Guide for NRICaribou

Transcription

NRICARIBOU
nricaribou.cc.umanitoba.ca
Multi-role virtual server
Overview and guide
Paul Galpern
pgalpern@gmail.com
Prepared for: Micheline Manseau
September 7, 2011
Please note:
For security reasons, usernames and passwords in this
document have been removed and replaced with a
reference code. Use the document sent under separate
cover to find these credentials.
NRICARIBOU Overview and Guide (September 7, 2011)
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1
An overview of the
structure of the
NRICARIBOU
virtual computer, with
some simplification.
Entry point
University of Manitoba IST Virtual Computing Facility
Runs many virtual computers using the VMWare operating system
World wide web server
Apache software
See next pages for
further description.
The figure also
attempts to show
hierarchical
relationships among
these elements.
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2
Database server
MySQL software
contains many databases (e.g. for MicroSatServer, lecol-ck.ca, etc.)
PHP programming language
A multi-purpose scripting tool that interfaces with the world wide web and the database server
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(a) http://www.lecol-ck.ca
website administered using Catalyst web application
(b) http://www.pademp.com
website administered using WordPress web application
Public functions
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R programming language
A multi-purpose scripting tool that
interfaces with PHP and the
database server
Tools
Boxes indicates an
entry point, tool or
public function
associated with
NRICARIBOU.
NRICARIBOU (a virtual computer/server running Windows Server 2003 operating system)
Windows computer name: \\nricaribou
DNS name: nricaribou.cc.umanitoba.ca; Aliases: lecol-ck.ca, pademp.com
Static IP address: 130.179.18.163
(c) http://nricaribou.cc.umanitoba.ca/allelematch/
website administered using WordPress web application
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(d) http://nricaribou.cc.umanitoba.ca/mss/
website containing MicroSatServer web application
administered using several tools that can be accessed from the NRICARIBOU desktop:
PHPMaker (template design and automatic PHP code generation for the database table pages)
Manual coding in R and PHP (with source code stored in C:\MicroSatServer)
Windows Server scheduled tasks that run Windows Powershell scripts
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File server
FileZilla FTP software
Windows VPN software
1. University of Manitoba IST Virtual Computing Facility
Purpose:
Provides the "cloud computing" or virtual computing framework (i.e. a facility to share
CPU, disk and network resources among multiple "virtual" computers). Entering via this
level of the hierarchy provides the most power. For example can recover complete
backups of the entire NRICARIBOU computer, as well as accessing the NRICARIBOU
desktop. Andrew Perchaluk (perchalu@cc.umanitoba.ca) at IST can provide assistance at
this level of the hierarchy, including issues with the Windows 2003 Server operating
system.
Control via: VMWare vSphere client: vcenter.cc.umanitoba.ca
Username:
<username1>
Password
<password1>
2. NRICARIBOU
Purpose:
This is a virtual windows computer that runs all the web, database, and other relevant
software. This can be accessed using the vSphere client. Andrew Perchaluk
(perchalu@cc.umanitoba.ca) at IST can provide assistance at this level of the hierarchy,
including issues with the Windows 2003 Server operating system.
Control via: VMWare vSphere client: vcenter.cc.umanitoba.ca OR
Remote desktop protocol client: nricaribou.cc.umanitoba.ca accessed only from a U.
Manitoba IP address. Note same username/password is used for vSphere and for
windows logon.
Username:
<username1>
Password
<password1>
3. World wide web server
Purpose:
Uses Apache software to send web pages when the computer receives an http:// request
through the network. Control at this level consists of either stopping/restarting the
Apache web server on the rare occasion it crashes, or when necessary, tweaking the
Apache configuration files. These tools can be found in c:\xampp\apache\.
Control via: NRICARIBOU desktop
4. Database server
Purpose:
A database running MySQL software that can store and quickly access large amounts of
data. Data can be queried, inserted, and changed using SQL statements. Data used to run
websites is stored here, as well as data that is stored for scientific purposes
(MicroSatServer data).
Control via: MySQL Query browser: nricaribou.cc.umanitoba.ca on port 3306 OR
Web-based query browser: http://nricaribou.cc.umanitoba.ca/phpmyadmin/
Username:
root
Password
<password2>
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5. File server
Purpose:
Provides remote access to the files on the NRICARIBOU computer. There are two means
of access: FTP and VPN (virtual private network, which lets the user treat folders on
NRICARIBOU as if they were on their own computer).
Control via: FileZilla FTP client: nricaribou.cc.umanitoba.ca using an active connection OR
Windows VPN client: nricaribou.cc.umanitoba.ca (then go to \\nricaribou in file
explorer) accessible only from a U. Manitoba IP address
Username:
<username1> (for both FTP and VPN)
Password
<password1> (for both FTP and VPN)
6. PHP programming language
Purpose:
A scripting language that is run by the web server, and is used to build web pages in real
time, often taking information from a database. It can also read and write files on
NRICARIBOU. Modifications to PHP code or configuration settings need to be done in a
text editor, and can be accessed from the NRICARIBOU desktop.
7. R programming language
Purpose:
A statistical programming language that for convenience was used to code the
MicroSatServer web application. Like PHP it can also access the database directly, and
read and write files on NRICARIBOU. It interfaces with the web via PHP (i.e. it is called
by PHP, and sends its information to the web through PHP). Modifications to R code
need to be done in a text editor, and these can be accessed from the NRICARIBOU
desktop.
8. http://www.lecol-ck.ca
Purpose:
