Skip to content

Commit 5e82dc2

Browse files
NEStockNEStock
committed
Format new Documentation Page
1 parent 078a92d commit 5e82dc2

File tree

1 file changed

+111
-60
lines changed

1 file changed

+111
-60
lines changed

‎frontend/src/pages/DocumentationPage.vue‎

Lines changed: 111 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -5,93 +5,140 @@
55
<q-card flat class="q-mt-lg">
66
<q-card-section>
77
<div class="text-h2">Uploading to and Downloading Data from the EMBER-DANDI Archive</div>
8-
<p>These instructions describe how to upload to and download data from the EMBER-DANDI Archive. The instructions are divided into two main sections: one set of instructions for novice users, and one set for experienced users of DANDI. Navigate to a section depending on your experience with each tool.</p>
9-
8+
<p>
9+
These instructions describe how to upload to and download data from the EMBER-DANDI
10+
Archive. The instructions are divided into two main sections: one set of instructions
11+
for novice users, and one set for experienced users of DANDI. Navigate to a section
12+
depending on your experience with each tool.
13+
</p>
14+
1015
<div class="text-h5">I'm new to Python, CLI, and/or DANDI</div>
11-
<p>If you're new to Python, follow these instructions to get Python and a virtual Anaconda environment installed:</p>
16+
<p>
17+
If you're new to Python, follow these instructions to get Python and a virtual Anaconda
18+
environment installed:
19+
</p>
1220
<ol>
13-
<li><LinkText text="Install Anaconda"
14-
uri="https://www.anaconda.com/docs/main"
15-
/>
16-
to get Python and standard data science/machine learning packages, and a desktop application</li>
21+
<li>
22+
<LinkText text="Install Anaconda" uri="https://www.anaconda.com/docs/main" /> to get
23+
Python and standard data science/machine learning packages, and a desktop application
24+
</li>
1725
<li>After installing, launch the Anaconda Navigator</li>
1826
<li>Navigate to the "Environments" tab on the left pane</li>
1927
<li>Create a new environment with your desired name</li>
2028

21-
<img src="/documentation-images/anaconda_navigator.png" alt="Anaconda Navigator" style="width: 1000px; height: auto;">
29+
<img
30+
src="/documentation-images/anaconda_navigator.png"
31+
alt="Anaconda Navigator"
32+
style="width: 1000px; height: auto"
33+
/>
2234

23-
<li>Click on the newly created environment, press the "Play" icon and select "Open Terminal"</li>
35+
<li>
36+
Click on the newly created environment, press the "Play" icon and select "Open
37+
Terminal"
38+
</li>
2439
</ol>
2540

2641
<div class="text-h6">How do I upload data?</div>
2742
<ol>
28-
<li>Create a GitHub account
29-
<LinkText
30-
text="here"
31-
uri="https://github.com/"
32-
/>
33-
(ideally with an .edu account for quicker approval)</li>
34-
<li>Register with
35-
<LinkText text="EMBER-DANDI"
36-
uri = "https://dandi.emberarchive.org/"
37-
/>
38-
using the "Log In With GitHub" button in the top right corner</li>
39-
<li>Wait for confirmation of review. In the meantime, convert your data to approved standards</li>
43+
<li>
44+
Create a GitHub account
45+
<LinkText text="here" uri="https://github.com/" />
46+
(ideally with an .edu account for quicker approval)
47+
</li>
48+
<li>
49+
Register with
50+
<LinkText text="EMBER-DANDI" uri="https://dandi.emberarchive.org/" />
51+
using the "Log In With GitHub" button in the top right corner
52+
</li>
53+
<li>
54+
Wait for confirmation of review. In the meantime, convert your data to approved
55+
standards
56+
</li>
4057
<li>Upon approval, log in with the "Log In With GitHub" button</li>
4158
</ol>
4259

4360
<div class="text-h6">Convert files to appropriate standards</div>
4461
<ol>
4562
<li>
46-
<LinkText text="Install NWB GUIDE"
47-
uri="https://nwb-guide.readthedocs.io/en/stable/installation.html"
48-
/>
49-
, which converts common neuroscience data formats into Neurodata Without Borders standards</li>
50-
<li>Complete key tutorials for NWB GUIDE:
63+
<LinkText
64+
text="Install NWB GUIDE"
65+
uri="https://nwb-guide.readthedocs.io/en/stable/installation.html"
66+
/>
67+
, which converts common neuroscience data formats into Neurodata Without Borders
68+
standards
69+
</li>
70+
<li>
71+
Complete key tutorials for NWB GUIDE:
5172
<ul>
5273
<li>
53-
<LinkText text="Generate a dataset"
54-
uri="https://nwb-guide.readthedocs.io/en/stable/tutorials/dataset.html"
55-
/>
74+
<LinkText
75+
text="Generate a dataset"
76+
uri="https://nwb-guide.readthedocs.io/en/stable/tutorials/dataset.html"
77+
/>
5678
</li>
57-
<li>Convert
58-
<LinkText text="a single session of data"
59-
uri="https://nwb-guide.readthedocs.io/en/stable/tutorials/single_session.html"
60-
/>
61-
</li>
62-
<li>Convert
63-
<LinkText text="a multi-session of data"
64-
uri="https://nwb-guide.readthedocs.io/en/stable/tutorials/multiple_sessions.html"
65-
/>
79+
<li>
80+
Convert
81+
<LinkText
82+
text="a single session of data"
83+
uri="https://nwb-guide.readthedocs.io/en/stable/tutorials/single_session.html"
84+
/>
85+
</li>
86+
<li>
87+
Convert
88+
<LinkText
89+
text="a multi-session of data"
90+
uri="https://nwb-guide.readthedocs.io/en/stable/tutorials/multiple_sessions.html"
91+
/>
6692
</li>
6793
</ul>
6894
</li>
69-
<li>Repeat with your own your data
95+
<li>Repeat with your own your data</li>
96+
<li>
97+
Ensure your data is supported by checking the
98+
<LinkText
99+
text="ecosystem compatibility"
100+
uri="https://nwb-guide.readthedocs.io/en/stable/format_support.html"
101+
/>
70102
</li>
71-
<li> Ensure your data is supported by checking the
72-
<LinkText text="ecosystem compatibility"
73-
uri="https://nwb-guide.readthedocs.io/en/stable/format_support.html"
103+
<img
104+
src="/documentation-images/ecosystem.png"
105+
alt="Ecosystem"
106+
style="width: 850px; height: auto"
74107
/>
75-
</li>
76-
<img src="/documentation-images/ecosystem.png" alt="Ecosystem" style="width: 850px; height: auto;">
77108
</ol>
78109

