fix: WG-400 absolute URLs and broken links (#112)

* fix: WG-400, abs URLs in usecases

* fix(curating): policies.md, broken links

* fix(curating): files with only a few broken links

* fix(curating): faq has linsk that do not appear

* enhance: use markdown not html for links

* docs: in commented text, use markdown for link

* fix: links to apps or app overview pages

* fix: update internal links

* fix: update old URLs to impact-of-data-reuse

* fix: new external link missing target blank

* fix: another new ext link without target blank

* fix: space inside link, link shoudl use markdown

* fix: fixed internal link should use markdown

* fix: fixed internal link should use markdown 2

* fix: unwanted quote replacement

* fix: space inside link

* fix: fixed internal link should use markdown 3

* fix: space inside link, link should use markdown 2

* fix: "." inside link, link should use markdown

* fix: fixed internal link should use markdown 4

* fix: fixed internal link should use markdown 5

* fix: internal links and malformed link

* fix: HTML lists break markup links

* fix: space inside link, link should use markdown 3

* fix: unwanted quote replacement 2

* fix: unwanted quote replacement 3

* fix: space inside link, link should use markdown 4

* fix: quotes, link syntax, missing period

* fix: extra space

* fix: bad internal link

* fix: "." inside link, link should use markdown 2

* fix: extra ".", unwanted quote replacement

* fix: fixed internal link should use markdown 6

* fix: unwanted quote replacement 4

* fix: HTML and target blank for internal links

* fix: eddited ext link should open in new window

* fix: HTML list and missing target blanks

* fix: "here" link and verbose grammar

* fix: extra period

* fix: help new ticket link not specific enough

* fix: remove redundant title

* fix: HTML list break markdown links

* fix: HTML list break markdown links

* fix: HTML list break markdown links 2

* fix: help new ticket not open in new tab

* fix: workspace link should open in new tab

* fix: HTML list break markdown links and images

* fix: "." outside link

* fix: missing punctuation

* fix: HTML lists malformed (includes updated link)

* fix: HTML table malformed

* fix: misc linsk during testing

README.md

@@ -17,7 +17,7 @@ How to Contribute **Other Changes**:
     <sup>(if comfortable using a command prompt)</sup>
 6. [Request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) a review.\
     <sup>(a.k.a. create a "Pull Request")</sup>
-   
+
 ### Resources
 
 * [Markdown syntax (extended)](https://www.markdownguide.org/extended-syntax/) via [MkDocs' Markdown support](https://www.mkdocs.org/user-guide/writing-your-docs/#writing-with-markdown)

user-guide/docs/curating/bestpractices.md

@@ -56,16 +56,16 @@ There are different ways to upload data to My Project:
 
 * Do not upload folders and files with special characters in their filenames. In general, keep filenames meaningful but short and without spacing. See file naming convention recommendations in the <a href="#organization">Data Organization and Description</a>
 * Select the Add button, then File upload to begin uploading data from your local machine. You can browse and select files or drag and drop files into the window that appears.  
-* Connect to your favorite cloud storage provider. <a href="../managingdata/#data-depot">We currently support integration with Box,  Dropbox, and Google Drive.</a> 
+* Connect to your favorite cloud storage provider. <a href="/user-guide/managingdata/datatransfer/#cloud">We currently support integration with Box,  Dropbox, and Google Drive.</a> 
 * You can also copy data to and from My Data.  
 * You may consider zipping files for purpses of uploading: however, you should unzip them for curation and publication purposes.  
-* For uploads of files bigger than 2 Gigabytes and or more than 25 files, consider using Globus, CyberDuck and  Command Line Utilities. Explanations on how to use those applications are available in our <a href="../managingdata/#data-transfer-guides">Data Transfer Guide.</a> 
+* For uploads of files bigger than 2 Gigabytes and or more than 25 files, consider using Globus, CyberDuck and  Command Line Utilities. Explanations on how to use those applications are available in our <a href="/user-guide/managingdata/datatransfer/">Data Transfer Guide.</a> 
 
-Downloading several individual files via our web interface could be cumbersome, so DesignSafe offers a number of alternatives. First, users may interact with data in the Workspace using any of the available tools and applications without the need to download; for this, users will need a DesignSafe account. Users needing to download a large number of files from a project may also use <a href="../managingdata/#globus">Globus</a>. When feasible, to facilitate data download from their projects users may consider aggregating data into larger files.
+Downloading several individual files via our web interface could be cumbersome, so DesignSafe offers a number of alternatives. First, users may interact with data in the Workspace using any of the available tools and applications without the need to download; for this, users will need a DesignSafe account. Users needing to download a large number of files from a project may also use <a href="/user-guide/managingdata/datatransfer/#globus">Globus</a>. When feasible, to facilitate data download from their projects users may consider aggregating data into larger files.
 