Micheline's website. It runs using the Catalyst Content Management system (which in
turn runs using PHP and the MySQL database). Content can be updated via the link given.
Please see the appendix for additional passwords that are required to manage this website.
In particular those that are used to access the Zonedit nameserver which creates the link
between the lecol-ck.ca domain name and the NRICARIBOU IP address.
Control via: http://lecol-ck.ca/admin/
Username:
See Micheline Manseau
Password
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9. http://www.pademp.com
Purpose:
A website created by Sones for the Peace-Athabasca Delta Ecological Monitoring
Program. It uses the WordPress content management system (which in turn uses PHP and
the MySQL database). Content can be updated via the link given. Please see the
appendix for additional passwords that are required to manage this website. In particular
those that are used to access the Zonedit nameserver which creates the link between the
pademp.com domain name and the NRICARIBOU IP address.
Control via: http://pademp.com/wp-admin/
Username:
Password
10. http://nricaribou.cc.umanitoba.ca/allelematch/
Purpose:
A website created by Paul Galpern to share his allelematch software for R, and allow
others to download the source code. It uses the WordPress content management system
(which in turn uses PHP and the MySQL database). Content can be updated via the link
given.
Control via: http://nricaribou.cc.umanitoba.ca/allelematch/wp-admin/
Username:
admin
Password
<password2>
11. http://nricaribou.cc.umanitoba.ca/mss/
Purpose:
The MicroSatServer web application. It provides a front-end to the genetic data stored in
the database server, as well as analysis tools specifically for this genetic data. Menu and
display pages are coded in PHP. Database table display pages are automatically generated
using the PHP templating tool PHPMaker. All analysis routines are coded in R.
Automated tasks (such as database table synchronization, backups and temporary file
deletion) are controlled using the Windows 2003 Scheduled Task application which in
turn runs Windows Powershell scripts. Modifying the functioning of this web application
is largely a programming task. Generally all tools required to modify the web application
can be accessed from the NRICARBIOU desktop. The operating web application requires
username/password credentials to access.
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Technical at a glance
IP address: 130.179.18.163 (static)
DNS names: nricaribou.cc.umanitoba.ca, lecol-ck.ca, ikpodcasts.lecol-ck.ca,
inuitknowledge.lecol-ck.ca, pademp.com
Open TCP ports (all IP addresses): 80 (HTTP), 20 (FTP), 21 (FTP), 3306 (MySQL)
Open TCP ports (restricted to U. Manitoba IP addresses): 3389 (RDP), 1723, 3306 (VPN)
Internet address registry: nricaribou.cc.umanitoba.ca (through umanitoba.ca), *.lecol-ck.ca
(CIRA through Visual Lizard?), pademp.com (?)
Nameservers: nricaribou.cc.umanitoba.ca (umanitoba.ca), *.lecol-ck.ca (zonedit.com1),
pademp.com (zonedit.com1)
Virtual platform: VMware vCenter server v4.1.0
Operating system: Windows Server 2003 R2 Enterprise Service Pack 2
Web hosting platform: XAMPP (Apache 2.0/PHP v5.3.0)
Database platform: MySQL 5.1.37
FTP platform: FileZilla server 0.9.32
Other Windows server roles: Routing and Remote Access (Firewall and VPN)
Backup and recovery: Weekly backup of entire NRICARIBOU hard disk. Most recent backup
is held (VMware). Daily backup of microsatserver, lecol-ck, inuitknowlege, and ikpodcasts
databases. A complete sequence of backups of these databases is retained.
University of Manitoba IST support: Andrew Perchaluk (perchalu@cc.umanitoba.ca)
administers Windows virtual machines, and ensures that the Windows operating system is
regularly updated. Any issues with the server's virtual hardware (i.e. disk, network, CPU),
network security or with the operating system can be addressed to him. Issues with any other
software on NRICARIBOU, including firewalls, the web and database servers should be
addressed to Paul Galpern (pgalpern@gmail.com).
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See Appendix for access to zonedit.com nameservers.
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How-to guides
How can I access the NRICARIBOU Windows desktop?
How can I move a file onto or off of NRICARIBOU?
How can I move a file onto NRICARIBOU so someone else can download it through the web?
How can I build a mini-website on NRICARIBOU to share files?
How can I restart MicroSatServer because it is not responding?
How can I query the MicroSatServer database?
Show me some SQL queries that I can do on the MicroSatServer database.
How can I recover a database backup for MicroSatServer?
How can I create a username/password to permit someone new to access to the MicroSatServer
web application?
I am a programmer tasked with modifying the MicroSatServer web application. Where do I
start?
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How can I access the NRICARIBOU Windows desktop?
There are two ways of doing this. The second (using an RDP client) is more technical, and will
not be explained here. (Note that NRICARIBOU blocks an RDP connection unless it originates
from a U. Manitoba IP address.)
1. Login to a computer on which the VMWare vSphere client is installed (e.g. GAMMA in
Micheline's office). You can install the client on a new computer by downloading the software
from: http://vcenter.cc.umanitoba.ca. The computer should not be on a network with a highly
restrictive firewall.
Windows login information for GAMMA in Micheline's office:
username: Micheline Manseau
password: <password1>
2. Run the vSphere client, and login using the following information:
IP address / Name: vcenter.cc.umanitoba.ca
User name: <username1>
Password: <password1>
3. Click on the "Virtual Machines" tab, and then right-click on nricaribou. Select Open Console.
You may have to click on Hosts and Clusters prior to clicking on Virtual Machines.
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4. The screen of NRICARIBOU should appear. Likely it will be showing the screen saver.
Click on the screen, and then press CTRL-ALT-INSERT to login. Note that it says to press
