons is available via POST at `/api/
 {"query":"query { project(first:0) {code, project_id, availability_type}}"}
 ```
 
-* First: 0 means return all, otherwise it defaults to the first 10. 
+* First: 0 means return all, otherwise it defaults to the first 10.
 * Project_id = <program>-<project> used to reference any projects
 * Code = project name in the project node
 * Availability_type = is this project open access to everyone or not

content/resources/developer/tech-intro.md

@@ -6,4 +6,3 @@ layout: withtoc
 menuname: developerMenu
 draft: true
 ---
-

content/resources/developer/ui-library.md

@@ -6,4 +6,3 @@ draft: true
 layout: withtoc
 menuname: developerMenu
 ---
-

content/resources/user/analyze-data.md

@@ -15,7 +15,7 @@ The Gen3 platform for creating data commons co-locates data management with anal
 
 * [1. Launch Workspace](#1-launch-workspace)
 * [2. Getting Files into the Gen3 Workspace](#2-getting-files-into-the-gen3-workspace)
-* [3. Working with the proxy and whitelists](#3-working-with-the-proxy-and-whitelists)
+* [3. Working with the proxy and allow lists](#3-working-with-the-proxy-and-allow-lists)
 * [4. Using the Gen3 Python SDK](#4-using-the-gen3-python-sdk)
 * [5. Jupyter Notebook Demos](#5-jupyter-notebook-demos)
 
@@ -133,7 +133,7 @@ GSM1558854_Sample40_3.CEL.gz  4.20 MiB / 4.20 MiB [====================....
 jovyan@jupyter-user:~$  mv *.gz files
 ```
 
-## 3. Working with the proxy and whitelists
+## 3. Working with the proxy and allow lists
 * * *
 
 <h4> Working with the Proxy </h4>
@@ -151,7 +151,7 @@ Alternatively, if you have a different service or a tool that needs to call out,
 https_proxy=https://cloud-proxy.internal.io:3128 aws s3 ls s3://gen3-data/ --profile <profilename>
 ```
 
-<h4> Whitelists </h4>
+<h4> Allow lists </h4>
 
 Additionally, to aid Gen3 Commons security, the installation of tools from outside resources is managed through a whitelist. If you have problems installing a tool you need for your work, contact <[email protected]> and with a list of any sites you might wish to install tools from. After passing a security review, these can be added to the whitelist to facilitate access.
 

content/resources/user/img/gen3_core_metadata_collection_template.tsv

@@ -1 +1 @@
-type	project_id	submitter_id	projects.code	contributor	coverage	creator	data_type	date	description	format	language	publisher	relation	rights	source	subject	titlecore_metadata_collection	example-training	collection-01	training														
+type	project_id	submitter_id	projects.code	contributor	coverage	creator	data_type	date	description	format	language	publisher	relation	rights	source	subject	titlecore_metadata_collection	example-training	collection-01	training

content/resources/user/submit-data/gen3_core_metadata_collection_template.tsv

@@ -1 +1 @@
-type	project_id	submitter_id	projects.code	contributor	coverage	creator	data_type	date	description	format	language	publisher	relation	rights	source	subject	titlecore_metadata_collection	example-training	collection-01	training														
+type	project_id	submitter_id	projects.code	contributor	coverage	creator	data_type	date	description	format	language	publisher	relation	rights	source	subject	titlecore_metadata_collection	example-training	collection-01	training

content/resources/user/template-tsvs/aliquot.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	samples.submitter_id	aliquot_container	clinical_or_contrived	hours_to_freezer_lower	hours_to_freezer_upper	preservation_method	storage_temperature	aliquot_quantity	aliquot_volume	contrivance_method	methanol_added	project_id
-aliquot													
+aliquot

content/resources/user/template-tsvs/analyte.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	aliquots.submitter_id	analyte_isolation_method	analyte_type	cell_identifier	cell_type	days_to_assay	frame_identifier	llod	project_id	run_identifier	sensitivity	specificity
-analyte													
+analyte

content/resources/user/template-tsvs/biospecimen.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	cases.submitter_id	biospecimen_anatomic_site	biospecimen_type	blood_tube_type	days_to_collection	days_to_procurement	method_of_procurement	procured_or_purchased	tissue_type	biospecimen_volume	biospecimen_weight	blood_draw_method	clinical_site	collaboration_id	disease_type	metastatic_bone	metastatic_lymph_node	metastatic_visceral	primary_site	procurement_temperature	project_id	shipping_temperature	tumor_code	tumor_descriptor
-biospecimen																									
+biospecimen

content/resources/user/template-tsvs/cell_image.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	analytes.submitter_id	data_category	data_format	data_type	file_name	file_size	md5sum	project_id
-cell_image									
+cell_image

content/resources/user/template-tsvs/contrived_expectations.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	aliquots.submitter_id	expected_allelic_fraction	expected_copy_number	expected_mutation_alt	expected_mutation_chromosome	expected_mutation_gene	expected_mutation_position	expected_mutation_reference	expected_mutation_type	project_id
-contrived_expectations											
+contrived_expectations

content/resources/user/template-tsvs/demographic.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	cases.submitter_id	cause_of_death	days_to_birth	days_to_death	ethnicity	gender	project_id	race	vital_status
-demographic										
+demographic

content/resources/user/template-tsvs/diagnosis.tsv

@@ -1,2 +1,2 @@
 type	submitter_id	cases.submitter_id	classification_of_tumor	days_to_diagnosis	morphology	primary_diagnosis	tissue_or_organ_of_origin	tumor_grade	ajcc_clinical_m	ajcc_clinical_n	ajcc_clinical_stage	ajcc_clinical_t	ajcc_pathologic_m	ajcc_pathologic_n	ajcc_pathologic_stage	ajcc_pathologic_t	best_overall_response	days_to_best_overall_response	method_of_diagnosis	overall_survival	prior_malignancy	prior_treatment	progression_free_survival	progression_free_survival_event	project_id	residual_disease
-diagnosis																									
+diagnosis