 Be aware that while you may store all of a project files in My Project, you may not need to publish all of them. During curation and publication you will have the option to select a subset of the uploaded files that you wish to publish without the need to delete them. 
 
-More information about the different Workspaces in DesignSafe and how to manage data from one to the other can be found <a href="../managingdata/#data-depot">here</a>.
+More information about the different Workspaces in DesignSafe and how to manage data from one to the other can be found <a href="/user-guide/managingdata/datatransfer/">here</a>.
 
 #### Selecting a Project Type { #selectingprojecttype }
 
@@ -95,7 +95,7 @@ Excel and Matlab are two proprietary file formats highly used in this community.
 
 ##### Compressed Data { #bestpractices-compresseddata }
 
-Users that upload data as a zip file should unzip before curating and publishing, as zip files prevent others from directly viewing and understanding the published data. If uploading compressed files to "My Data" , it is possible to unzip it using the extraction <a href="https://www.designsafe-ci.org/rw/workspace/#!/extract-0.1u1">utility</a> available in the workspace before copying data to My Project for curation and publication.
+Users that upload data as a zip file should unzip before curating and publishing, as zip files prevent others from directly viewing and understanding the published data. If uploading compressed files to "My Data" , it is possible to unzip it using [the extraction utility available in the workspace](https://www.designsafe-ci.org/workspace/extract){target=_blank} before copying data to My Project for curation and publication.
 
 ##### Simulation Data { #bestpractices-simulationdata }
 
@@ -750,7 +750,7 @@ Depositing your data and associated research project materials in the DDR meets
 Follow the curation and publication onboarding instructions and steps -documented in the <a href="#curation-publication-guides">Data Curation and Publication Guides</a> - to ensure that your data curation and publication process is smooth and that your public datasets are well organized, complete, and understandable to others.
 
 
-To facilitate long term access to your published data, when possible, we recommend using open file formats. Open file formats facilitate interoperability between datasets and with applications, which in turn facilitates long term access to the datasets. <!-- The Data Curation and Publication Best Practices have information about <a href="/rw/user-guides/curating-publishing-projects/best-practices/">file formats</a> . -->
+To facilitate long term access to your published data, when possible, we recommend using open file formats. Open file formats facilitate interoperability between datasets and with applications, which in turn facilitates long term access to the datasets. <!-- The Data Curation and Publication Best Practices have information about [file formats](/user-guide/curating/bestpractices/#acceptedfileformats). -->
 
 
 DDR data is stored in high performance storage (HPC) resources deployed at the <a href="https://www.tacc.utexas.edu" target="_blank">Texas Advanced Computing Center</a>. These storage resources are reliable, secure, monitored 24/7, and under a rigorous maintenance and update schedule.

user-guide/docs/curating/faq.md

@@ -6,7 +6,7 @@
 **A**: For long-term preservation purposes it is best to publish data in interoperable and open formats. For example, instead of Excel spreadsheet files -which are proprietary- it is best to convert them to CSV for publication. And, instead of Matlab files -also proprietary- it is best to publish data as simple txt (ascii) so it can be used by many different software. However, be aware that conversion may distort the data structure, so retain an original copy of any structured data (e.g. Matlab, Excel files) before attempting conversions and then check between the two for fidelity. In addition, you may publish both the proprietary and the open format, and/or consult the Data Curation Primers to find out how to better curate research data.
 
 **Q: What does DesignSafe recommend for zip files?**  
-**A**: If you uploaded your data as zip files, you should unzip before publishing. Zip files prevent others from directly viewing and understanding your data in the cloud. You may upload zip files to your "MyData" and unzip them using the utilities available in the workspace at: <https://www.designsafe-ci.org/rw/workspace/#!/extract-0.1u1> before copying them to your project.
+**A**: If you uploaded your data as zip files, you should unzip before publishing. Zip files prevent others from directly viewing and understanding your data in the cloud. You may upload zip files to your "MyData" and unzip them using the [Extract utility](https://www.designsafe-ci.org/workspace/extract) before copying them to your project.
 