79110
<div class="text-h6">Create an EMBER-DANDIset</div>
80111
<ol>
81112
<li>Log in to EMBER-DANDI with your approved GitHub account</li>
82113
<li>Select the "New Dandiset" button in the top right corner</li>
83114
<li>Fill out basic metadata and hit "Register Dandiset"</li>
84-
<img src="/documentation-images/register_new_dandiset.png" alt="New Dandiset" style="width: 1200px; height: auto;">
115+
<img
116+
src="/documentation-images/register_new_dandiset.png"
117+
alt="New Dandiset"
118+
style="width: 1200px; height: auto"
119+
/>
85120
</ol>
86121

87122
<div class="text-h6">Upload the converted files</div>
88123
<ol>
89-
<li>In the python terminal in your ember-dandi specific environment, run: `pip install -U dandi`</li>
90-
<li>Validate the converted files, replacing `source_folder` with the path to your .nwb files: `dandi validate --ignore DANDI.NO_DANDISET_FOUND "source_folder"`</li>
124+
<li>
125+
In the python terminal in your ember-dandi specific environment, run: `pip install -U
126+
dandi`
127+
</li>
128+
<li>
129+
Validate the converted files, replacing `source_folder` with the path to your .nwb
130+
files: `dandi validate --ignore DANDI.NO_DANDISET_FOUND "source_folder"`
131+
</li>
91132
<li>Navigate to your dataset in the EMBER-DANDI archive and note the ID number</li>
92-
<img src="/documentation-images/test_number_data.png" alt="Test Number Data" style="width: 900px; height: auto;">
93-
<li>Upload your validated .nwb files using the following commands, replacing `&lt;dataset_id&gt;` and `source_folder` with your specific information:
94-
<pre>
133+
<img
134+
src="/documentation-images/test_number_data.png"
135+
alt="Test Number Data"
136+
style="width: 900px; height: auto"
137+
/>
138+
<li>
139+
Upload your validated .nwb files using the following commands, replacing
140+
`&lt;dataset_id&gt;` and `source_folder` with your specific information:
141+
<pre>
95142
dandi download https://dandi.emberarchive.org/dandiset/&lt;dataset_id&gt;/draft
96143
cd &lt;dataset_id&gt;
97144
dandi organize "source_folder" -f dry
@@ -108,32 +155,36 @@ dandi upload -i ember
108155
<li>Click the "Download" tab on the right-hand panel</li>
109156
<li>Copy the command into your python terminal</li>
110157
</ol>
111-
<img src="/documentation-images/download_dandiset.png" alt="Download Dandiset">
158+
<img src="/documentation-images/download_dandiset.png" alt="Download Dandiset" />
112159
<p>To download specific files:</p>
113160
<ol>
114161
<li>Navigate to the URL of the dataset of interest</li>
115162
<li>Click on the "Files" tab on the right-hand panel</li>
116-
<img src="/documentation-images/files_tab.png" alt="Files Tab" style="width: 1200px; height: auto;">
163+
<img
164+
src="/documentation-images/files_tab.png"
165+
alt="Files Tab"
166+
style="width: 1200px; height: auto"
167+
/>
117168
<li>Navigate to the folder containing the desired file</li>
118169
<li>Click the downward pointing arrow icon to download the file</li>
119170
</ol>
120171

121172
<div class="text-h5">I've used DANDI or CLI tools before!</div>
122173
<p>For experienced users, the steps for uploading data are as follows:</p>
123-
<pre class="commands">
174+
<pre class="commands">
124175
dandi download https://dandi.emberarchive.org/dandiset/&lt;dataset_id&gt;/draft
125176
cd &lt;dataset_id&gt;
126177
dandi organize "source_folder" -f dry
127178
dandi organize "source_folder"
128179
dandi validate .
129180
dandi upload -i ember
130-
</pre>
131-
<p>For downloading data, use the standard procedures from the DANDI documentation
132-
<LinkText
133-
text="here"
134-
uri="https://docs.dandiarchive.org/12_download/"
135-
/>
136-
.</p>
181+
</pre
182+
>
183+
<p>
184+
For downloading data, use the standard procedures from the DANDI documentation
185+
<LinkText text="here" uri="https://docs.dandiarchive.org/12_download/" />
186+
.
187+
</p>
137188
</q-card-section>
138189
</q-card>
139190
</div>

0 commit comments

Comments
 (0)