Season Of Docs-Community Bonding Period, Meeting-3
Tags: opensource, documentation, gsod
Published: 2020-09-16 13:08:20

On 9th of September, I had a meeting with my mentors with regards to my Google's Season Of Docs project. On 14th September 2020 the community bonding phase had ended and we'd formally entered into the Doc development phase which'll run till the 30th of November.
I was able to accomplish the following tasks this week:-

1. I made some changes to the "About SynBioHub" page & added some material to the "Further References page". Also I made some changes to the "Installations" page under the docker section.

2. Proof-read all the API documentation that was copied to the new documentation to search for any grammatical/spelling errors in the documentation.

3. Pushed the Hugo files to the following github repo's: [synbiohub-docs](https://github.com/SynBioHub/synbiohub-docs) & [synbiohub.github.io](https://github.com/SynBioHub/synbiohub.github.io)
The synbiohub-docs repo contains the Source code of the website and synbiohub.github.io repo contains a fully rendered version of the website. Made quite a few PR's on both the repo's trying to get the right configuration.

4. Was successfully able to install SynBioHub on Mac OS by following the following steps:-

a) Download git onto your Mac using ```brew install git``` and then configure you name and email using the following commands
```git config --global user.name "<your name>"```  and ```git config --global user.name "<your email>" ``` respectively.

b) Download Docker for Mac OS from [here](https://docs.docker.com/docker-for-mac/install/).

c) Start Docker-desktop.

d) Open your terminal and enter ``` cd ``` just to make sure that you're in your home directory at that instant.

e) Clone the synbiohub-docker repo using the following command ```git clone https://github.com/synbiohub/synbiohub-docker```.

f) Start a synbiohub instance with ```docker-compose --file ./synbiohub-docker/docker-compose.yml up```.
or you may follow the alternate method, i.e using SBOL explorer:
```sysctl -w vm.max_map_count=262144```

```docker-compose --file ./synbiohub-docker/docker-compose.yml --file ./synbiohub-docker/docker-compose.explorer.yml up```

g) In your browser search for localhost:7777 and it'll take you to a setup page when you'll run it for the very first time.

I was successfully able to run SynBioHub on Ubuntu 20.04 a few months ago, but a couple of days back while trying to reconfigure, I encountered an error. I've mentioned the first few steps for Ubunutu 20.04.

Step 1: Install Git for linux and configure it.[Steps are similar to Mac OS]

Step 2: Install Docker from https://docs.docker.com/engine/install/ for Linux.

Step 3: Open the Terminal using Ctrl+Alt+t.

Step 4: Enter the command “systemctl start docker” and press “Enter/Return” command. It’ll ask you to enter your password after which docker will successfully start without giving any output.

Step 5: Then, enter the command “cd” into your terminal, which’ll take you to your home directory.

Step 6: Pull the docker-compose composition by entering the following command into you terminal: “git clone https://github.com/synbiohub/synbiohub-docker”.

Step 7: After executing the following command: ```docker-compose --file ./synbiohub-docker/docker-compose.yml up```
I received the follwing error:
```
virtuoso_1   | chmod: cannot access '/clean-logs.sh': No such file or directory
virtuoso_1   |
virtuoso_1   | Wed Sep 16 2020
virtuoso_1   | 12:44:27 { Loading plugin 1: Type `plain', file `wikiv' in `/usr/local/virtuoso-opensource/lib/virtuoso/hosting'
virtuoso_1   | 12:44:27   WikiV version 0.6 from OpenLink Software
virtuoso_1   | 12:44:27   Support functions for WikiV collaboration tool
virtuoso_1   | 12:44:27   SUCCESS plugin 1: loaded from /usr/local/virtuoso-opensource/lib/virtuoso/hosting/wikiv.so }
virtuoso_1   | 12:44:27 { Loading plugin 2: Type `plain', file `mediawiki' in `/usr/local/virtuoso-opensource/lib/virtuoso/hosting'
virtuoso_1   | 12:44:27   MediaWiki version 0.1 from OpenLink Software
virtuoso_1   | 12:44:27   Support functions for MediaWiki collaboration tool
virtuoso_1   | 12:44:27   SUCCESS plugin 2: loaded from /usr/local/virtuoso-opensource/lib/virtuoso/hosting/mediawiki.so }
virtuoso_1   | 12:44:27 { Loading plugin 3: Type `plain', file `creolewiki' in `/usr/local/virtuoso-opensource/lib/virtuoso/hosting'
virtuoso_1   | 12:44:27   CreoleWiki version 0.1 from OpenLink Software
virtuoso_1   | 12:44:27   Support functions for CreoleWiki collaboration tool
virtuoso_1   | 12:44:27   SUCCESS plugin 3: loaded from /usr/local/virtuoso-opensource/lib/virtuoso/hosting/creolewiki.so }
virtuoso_1   | 12:44:27 OpenLink Virtuoso Universal Server
virtuoso_1   | 12:44:27 Version 07.20.3229-pthreads for Linux as of Aug 21 2019
virtuoso_1   | 12:44:27 uses parts of OpenSSL, PCRE, Html Tidy
virtuoso_1   | 12:44:27 Database version 3100
virtuoso_1   | 12:44:27 Trying to access the database schema data before the schema has been initialized. This is usually caused by an unrecoverable corrupted database file.
virtuoso_1   | 12:44:27 Server exiting
```

5) I was able to go through the research paper sent by Prof. Myers.

6) I'd already implemented quite a few of the API operations using the UI at `https://synbiohub.org`. The one's I haven't are Permission, attachment and admin endpoints.


Following are the issues that I faced while completing this week's tasks:
1. It took me quite a long time, i.e almost this whole week to configure the documentation hosted at synbiohub.github.io . I'd also opened a PR in ACE documentation's repo and based on their instructions I corrected my "config.toml" file, which has partially solved the problem.

2. I was unable to reinstall synbiohub's local instance onto my PC running Ubuntu 20.04

3. I didn't have access to a Windows PC, hence was unable to perform SynBioHub's installation.

4. I also have some doubts pertaining to the research paper shared by Prof. Myers.

5. I was unable to read the doc shared by Jet Mante, due to lack of time this week. I'll surely try to read it before the next meeting.

The next meeting is scheduled to be on 16th September & I hope to discuss quite a few points including synbiohub.github.io's configuration, basic layout of the GUI documentation and also a few queries that I have in the research paper.