Merge pull request #292 from NFDI4Chem/development

Development

docs/FAQs.md

@@ -48,7 +48,7 @@ You can assign roles to people with whom you share content:
 * **Reviewer** - Can only read the project, study, and dataset.
 
 ### How can I delete or edit my account?
-You can edit your account details by heading to your name at the top right corner and clicking on the `Account` tab from the drop-down. To delete your account, please reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/), or write to us at info@nmrxiv.org.
+You can edit your account details by heading to your name at the top right corner and clicking on the `Account` tab from the drop-down. To delete your account, please reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/), or write to us at info.nmrxiv@uni-jena.de.
 
 ### How can I license my resources, and which license to choose?
 You can license your project during or after submission as long as it is private. The license will propagate to the underlying studies, but you can still change the studies licenses. For more details about licenses and when to use each one, please visit the [licenses page](/docs/submission-guides/licenses.md).
@@ -67,6 +67,6 @@ If the above criteria are not met
 * Click [here](https://github.com/NFDI4Chem/nmrxiv/issues/new/choose) to report a new one under appropiate category.
 
 ### How to reach to you?
-Please write to us at info@nmrxiv.org or reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/). 
+Please write to us at info.nmrxiv@uni-jena.de or reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/). 
 You can also leave us a message via our support bubble which you find in the left down corner on our [application](https://nmrxiv.org/) page. 
 We will try to get back to your queries as soon as possible.

docs/contributing/nmrxiv.mdx

@@ -6,7 +6,7 @@ title: nmrXiv App
 
 ### Did you find a bug?
 
-* **Do not open up a GitHub discussion issue if the bug is a security vulnerability in nmrXiv**, and instead contact us here: <i>info@nmrxiv.org</i> (This email is not ready yet).
+* **Do not open up a GitHub discussion issue if the bug is a security vulnerability in nmrXiv**, and instead contact us here: <i>info.nmrxiv@uni-jena.de</i> (This email is not ready yet).
 
 * **Ensure the bug was not already reported** by searching on GitHub under [nmrXiv issues](https://github.com/NFDI4Chem/nmrxiv/issues).
     When searching change the filter box to both open and closed issues like this:

docs/introduction/data/exemplary-data.md

@@ -0,0 +1,68 @@
+---
+sidebar_position: 4
+id: exemplary-data
+title: Exemplary Data
+---
+
+In this section, you can find links and explanations about exemplary data ready for submission to **[nmrXiv](https://nmrxiv.org)**.
+
+## Bruker Datasets
+[Following this link](https://cloud.uni-jena.de/s/W3JHNPDY5isXo5F), you can download a project with two samples analyzed with Bruker instrument. After unzipping, the project "Bruker Example" is ready for submission.
+You can find the needed hierarchy for submission there : 
+- The main folder "Bruker Example" corresponds to the project. This is the folder that should be submitted (dragged and dropped) to nmrXiv.
+  - Within "Bruker Example" you find two folders, each corresponding to a sample (Eserine and Cucurbitacin E). 
+    - Within each sample folder, you find separate **folders** each corresponding to the spectrum/dataset folder. at the same level (within the sample folder), you can find additional files representing the whole sample, such as mol files for the structure or NMReData files and such.
+
+<div style={{textAlign: 'center'}}>
+<img src="/img/examples/Bruker.png" width="350"/>
+<figcaption>The hierarchy needed for a Bruker samples project</figcaption>
+</div>
+
+### Wrong Bruker Hierarchy
+
+:::danger Wrong Hierarchy
+It is common in Bruker datasets to find, for instance, the 2D datasets provided in a parent folder with the experiment name (e.g., HSQC), and within this folder you find the traditional Bruker named folders such as 1,2,3, etc. Such hierarchy will result in considering the HSQC dataset as a separate sample by nmrXiv, thus you need to be careful and avoid such inconveniences
+:::
+
+In the following photo, because there is an "HSQC" folder above the actual spectrum folder "58", nmrXiv recognizes 3 studies (Eserine, Cucurbitacin E, and HSQC)
+
+<div style={{textAlign: 'center'}}>
+<img src="/img/examples/Bruker-wrong.png" width="350"/>
+<figcaption>Adding a parent "HSQC folder to dataset 58 makes that folder a new sample to nmrXiv system."</figcaption>
+</div>
+
+<div style={{textAlign: 'center'}}>
+<img src="/img/examples/Bruker-studies.png" width="700"/>
+<figcaption>The studies in nmrXiv resulting from submitting the project in the above image.</figcaption>
+</div>
+
+## JCAMP Datasets
+
+[Following this link](https://cloud.uni-jena.de/s/CrNXN46N9GBQ7cG), you can download a project with two analyzed samples. The analysis output is provided in JCAMP format.  After unzipping, the project "JCAMP Example" is ready for submission.
+You can find the needed hierarchy for submission there : 
+- The main folder "JCAMP Example" corresponds to the project. This is the folder that should be submitted (dragged and dropped) to nmrXiv.
+  - Within "JCAMP Example" you find two folders, each corresponding to a sample (196793-29-0 and 1155308-25-0). 
+    - Within each sample folder, you find separate **JCAMP files** each corresponding to the spectrum/dataset file. At the same level (within the sample folder), you can find additional files corresponding to the whole sample, such as mol files for the structure or NMReData files and such.
+
+<div style={{textAlign: 'center'}}>
+<img src="/img/examples/JCAMP.png" width="350"/>
+<figcaption>The hierarchy needed for a Bruker samples project</figcaption>
+</div>
+
+### Wrong JCAMP Hierarchy
+
+:::danger Wrong Hierarchy
+It is common in JCAMP datasets to find, for instance, the 2D datasets provided in a parent folder with the experiment name (e.g., HSQC), and within this folder, you find the jcamp file such as hsqc.dx. Such hierarchy will result in considering the HSQC dataset as a separate sample by nmrXiv, thus you need to be careful and avoid such inconveniences
+:::
+
+In the following photo, because there is an "HSQC" folder above the actual spectrum file "hsqc.dx", nmrXiv recognizes 3 studies (196793-29-0, 1155308-25-0, and HSQC)
+
+<div style={{textAlign: 'center'}}>
+<img src="/img/examples/JCAMP-wrong.png" width="350"/>
+<figcaption>Adding a parent "hsqc folder to dataset hsqc.dx makes that folder a new sample to nmrXiv system."</figcaption>
+</div>
+
+<div style={{textAlign: 'center'}}>
+<img src="/img/examples/JCAMP-studies.png" width="700"/>
+<figcaption>The studies in nmrXiv resulting from submitting the project in the above image.</figcaption>
+</div>

docusaurus.config.js

@@ -19,7 +19,7 @@ module.exports = {
     themeConfig: {
         announcementBar: {
             id: 'support_us', // Any value that will identify this message.
-            content: 'You’re browsing the docs for beta version of nmrXiv. Please provide your feedback / suggestions <a target="_blank" rel="noopener noreferrer" href="mailto:info@nmrxiv.org?subject=nmrXiv feedback/suggestions&body=Hi,<Add your suggestions here>">here</a>',
+            content: 'You’re browsing the docs for beta version of nmrXiv. Please provide your feedback / suggestions <a target="_blank" rel="noopener noreferrer" href="mailto:info.nmrxiv@uni-jena.de?subject=nmrXiv feedback/suggestions&body=Hi,<Add your suggestions here>">here</a>',
             backgroundColor: '#fafbfc', // Defaults to `#fff`.
             textColor: '#091E42', // Defaults to `#000`.
             isCloseable: true, // Defaults to `true`.