 **Q: My project has many individual files. It will be cumbersome for a user to download them one by one. What do you suggest?**  
 **A**: Through the web interface, downloading a lot of individual files is cumbersome. However, DesignSafe offers a number of solutions for this issue. First, users may interact with data in the cloud, without the need to download, using Matlab scripts as well as Jupyter notebooks. In this case, users may find downloading large quantities of data to be unnecessary. If users want to download a large number of files from a project, we recommend that they use Globus or include zip files for your data files. However, if you include zip files you should include the unzipped files in your project as well. If you wish to make your data easy to download, it is best to aggregate small individual files into a smaller number of larger files when feasible.
@@ -52,10 +52,10 @@
 ### Publishing { #publishing }
 
 **Q: Which license is appropriate for my publication?**  
-**A**: Licenses indicate the conditions in which you, as a data creator, want the data to be used by others. Due to the variety of resources published in DesignSafe, we provide four different types of open licenses. These cover datasets, software, materials with intellectual property rights, and the different ways in which you want your work to be attributed. You can find relevant information under licensing here: <https://www.designsafe-ci.org/rw/user-guides/data-publication-guidelines/>.
+**A**: Licenses indicate the conditions in which you, as a data creator, want the data to be used by others. Due to the variety of resources published in DesignSafe, we provide four different types of open licenses. These cover datasets, software, materials with intellectual property rights, and the different ways in which you want your work to be attributed. [Read more.](/user-guide/curating/bestpractices/#licensing)
 
 **Q: What is a DOI?**  
-**A**: A Digital Object Identifier (DOI) is a unique alphanumeric string assigned by a registration agency (the International DOI Foundation) to identify a resource and provide a persistent link to its location on the Internet. You can find a registered resource by its DOI using the "Resolve a DOI Name" function at: <http://www.doi.org/>. In addition, you may find the citation information for that DOI in DataCite at <https://search.datacite.org/>.
+**A**: A Digital Object Identifier (DOI) is a unique alphanumeric string assigned by a registration agency (the International DOI Foundation) to identify a resource and provide a persistent link to its location on the Internet. You can find a registered resource by its DOI using the "Resolve a DOI Name" function at: [http://www.doi.org/](http://www.doi.org/){target="_blank"}. In addition, you may find the citation information for that DOI in DataCite at [https://search.datacite.org/](https://search.datacite.org/){target="_blank"}.
 
 **Q: What is the relation between a DOI and a data citation?**  
 **A**: The DOI is a component of a citation for a work that is stored online. Therefore, it provides access to the permanent URL and the cited resource.
@@ -72,7 +72,7 @@
 **Q: How can I give credit to DesignSafe?**  
 **A**: Please include the citation of the marker paper in the references/bibliography section of your publication. This is more effective than you providing in-text acknowledgements.
 
-<blockquote>Rathje, E., Dawson, C. Padgett, J.E., Pinelli, J.-P., Stanzione, D., Adair, A., Arduino, P., Brandenberg, S.J., Cockerill, T., Dey, C., Esteva, M., Haan, Jr., F.L., Hanlon, M., Kareem, A., Lowes, L., Mock, S., and Mosqueda, G. 2017. "DesignSafe: A New Cyberinfrastructure for Natural Hazards Engineering," ASCE Natural Hazards Review, doi:10.1061/(ASCE)NH.1527-6996.0000246.</blockquote>
+> Rathje, E., Dawson, C. Padgett, J.E., Pinelli, J.-P., Stanzione, D., Adair, A., Arduino, P., Brandenberg, S.J., Cockerill, T., Dey, C., Esteva, M., Haan, Jr., F.L., Hanlon, M., Kareem, A., Lowes, L., Mock, S., and Mosqueda, G. 2017. "DesignSafe: A New Cyberinfrastructure for Natural Hazards Engineering," ASCE Natural Hazards Review, doi:10.1061/(ASCE)NH.1527-6996.0000246.
 
 ### Data Reuse { #datareuse }
 
@@ -95,7 +95,7 @@
 
 1. If you have reused images from other sources (online, databases, publications, etc.), be aware that they may have copyrights. We recommend using the following instructions for how to cite them:
 
-	<http://guides.library.ubc.ca>
+	[https://guides.library.ubc.ca](https://guides.library.ubc.ca){target="_blank"}
 
 **Q: Are there any conditions regarding the usage of data published in DesignSafe?**
 **A**: Yes, users that download and reuse data agree to the Data Usage conditions published here: These conditions outline the responsibilities of and expectations for data usage including aspects of data licensing, citation, privacy and confidentiality, and data quality.