11. Copy Old Wiki Contents¶

Start biol300_2017 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 (2016) 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 spring’s semester ended to make some changes to these pages on either the live wiki (biol300.case.edu) or the development wiki (biol300dev.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:

BIOL 300 Wiki pages to export

Course policies
    Class attendance
    Team evaluations
    Concepts and attitudes surveys
    Problem benchmarks
    Comments on other students' term paper benchmarks
    Term Paper Template
    Model Plan
        Exemplary Model Plan
    Selecting a published model to reproduce
    Term paper proposal
        Exemplary Term Paper Proposal 1
        Exemplary Term Paper Proposal 2
    Benchmark I: Introduction
        Exemplary Introduction Draft 1
        Exemplary Introduction Draft 2
        Exemplary Introduction Draft 3
        Exemplary Introduction Draft 4
        Exemplary Introduction Draft 5
    Benchmark II: Model Description
        Exemplary Model Description Draft 1
        Exemplary Model Description Draft 2
        Exemplary Model Description Draft 3
        Exemplary Model Description Draft 4
        Exemplary Model Description Draft 5
    Benchmark III: Results
        Exemplary Results Draft 1
        Exemplary Results Draft 2
        Exemplary Results Draft 3
        Exemplary Results Draft 4
        Exemplary Results Draft 5
    Benchmark IV: Discussion
        Exemplary Discussion Draft 1
        Exemplary Discussion Draft 2
        Exemplary Discussion Draft 3
        Exemplary Discussion Draft 4
        Exemplary Discussion Draft 5
    Term paper
        Exemplary Final Term Paper 1
        Exemplary Final Term Paper 2
        Exemplary Final Term Paper 3
        Exemplary Final Term Paper 4
        Exemplary Final Term Paper 5
        Exemplary Final Term Paper 6
    Student Presentations
        Presentation Guidelines
    Rationale for modeling and modeling tools
    Plagiarism
    Don't Cheat
    The rules apply to everyone, including you

Course syllabus
    List of Discussion benchmarks
    List of final term papers
Student list
Help:Editing
BIOL 300 Wiki:Copyrights
Template:Instructor links
User:Hjc
User:Jpg18
Sandbox
Wiki Todo list
Hjc Todo list

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

On the 2017 virtual machine, visit Special:Import and upload the XML file obtained from the 2016 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 /Model Plan. These appear in the list because the Template:Termpaper page uses relative links for the 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 benchmark exemplars:

wget -P ~ https://biol-300-wiki-docs.readthedocs.io/en/latest/_downloads/BIOL-300-Files-to-Import.tar.bz2
tar -xjf ~/BIOL-300-Files-to-Import.tar.bz2 -C ~
php /var/www/mediawiki/maintenance/importImages.php --user=Hjc ~/BIOL-300-Files-to-Import
sudo apache2ctl restart
rm -rf ~/BIOL-300-Files-to-Import*

If you’d like to view the collection of files, you can download it to your personal machine here: BIOL-300-Files-to-Import.tar.bz2

Todo

Update this step with instructions for adding files to the online “BIOL-300-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://biol300.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 “2016 wiki contents migrated”.