CTRL-ALT-DELETE to login, but because you are remote use INSERT instead.
5. You are now logging on to Windows. Use the following credentials:
username: <username1>
6. The desktop of NRICARIBOU should appear. On the desktop are several shortcuts that may
be useful. This virtual computer should be treated like any other computer.
7. Make sure to logoff Windows when you are finished. Also exit the vSphere client for
security reasons.
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How can I move a file onto or off of NRICARIBOU?
There are numerous reasons why this might be necessary. There are two ways to do this. FTP is
reliable and easy, but it is also slow and best suited for a small number of files. VPN is the way
to go for frequent file transfers. There is a folder on NRICARIBOU where files are
uploaded/downloaded to and from. See the end of this section.
Moving files using FTP
1. Make sure that the computer from which you are sending or receiving the files has an FTP
client installed, and is not behind a restrictive firewall. FileZilla has been installed on GAMMA
in Micheline's office for convenience. You can install FileZilla to another computer by
downloading the client from: http://filezilla-project.org/download.php. Other FTP clients will
also work.
2. Load FileZilla. Enter the following information, and press Quickconnect.
host: nricaribou.cc.umanitoba.ca
passowrd: <password1>
3. If this is a new installation you will also have to set it to Active mode. Go to
EditSettingsFTPActive.
4. Drag the files to the yellow area on FileZilla and they will be uploaded to NRICARIBOU.
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5. To download files from FileZilla, click on a file in the yellow area and drag it to the desktop
or some other location on your computer.
Moving files using a VPN (Virtual Private Network)
Steps for doing this from GAMMA in Micheline's office are given, as VPN functionality has
already been established on this machine. To install VPN on another computer requires many
manual steps, including tweaking firewalls. Instructions are not given.
1. Login:
2. Click on "nricaribou_vpn" icon on GAMMA. Then click on "manseau_transfer_ftp on
nricaribou" icon on GAMMA.
3. The resulting window that opens is like any windows file
folder. Files can be copied to or from this folder.
Where do the files I transfer go to/come from on NRICARIBOU?
All files transferred using FTP or VPN illustrated above are coming from, or going to a folder on
the desktop of NRICARIBOU called manseau_transfer_ftp.
To access this folder on NRICARIBOU:
1. Login to the NRICARIBOU desktop (see: How can I access the NRICARIBOU Windows
desktop?)
2. Click on the manseau_transfer_ftp folder on the desktop.
3. Move files to or from this folder in the usual manner.
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How can I move a file onto NRICARIBOU so someone else can
download it through the web?
This is very useful when a file must be sent that is too large for email. Or, when you wish to
make some materials available for others to download at their convenience.
1. Follow steps from How can I move a file onto or off of NRICARIBOU?.
2. Access the NRICARIBOU desktop (see: How can I access the NRICARIBOU Windows
desktop?) File will now be stored in the folder manseau_transfer_ftp visible on the desktop.
3. Move the file to one of two locations depending on how you want others to access it.
a) To have users download a file at nricaribou.cc.umanitoba.ca move the file you just
transferred to the folder c:\xampp\htdocs. You can tell others to download this file
(abcdefgh.zip) using their browser. The address for this file would then be:
http://nricaribou.cc.umanitoba.ca/abcdefgh.zip
b) To have users download a file at lecol-ck.ca move the file you just transferred to the
folder c:\xampp\htdocs\lecol-ck. You can tell others to download this file (abcdefgh.zip)
using their browser. The address for this file would then be:
http://lecol-ck.ca/abcdefgh.zip
Note that, when giving a web address for your file, the capitalization must be exact. For
simplicity, don't create files for web download that have spaces or unusual characters in
their names. It is also good practice to go with all lower case in order to avoid typing
errors.
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How can I build a mini-website on NRICARIBOU to share files?
There is a conference coming up and you want to share some files. Or a course, and we need a
repository for papers and other reference material. A simple page with links to these files
constitutes a website and can quickly be put together by moving the files onto NRICARIBOU,
and creating an index page in HTML (Microsoft Word can be used to save pages in this format).
1. Create an index page using Microsoft Word. You can use this file as a template and open it in
Microsoft Word. The index can be very simple: some text, with some of the words hyperlinked.
Hyperlink by highlighting a word or words and pressing CTRL-K in Microsoft Word, and
entering the filename and extension you want to link in the "Address" part of the dialog (no path
is required).
2. Save the file as web page in Microsoft Word with the name index.html. This will create a file
with this name and a folder called index_files in the folder where you saved it.
3. Move this file (index.html) and the folder it created (index_files) and all other files that are
hyperlinked on it onto NRICARIBOU. Follow steps from How can I move a file onto or off of
NRICARIBOU? This process will also work for folders containing files.
desktop?) Files will now be stored in the folder manseau_transfer_ftp visible on the desktop.
5. Go to the folder c:\xampp\htdocs\ and create a new folder with a short name that will be the
de facto name of your website. New folder example: c:\xampp\htdocs\examplesite\.
6. Copy the files from manseau_transfer_ftp to the new folder.
7. Using your browser go to http://nricaribou.cc.umanitoba.ca/whatever/, replacing whatever
with the name of the new folder. The browser should automatically load the index page you
created, and the links should load the files.
