12. Copy Old Wiki Contents¶

Start neurowiki_2016 and log in:
```
ssh -p 8015 hjc@dynamicshjc.case.edu
```

Check for and install system updates on the virtual machine:

sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get autoremove

Start the old (2015) virtual machine if it is not already running.

Export the policy and unit pages from last year’s wiki. You may have decided after last fall’s semester ended to make some changes to these pages on either the live wiki (neurowiki.case.edu) or the development wiki (neurowikidev.case.edu). To determine where the latest changes can be found, visit these pages to view the latest edits on each wiki:

If you made changes in parallel to both wikis that you want to keep, you may need to manually propogate some of those edits.

After determining where you should export pages from, visit Special:Export on that wiki (live wiki | dev wiki). Select these options,

Check “Include only the current revision, not the full history”
Do NOT check “Include templates”
Check “Save as file”

and paste the names of the following pages into the text field:

NeuroWiki pages to export

Course policies
    Attendance
    Lab notebook
    Conceptual checkoffs
    Pre-Unit Quizzes
    Post-Unit Quizzes
    Surveys
    Comments on Course Materials
    Term Paper
        Term Paper Exemplars
            Term Paper Proposal ixk51
            Benchmark I ixk51
            Benchmark II ixk51
            Benchmark III ixk51
            Talk:Benchmark III ixk51
            Benchmark IV ixk51
            Talk:Benchmark IV ixk51
            Final Term Paper ixk51

            Term Paper Proposal agv13
            Benchmark I agv13
            Benchmark II agv13
            Benchmark III agv13
            Talk:Benchmark III agv13
            Benchmark IV agv13
            Talk:Benchmark IV agv13
            Final Term Paper agv13

            Term Paper Proposal axl90
            Benchmark I axl90
            Benchmark II axl90
            Talk:Benchmark II axl90
            Benchmark III axl90
            Talk:Benchmark III axl90
            Benchmark IV axl90
            Talk:Benchmark IV axl90
            Final Term Paper axl90
        Term Paper Proposal
        Term Paper Benchmarks
            Instructions for Grant Proposals
    Term Paper Presentation
    Writing and Editing
    Plagiarism
    Don't Cheat
    The rules apply to everyone, including you.
    Critical Thinking
    The Structure of a Scientific Paper
    How to Read a Scientific Paper
    Fundamental questions about nature
    What does it mean to understand a phenomenon scientifically?
    Course Topics
    The Goals and Promise of Neuroscience

Course syllabus
    Equilibrium Potentials I
        Problem Set 1, Problem 1
        Equilibrium Potentials I Answer 1
    Equilibrium Potentials II
        Equilibrium Potentials II Answer 1
        Equilibrium Potentials II Answer 2
        Equilibrium Potentials II Answer 3
        Equilibrium Potentials II Answer 4
        Problem Set 2, Problem 1
        Problem Set 2, Problem 2
            Equilibrium Potentials II Lab Notebook Table
        Equilibrium Potentials II Answer 5
        Equilibrium Potentials II Answer 6
        Equilibrium Potentials II Answer 7
        Problem Set 2, Problem 3
    Passive Membrane Properties, the Resting Potential, and Electrical Models of Passive Properties
        Passive Membranes Answer 1
        Passive Membranes Answer 2
        Passive Membranes Answer 3
        Passive Membranes Answer 4
        Passive Membranes Answer 5
        Passive Membranes Answer 6
        Passive Membranes Answer 7
    Action Potential I: Qualitative Introduction and Current Clamp
    Action Potential II: Voltage Clamp and Analysis of the Potassium Current
    Action Potential III: Sodium Current, Patch Clamp, and Ion Channels
        Action Potentials III Answer 1
        Action Potentials III Answer 2
    Action Potential IV: Hodgkin-Huxley Equations and Other Conductances
        FirstOrderEquationDerivation
        HodgkinHuxleyModelParameters
    Action Potential V: Design and Analysis of Complex Neurons
        Action Potentials V Lab Notebook Table
    Cable Properties I: Passive Properties
        Cable Theory Parameters and Units‏‎
        DerivationSphericalCell
        CablePropertiesIQuestion4
    Cable Properties II: Temporal Characteristics and Myelination
        Cable Theory Parameters
        CablePropertiesIIQuantities
    Cable Properties III: Design and Analysis of Branching Neurons
    Synaptic Physiology I: Postsynaptic Mechanisms
    Synaptic Physiology II: Presynaptic Mechanisms and Quantal Analysis
    Synaptic Plasticity I: Facilitation and Depression
    Synaptic Plasticity II: Introduction to Long-Term Potentiation
    Synaptic Plasticity III: Design and Analysis of a Plastic Synapse
    Novel Transmitters I: Introduction to Nitric Oxide
    Novel Transmitters II: Design and Analysis of a Nitric Oxide Synapse
    Sensory Neurons: Mechano-Afferent Neurons
    Simple Neuromuscular Models
        Neuromuscular Lab Notebook Table
    A Simple Reflex Loop
    Central Pattern Generators I: From Behavior to a Circuit
        Circuit Analysis Lab Notebook Table
        Cell Identification Table
        Bursting Identification Table
    Central Pattern Generators II: Analysis of Tritonia Escape Swim Circuit Interneurons
    Central Pattern Generators III: Role of Modulation in a Central Pattern Generator
    Neural Correlates of Consciousness
    Student Presentations

Simulations
Help:Editing
NeuroWiki:About
NeuroWiki:Copyrights
Template:Instructor links
User:Hjc
User:Jpg18
Sandbox
Student list
To Do List

Export the pages and save the XML file when given the option.

On the 2016 virtual machine, visit Special:Import and upload the XML file obtained from the 2015 wiki (choose “Import to default locations”).
Since it is possible that the list above is incomplete, visit Special:WantedPages to determine which pages are still missing.

