Developing Online Databases and Serving Biological Research Data

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1 Developing Online Databases and Serving Biological Research Data 1

2 Last Time HTML Hypertext Markup Language Used to build web pages Static, and can't change the way it presents itself based off of user interaction HTML files are created by using HTML elements HTML files can be stored on a web server and accessed via a URL in a web browser 2

3 Last Time HTML elements are a set of 'tags' that suggest to the browser what type of data is being presented Tags are 'wrapped' with angle brackets <> Tags come in pairs Opening HTML tag: <html> Closing HTML tag: </html> Some tags are 'self closing' <input type= text name= sometext /> 3

4 Last Time Any sequence of spaces is treated as a single space White space is typically used to indent HTML to make it more legible Hard to see matching tags Easier to see matching tags Treated the Same 4

5 Last Time HTML is an ever growing standard maintained by the W3C (World Wide Web Consortium) New versions of HTML are developed every so often, include new tags, backwards compatibility with old versions Year Version 1995 HTML HTML HTML 4.0 5

6 Last Time The latest version, yet to be completely adopted, is HTML 5 Currently it's a working draft Canvas, video and audio elements 6

7 Last Time A fairly good reference of HTML tags: 7

8 Last Time PHP (Personal Hypertext Processor Hypertext Processor) is a scripting language that can be used to generate HTML 'on the fly' Web oriented, designed to address the shortcomings of static HTML 8

9 Last Time PHP code can be embedded into HTML, generate HTML or any mix of the two Code is written between the PHP opening and closing tag: <?php?> The same as: //code here <?php //'inline' code?> 9

10 Last Time test.php 10

11 Last Time test.php 11

12 Last Time test.php 12

13 Last Time Values can be stored inside variables, and used again later Variables must be named starting with a dollar sign ($) Variable names cannot have spaces in them camelcasing is a best practice 13

14 Last Time Lines of code must end with a semicolon (;) 14

15 Last Time Functions are named bodies of code that exist 'somewhere else', and can be called by their name Calling a function performs some operations for you and may return a result //call the gettimeofday function gettimeofday(); 15

16 Last Time Parameters or 'arguments' may be and sometimes are required to be given to a function upon calling it Parameters tell the function how more specifically to do it's job // gives hours:minutes:seconds gettimeofday(); // seconds since Jan gettimeofday(true); 16

17 Last Time Parameters can be stored and passed into a function call as string literals, or variables 17

18 Last Time PHP provides the special variables $_GET and $_POST variables to retrieve user input from forms and pass values between web pages These special variables capture user input from a form submission so that PHP can process it 18

19 Last Time $_GET shows the name value pairs in the URL There is a character number limitation, so you can only store so much $_POST doesn't show the name value pairs in the URL 19

20 Last Time The HTML form: <form action='processor.php' method='get'> <input type='text' name='firstname' />... The PHP code to grab user input: $_GET['firstName']; // what the user entered 20

21 Last Time The HTML form: <form action='processor.php' method='post'> <input type='text' name='firstname' />... The PHP code to grab user input: $_POST['firstName']; // what the user entered 21

22 Last Time PHP is a great first scripting language; I can only scratch the surface Tutorial book: Learning PHP, MySQL, and JavaScript ISBN: PHP's website has documentation of just about anything you would want or need to know: (use 'search for' in 'function list' at top right or just read the fine manual) 22

23 Last Time Scaffolding is a term used to describe web interfaces that facilitate CRUD operations within a browser PHPMyAdmin generates scaffolding on the fly from your schema You can see what scaffolding looks like inside PHPMyAdmin by clicking on any table's name 23

24 Database Tier Server Tier Intermediary Tier Client Tier Day 1&2 Day 3 &4 Day 5 Client Browser Database Server Web Server GBIF Server Network Network Network Network 24

25 Today Scaffolding is great, but we can do better Follow along: Building off of scaffolding Exercises No coding (given example code) 25

26 Follow along: Building off of scaffolding Download: Unzip into a directory, and leave that directory open 26

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28 Follow along: The following directions assume that Uconn's central web server, directions for different hosting companies will differ If you have your own hosting, you can upload this file to your own web server, via any means they provide, such as FTP or SSH 28