Note that when naming files and folders for the web capitalization must be exact. Don't create
files for web download that have spaces or unusual characters in their names. It is also good
practice to go with all lower case in order to avoid typing errors.
8. You can advertise this link as your mini-website!
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How can I restart MicroSatServer because it is not responding?
You will know the MicroSatServer web application is non-responsive if you try to login in the
usual way (e.g http://nricaribou.cc.umanitoba.ca/mss/) and after you enter your information
nothing happens for more than 5 seconds. This occurs because the Apache web server software
has crashed. The reason for the crash is complex, but ultimately it is caused by a bug in the
Apache software. Many attempts have been made to work around this bug with good success,
but likely such freezes will still appear from time to time.
The following steps are required to restart the Apache web server software. This will also restart
MicroSatServer.
1. Login to the NRICARIBOU desktop (see: How can I access the NRICARIBOU Windows
desktop?)
2. Click on the "Control web and ftp server" icon.
3. The following dialog should appear. If you receive an error message, then it is already active.
So, click on the orange icon near the clock.
4. Click the Stop button for Apache (highlighted above).
A message saying the server has stopped should appear
below. Wait about 30 seconds. Click the start button for
Apache. In about 5 seconds the word Running should
appear highlighted in green. If it does not appear, repeat
these steps. Patience is key. Eventually the server will
restart and "Running" will appear indicating everything is
okay.
5. Go to http://nricaribou.cc.umanitoba.ca/mss/ on any
computer and check you can login normally.
6. If nothing seems to work, do an old-fashioned reboot. Click on the Start button on the
NRICARIBOU desktop. Then click the shut-down button. Make sure you choose restart in the
drop-down box. You'll need to enter a few random characters under "Comments" When the
computer restarts all the servers will start too, and you should be able to login again.
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How can I query the MicroSatServer genetic database?
Background
There are two types of MySQL databases on NRICARIBOU: (1) website content databases;
and, (2) scientific databases. The first type can generally be ignored because content
management software maintains and queries them. MicroSatServer is a web application built
around a database of the second type, and occasionally queries will be required that are not
performed automatically by MicroSatServer.
Two methods for sending SQL queries to NRICARIBOU databases are given. The first uses a
web application called phpMyAdmin that will work from locations with highly restrictive
firewalls. A second alternative uses MySQL client software. It is fast, efficient, and
recommended for serious users, but will not work from restricted locations.
Using the phpMyAdmin web application
1. Open a web browser on any computer, and go to:
http://nricaribou.cc.umanitoba.ca/phpmyadmin/
2. Use the following credentials to login:
username: root
3. Click on microsatserver in the left panel to
browse and query the MicroSatServer database.
4. Click on a table in the left panel to begin
browsing the contents of that table.
5. Select the SQL tab to enter an SQL query. For
example enter the following and click "Go"
SELECT * FROM pellet WHERE population_id = 'North Interlake' AND collection_year =
2004;
6. Many additional operations on database tables can be performed using the tabs. Note
specifically Import and Export which can interface with Excel using CSV files.
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Using the MySQL client web application
This has been installed on GAMMA in Micheline's office. If you wish to install this software on
a Windows computer, please download an installation package from this address:
http://nricaribou.cc.umanitoba.ca/repository/ mysql-gui-tools-5.0-r17-win32.msi. Other MySQL
clients are also available online and work in a similar manner.
1. Open the MySQL Query browser.
2. Enter the following:
host: nricaribou.cc.umanitoba.ca
port: 3306
username: root
default schema: microsatserver
3. Queries can be entered in the top left box, and results appear in the bottom box.
4. It is also possible to edit a datum in a table by clicking on Edit at the bottom of the screen,
making changes as if using a spreadsheet, and then clicking Apply changes. Keep in mind it is
not possible to "undo" a change to a database table as it would be using spreadsheet software.
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Show me some SQL queries that I can do on the MicroSatServer genetic
database
The MicroSatServer web application automatically handles most of the common queries on the
database. On occasion, however, it may be necessary to find records in a table that fulfil certain
complex criteria, or to use the contents of one table to look up information on a second table.
Another common query is to replace the fields in multiple records with a new value, avoiding
tedious manual editing of each record in MicroSatServer.
Structured Query Language (SQL) qualifies as a simple programming language, although
programming experience is not required to use it. An SQL query is most often a command
written in English that asks the database to find records (SELECT), add records (INSERT),
remove records (DELETE), or change records (UPDATE) in a table. The format of these
commands is highly structured, and many excellent references and tutorials are available on the
web that explain this syntax. A good place to start is the MySQL reference manual:
http://dev.mysql.com/doc/refman/5.1/en/.
To perform any of the following example queries first open phpMyAdmin or a query browser by
following the steps in How can I query the MicroSatServer database? The intention, here, is not
to give an introductory tutorial in SQL, but rather indicate some common applications of queries
and demonstrate broadly what is possible.
Example 1: View all records in a table
SELECT * FROM goldgenotype
SQL
Query