There will be several missing pages related to the class that should be ignored. These are the pages begining with the slash (“/”) character, such as /Equilibrium Potentials I, or with “Private:Template:”, such as Private:Template:Termpaper ‘s Term Paper Proposal‏‎. These appear in the list because the Template:Notebook and Template:Termpaper pages use relative links or name substitution in links for the lab notebooks and term paper benchmanks.

If necessary, repeat steps 4-5 until no relevant pages are missing.
The following pages need to be updated with new dates, personnel, office hours times, etc., or out-dated contents need to be cleared:
If you’d like to add or remove term paper benchmark exemplars, now is a good time to do so. If you remove any, be sure to also delete associated files and images from the “Files to Import” directory.

Todo

The “Files to Import” directory is now hosted online. Add instructions for modifying it.
On the virtual machine, download and then import into the wiki a collection of images and files. This includes the wiki logo, favicon, and figures from the units and benchmark exemplars:
```
wget -P ~ https://neurowiki-docs.readthedocs.io/en/latest/_downloads/BIOL-373-Files-to-Import.tar.bz2
tar -xjf ~/BIOL-373-Files-to-Import.tar.bz2 -C ~
php /var/www/mediawiki/maintenance/importImages.php --user=Hjc ~/BIOL-373-Files-to-Import
sudo apache2ctl restart
rm -rf ~/BIOL-373-Files-to-Import*
```
If you’d like to view the collection of files, you can download it to your personal machine here: BIOL-373-Files-to-Import.tar.bz2

Todo

Update this step with instructions for adding files to the online “BIOL-373-Files-to-Import.tar.bz2” archive, and move the fetch_wiki_files.sh script to an external file in the docs source.

Visit Special:WantedFiles to determine which files are still missing. Files on this list that are struckthrough are provided through Wikimedia Commons and can be ignored.

If there are only a few files missing, download them individually from the old wiki, add them to the “Files to Import” directory, and upload them manually.

If there are many files missing (which is likely to happen if you added a new exemplar), you can use the following script to download them from the old wiki in a batch.

On your personal machine, create the file

vim fetch_wiki_files.sh

and fill it with the following:

fetch_wiki_files.sh

#!/bin/bash

# This script should be run with a single argument: the path to a file
# containing the names of the files to be downloaded from the wiki,
# each on its own line and written in the form "File:NAME.EXTENSION".
INPUT="$1"
if [ ! -e "$INPUT" ]; then
    echo "File \"$INPUT\" not found!"
    exit 1
fi

# MediaWiki provides an API for querying the server. We will use it
# to determine the URLs for directly downloading each file.
WIKIAPI=https://neurowiki.case.edu/w/api.php

# The result of our MediaWiki API query will be provided in JSON and
# will contain some unnecessary meta data. We will use this Python
# script to parse the query result. It specifically extracts only the
# URLs for directly downloading each file.
SCRIPT="
import sys, json

data = json.loads(sys.stdin.read())['query']['pages']

for page in data.values():
    if 'invalid' not in page and 'missing' not in page:
        print page['imageinfo'][0]['url']
"

# Create the directory where downloaded files will be saved
DIR=downloaded_wiki_files
mkdir -p $DIR

# While iterating through the input line-by-line...
while read FILENAME; do
    if [ "$FILENAME" ]; then
        echo -n "Downloading \"$FILENAME\" ... "

        # ... query the server for a direct URL to the file ...
        JSON=`curl -s -d "action=query&format=json&prop=imageinfo&iiprop=url&titles=$FILENAME" $WIKIAPI`

        # ... parse the query result to obtain the naked URL ...
        URL=`echo $JSON | python -c "$SCRIPT"`

        if [ "$URL" ];
        then
            # ... download the file
            cd $DIR
            curl -s -O $URL
            cd ..
            echo "success!"
        else
            echo "not found!"
        fi
    fi
done < "$INPUT"

Make the script executable:

chmod u+x fetch_wiki_files.sh

Copy the bulleted list of missing files found at Special:WantedFiles and paste them into this file:

vim wanted_files_list.txt

You can use this Vim command to clean up the list:

:%s/^\s*File:\(.*\)\%u200f\%u200e (\d* link[s]*)$/File:\1/g

Finally, execute the script to download all the files in the list:

./fetch_wiki_files.sh wanted_files_list.txt

The downloaded files will be saved in the downloaded_wiki_files directory. Copy these to the “Files to Import” directory and upload them to the new wiki manually or using the importImages.php script used in step 9.

Protect every image and media file currently on the wiki from vandalism. Access the database:

mysql -u root -p wikidb

Enter the <MySQL password> when prompted. Execute these SQL commands (the magic number 6 refers to the File namespace):

INSERT IGNORE INTO page_restrictions (pr_page,pr_type,pr_level,pr_cascade,pr_expiry)
    SELECT p.page_id,'edit','sysop',0,'infinity' FROM page AS p WHERE p.page_namespace=6;
INSERT IGNORE INTO page_restrictions (pr_page,pr_type,pr_level,pr_cascade,pr_expiry)
    SELECT p.page_id,'move','sysop',0,'infinity' FROM page AS p WHERE p.page_namespace=6;
INSERT IGNORE INTO page_restrictions (pr_page,pr_type,pr_level,pr_cascade,pr_expiry)
    SELECT p.page_id,'upload','sysop',0,'infinity' FROM page AS p WHERE p.page_namespace=6;

Type exit to quit.

You do not need to protect any wiki pages because the Lockdown extension for MediaWiki does this for you!

Shut down the virtual machine:
```
sudo shutdown -h now
```
Using VirtualBox, take a snapshot of the current state of the virtual machine. Name it “2015 wiki contents migrated”.