29 Follow along: Building off of scaffolding Log in to UITS's PHPMyAdmin (or your own web hosts phpmyadmin and load the sql file...) 29

30 If Necessary Select your one and only database by clicking it's name at the top left 30

31 Follow along: Building off of scaffolding Check all, select drop 31

32 Follow along: Building off of scaffolding Click the yes button 32

33 Follow along: Building off of scaffolding You just wiped your database clean Next, import a fresh schema Click on the import tab 33

34 Follow along: Building off of scaffolding Choose file, locate the schema.sql file inside the scaffolding folder that you just unzipped, click go on bottom right 34

35 Follow along: Building off of scaffolding Now that we have a fresh copy of the schema in the database, we'll copy the basic and advanced folders to the web server Last class we 'mapped a network drive'; it should still be there; we need to re-open the connection, and leave the folder open (If you are using your own web-hosting these directions, will be different) 35

36 Follow along: Building off of scaffolding Windows Mac Start button My Computer web2.uconn.edu... In a new finder window look for web2.uconn.edu... If you can't find it there, still in finder select the 'go' menu, is it there? If all else fails, re-map the drive 36

37 Re-Map if necessary (skip otherwise) In order to transfer the modified example HTML file to your web server account, we first need to open a WebDAV connection Follow the instructions at: Make sure to follow the directions that pertain to the operating system you use, there are instructions for OSX (Macintosh), and several versions of Windows 37

38 Re-Map if necessary (skip otherwise) The correct WebDAV URL you will need to use is: You must replace the number with the one I sent you for your PHPMyAdmin login This time the username and password is just your NetID and NetID password (TRY using capitol letters in your netid for username first JAS02001 instead of jas02001) 38

39 Follow along: Building off of scaffolding The files we'll be storing on our web accounts need to go in a secure location, so not just anyone can go in and modify your database If you completed the exercises from last time, you should already have a folder named 'scaffolding' that is secured using CAS If you don't have this folder complete the steps of the next slide, otherwise skip it 39

40 If Necessary If you didn't complete the exercises, and therefore don't have a secured 'scaffolding' folder, follow these directions: No 's' in http 40

41 Follow along: Building off of scaffolding Before copying any files over to the web server, we need to configure PHP to connect to your specific database Open config.php in the basic folder and change both $database and $user to: 'cyberinfra#' Replace # with the number I sent you via e.g.: cyberinfra4 Change the $password to match the one I sent via as well Save the file 41

42 Follow along: Building off of scaffolding Either repeat the steps of the last slide or copy the basic folder's config.php to the advanced folder (replace the file) Copy the basic and advanced folders over to the web server's scaffolding folder via our 'mapped network drive' folder 42

43 Follow along: Building off of scaffolding The basic folder consists of the complete scaffolding generated from the website I added an additional index.php file to navigate between different tables Go to: Click around, notice that you still need to specify foreign key values for child table records 43

44 Follow along: Building off of scaffolding The advanced folder was built off of the basic scaffolding; it's incomplete, but serves as an example of how you might want to build a better interface using the scaffolding The main interface is essentially just the select.php of the CestodeSpecies table, with additional links for the species names: (replace # with the number your assigned number) (If you're using your own web hosting it will be your.web.host/scaffolding/advanced/index.php) 44

45 Follow along: Building off of scaffolding 45

46 Follow along: Building off of scaffolding 46

47 Follow along: Building off of scaffolding Now, when adding a species, you can enter all data for a single record at once, instead of table by table Open addspecies.php in the advanced folder on your computer ( NOT the web server) 47

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49 Follow along: Building off of scaffolding Adding a record takes you to a 'complete record view' provided by specific.php Specific view can also be accessed for any record by clicking on a species name in advanced/index.php 49

50 Follow along: Building off of scaffolding 50

51 Follow along: Building off of scaffolding The advanced folder isn't complete What should work: Editing a record's Species Name Editing a record's Genus Everything else should cause an error; we'll fill in one of these blanks in exercises 51

Developing Online Databases and Serving Biological Research Data

Developing Online Databases and Serving Biological Research Data 1 Last Time PHP scripts can be used to create better web interfaces for specific database schemas If you want something more user friendly