SELECT means
that records should be returned
return all columns (or fields) from the table
goldgenotype indicates the name of the table
The full analysis-ready "gold" genotype table should be returned (where -99 indicates data that
is not "gold" or missing due to amplification failure)
* means
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Example 2: View specific records from a table
SELECT * FROM pellet WHERE (population_id =
SQL
'Maligne' OR population_id = 'Tonquin') AND
Query 2006, 2007, 2008, 2009, 2010)







SELECT means
* means return all columns (or fields) from the table
pellet indicates the name of the table
WHERE indicates that a series of conditions follow
Conditions are in the form of the column name, and operator (=, <, > etc.) and a value. If the
value is text it should be surround in single quotation marks. To specify a range of conditions
IN followed by comma separated list surrounded in brackets is given.
AND and OR are logical terms
Only the specific records from the pellet collection table are returned
Example 3: View specific columns from a table
SELECT pcid, gold_flag FROM bm848 WHERE
SQL
batch_id = 'Tonquin 2009'
Query





'Brazeau' OR population_id =
collection_year IN (2004, 2005,
(bm848a=-99 OR bm848b=-99) AND
SELECT means
pcid, gold_flag means return only these columns
bm848 indicates the name of the table
This query returns the PCID and gold flag status for all missing (-99) bm848 genotypes in the
Tonquin 2009 batch.
Example 4: View specific records from a table using a fragment of text
SELECT pcid, abi_filename FROM map2c WHERE abi_filename REGEXP
SQL
Query






'mkabi'
SELECT means
pcid, abi_filename means return only these columns
map2c indicates the name of the table
REGEXP indicates that the condition will be met if the text fragment mkabi is found in the
abi_filename column of a record
This query returns the PCID and abi_filenames in the map2c table for data generated by Marina
Kerr (mkabi)
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Example 5: View specific records from a table and remove duplicates
SELECT DISTINCT rt5a FROM rt5 WHERE batch_id REGEXP 'North
SQL
BY rt5a ASC
Query








SELECT means
throw out exact duplicates
rt5a means return only this column for the selected records
rt5 indicates the name of the table
ORDER BY indicates that the results should be sorted by the given column
ASC indicates that this sort should be in ascending order
This query returns the unique alleles in rt5 for the North Interlake population in increasing order
DISTINCT means
Example 6: Count how many records meet a simple criterion
SELECT population_id, collection_year, count(PCID)
SQL
population_id, collection_year
Query





Interlake' ORDER
FROM pellet GROUP BY
SELECT means
population_id, collection_year means return only these columns
count(PCID) indicates that a count should be returned
GROUP BY indicates records should first be grouped according to two criteria before counting the
number in each group
This query returns the number of pellets collected by population and collection year
Example 7: View records from one table using criteria from another table
SELECT pcid, utm_easting, utm_northing FROM pellet WHERE PCID IN
SQL
FROM rt5 WHERE rt5a=100 OR rt5b=100)
Query






(SELECT PCID
SELECT means
pcid, utm_easting, utm_northing means return only these columns
pellet indicates the name of the table
(SELECT ...) indicates a sub-query that returns only PCID which is then used as a criterion for
the first query.
This query returns the sampling locations of individuals with a very rare rt5 allele (100).
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Example 8: Count how many records meet a complex criterion
SELECT population_id, collection_year, count(PCID) FROM goldgenotype WHERE
SQL
PCID IN (SELECT PCID FROM pellet WHERE sampled_by regexp 'Kent') GROUP BY
Query population_id, collection_year;








SELECT means
population_id, collection_year, means return only these columns
count(PCID) indicates that a count of the index should be returned
goldgenotype indicates the name of the table (the analysis-ready genotype table)
(SELECT ...) indicates a sub-query that returns only PCID which is then used as a criterion for
the first query.
GROUP BY indicates records should first be grouped according to two criteria before counting the
number in each group
This query returns the number of partial or complete genotypes in the database by population
and collection year in which someone name Kent was credited as doing the pellet sampling. In
other words: how much credit to we owe Kent for building our analysis-ready dataset!
Example 9: Create a new table
CREATE TABLE example (id
SQL
score FLOAT)
Query




INT, firstname VARCHAR(50), lastname VARCHAR(50),
CREATE TABLE means
make a new table
example indicates the name of the new table
The remaining information in brackets give the name of the columns followed by the type of
column separated by commas. Please see MySQL documentation for details. An alternative
means of creating tables by point-and-click is provided by phpMyAdmin.
This creates a table that is used in the subsequent examples.
Example 10: Insert records into a table
INSERT INTO example (id, firstname,
SQL
'Galpern', 0.95);
Query INSERT INTO example (id, firstname,
lastname, score) VALUES (1, 'Paul',
lastname, score) VALUES (2, 'Micheline',
'Manseau', 0.96);
INSERT INTO example (id, firstname, lastname, score) VALUES (3, 'New',
'Student', 0);







INSERT INTO means
add a record to an existing table
example indicates the name of the new table
The first set of brackets gives the name of the columns separated by commas.
VALUES indicates that values for those columns follow in brackets
Semi colons at the end of each line indicate that multiple SQL statements are given together
An alternative means of inserting records by point-and-click or by CSV import is provided by
phpMyAdmin and the MySQL client.
This adds three records to the table example
21
Example 11: Change records in one or multiple records in a table
UPDATE example SET score = 0.95 WHERE firstname = 'New'
SQL
'Student'
Query







UPDATE means
change a record or records in an existing table
indicates the name of the new table
SET indicates that a column name and value follow
WHERE gives the conditions under which the value in that column should be changed
This changes the score for only one record, as there is only one that meets this condition
An alternative means of editing single records by point-and-click is provided by phpMyAdmin
and by the MySQL client.
NOTE THAT WHEN A FIELD IS CHANGED NO BACKUP IS KEPT OF THE
PREVIOUS VALUE. UPDATE SHOULD BE DONE WITH CAUTION. FIXING AN
INCORRECT UPDATE REQUIRES RECOVERING A DATABASE BACKUP
example
Example 12: Delete records in a table
DELETE FROM example WHERE firstname
SQL
Query





and lastname =
= 'New' and lastname = 'Student'
DELETE FROM means
delete a record
indicates the name of the new table
WHERE gives the conditions under which the record should be deleted
An alternative means of deleting records by point-and-click is provided by phpMyAdmin and by
the MySQL client.
NOTE THAT WHEN A RECORD IS DELETED NO BACKUP IS KEPT. DELETE FROM
SHOULD BE DONE WITH CAUTION. REVERSING THIS REQUIRES
RECOVERING A DATABASE BACKUP
example
Example 13: Delete an entire table
DROP TABLE example
SQL
Query
 NOTE THAT WHEN A TABLE DROP IS USED NO BACKUP IS KEPT.
SHOULD
BE DONE WITH CAUTION. REVERSING THIS REQUIRES RECOVERING A
DATABASE BACKUP
DROP
22
How can I recover a database backup for MicroSatServer?
Disaster can strike the MicroSatServer database in many--fortunately uncommon--ways. The
most likely case is a manual SQL query that has been improperly formed. Equally, incorrect
score data could be uploaded by a user, and determining which records this represents can
sometimes be extremely tedious. Because the database does not remember its previous state, it is
not possible to quickly "undo" the last action as it might be in a word processor or spreadsheet
program. In a variety of scenarios it will be desirable to revert to the last backed-up state of the
database.
Fortunately, the entire contents of the MicroSatServer database are backed-up daily at midnight,
and a record of every backup is retained, making it possible to revert to the state of the database
as it was at any point in the past. Keep in mind that while reverting to a backup made
immediately before the event will fix the problem, it will also remove any desired changes
to the database that have been made in the interim. Use with caution!
desktop?)
2. Find the folder: D:\MicroSatServer\Backups\MySQL\Backups
3. Find the backup you wish to restore to (the most recent will be this morning). They are
named as follows: mssYYMMDD_XXXXXX.sql where "mss" indicates MicroSatServer, YY,
MM and DD are two digit representations of the year, month and day respectively, and
XXXXXX is the size of the database in rows.
4. Copy this backup file to the folder: C:\xampp\mysql\bin
5. Go to the start button and click on Run.
6. Type "cmd" (without quotes)
which runs the shell (right).
7. Type: "cd\xampp\mysql\bin"
8. Type: "mysql –u root –p microsatserver < mssYYMMDD_XXXXXX.sql" replacing the capital
letters as appropriate. Then enter the password: <password2>
10. The database will be restored to its state on YYMMDD at 12:00am.
23
How can I create a username/password to permit someone new
to access the MicroSatServer web application?
The MicroSatServer web application requires a username and password to access it. Granting a
new user access must be done using an SQL query. Two levels of user access are possible.
1. Open phpMyAdmin or a query browser by following the steps in How can I query the
MicroSatServer database?
1. View the existing usernames and passwords. The passwords appear in an encrypted form.
SELECT * FROM caribou_genetics_users
2. Enter the following SQL statement, replacing newuser with a unique username for the person
(typically first initial last name is used). Note that it is necessary to type the long string of
characters giving the encrypted password exactly as shown.
INSERT INTO caribou_genetics_users (username, password, userlevel) VALUES ('newuser',
'4c7e0210b2cc9120dd2a8989677ff205', -1)
3. The new user should be able to login using the username you gave them and the default
password: ran91fer. They should promptly change this password to something else using the
link on the left panel in the MicroSatServer web application.
4. It is also possible to grant access to someone who can only view the analysis-ready results.
Replace -1 with 3 in the query above. Userlevel management has not been robustly
implemented, however, so a malicious and determined person with even this reduced access
could find a way to change some elements of the database.
24
I am a programmer tasked with modifying the MicroSatServer
web application. Where do I start?
The goal of this "Guide" document was to describe the NRICARIBOU computer, and not to
focus on the MicroSatServer web application. Indeed, this is another document in itself! In the
event that such a document does not get written, the following should provide some basic
information from which a programmer could build an understanding of how the web application
operates. Comments included in the PHP and R code may also be helpful.
Below the most important files associated with running the web application are listed, with some
brief comments on their purpose and how they interact with others. Apologies that is not
comprehensive or detailed, but hopefully it provides a place to start!
C:\xampp\htocs\mss\
*list.php
*info.php
*delete.php
menu.php
mssToR_public.php
C:\microsatserver\PHP
This is the root folder of the web application and contains
the public interface of the web application
These files are generated by the PHP templating tool
PHPMaker v6. This version of the software must be used
to edit them. The master template file is C:\Documents
and Settings\pgalpern\My
Documents\PHPMaker\Projects\MicroSatServer_v1.pmp
No changes to these PHP files should be attempted
manually. Use PHPMaker exclusively for this purpose.
Numerous defaults have been tweaked, so the installed
version on the server should be used. In the case of the
pages named for genotype loci, PHPMaker produces a
series of locus*.php templates, and routines in R are
manually called to roll out the PHP pages and search and
replace "locus" as required (see microsatserver_v1.r)
This is the menu page of the MicroSatServer application.
It and its associated includes are the nexus of
MicroSatServer. Using a database lookup it "includes"
any of a number of pages.
This is the configuration file for MicroSatServer's PHP
interface with R. It establishes how PHP will call R
routines. (i.e. using PHP system() calls, and sending
POST data to a MySQL database intermediary)
This folder contains the PHP interface for
MicroSatServer analyses and additional functions coded
by Paul Galpern (pgalpern@gmail.com) .
25
mssToR.php
db_fsa.php
db_fsa.php
importgenetic.php
importpellet.php
importtelem.php
mss_analysis.php
mss_automation.php
mss_sandbox.php
C:\microsatserver\R
mssToR.R
microsatserver_v1.R
pg_genetic.R
C:\microsatserver\PS1
mss_tmpfilecleanup.ps1
D:\microsatserver
D:\microsatserver\backups\mys
ql
microsatserver_backup.ps1
D:\microsatserver\abifiles
This is the PHP side of the MicroSatServer to R interface
Routines to associated with the upload and download of
FSA files from the FSA repository.
Routines to associated with the upload and download of
FSA files from the FSA repository.
PHP interface to R for importing genotype data
Routines to import pellet data (100% PHP)
Routines to import telemetry data (100% PHP)
PHP interface to R for analyses contained in the
"Analysis-ready" section of MicroSatserver
PHP interface to R synchronization of database tables.
This is called twice a day by Windows Task Scheduler,
and also called when a manual synchronization is
requested.
PHP interface to R Technician's Sandbox routines
This folder contains the R routines for MicroSatServer
analyses and additional functions coded by Paul Galpern
(pgalpern@gmail.com) .
This is the R side of the MicroSatServer PHP to R
interface
The guts of MicroSatServer. Contains R code that
provides most of the additional functionality and analysis
routines.
Some genetic support routines called by
microsatserver_v1.R
This folder contains some of the Windows Powershell
routines that are called by the Windows Task Scheduler
Called every hour by the Windows Task Scheduler to
delete temporary files that are older than 24 hours.
Folder on D drive containing file repository and backups
for MicroSatServer. Stored on this drive as there is more
storage space.
Root folder for the daily backups of MicroSatServer
Windows Powershell script called at midnight by the
Windows Task Scheduler to create SQL backups of
MicroSatServer
Folder in which all the ABI raw data is stored as ZIP
files. This folder is controlled directly by the File
Repository section of the MicroSatServer application.
26
Appendix 1 – Additional information for *.lecol-ck.ca
1. Domain name registration for lecol-ck.ca
username/password (?)
This registration will be held by CIRA, and likely managed by Visual
Lizard until a transfer in management is initiated and approved.
2. FTP Account
username: lecol
Full privileges for file and folder creation/deletion etc.
3. MySQL Account
username: lecol
database: lecol, inuitknowledge, ikpodcasts
Full privileges for only these three databases
Can be accessed at localhost using
http://nricaribou.cc.umanitoba.ca/phpmyadmin or remotely using a MySQL
client
4. DNS Service
Zonedit.com (http://zonedit.com)
domains: lecol-ck.ca, www.lecol-ck.ca, inuitknowledge.lecol-ck.ca,
ikpodcasts.lecol-ck.ca
nameservers: ns13.zoneedit.com (66.223.40.121), ns9.zoneedit.com
(66.240.231.42)
These nameservers redirect requests for the above domains to
nricaribou.cc.umanitoba.ca (130.179.18.163)
5. Virtual hosting at nricaribou.cc.umanitoba.ca
Modifications to virtual hosting require manual editing of the
c:\xampp\apache\conf\extra\httpd-vhosts.conf on nricaribou.
Web server at nricaribou.cc.umanitoba.ca will serve pages from the
following folders, according to the domains from which the page is
requested:
lecol-ck.ca,
www.lecol-ck.ca (http://nricaribou.cc.umanitoba.ca/lecol-ck/)
inuitknowledge.lecol-ck.ca (http://nricaribou.cc.umanitoba.ca/lecolck/inuitknowledge/)
ikpodcasts.lecol-ck.ca (http://nricaribou.cc.umanitoba.ca/lecolck/ikpodcasts/)
27

Guide for NRICaribou

Transcription

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