LIGO e-Lab Design Notes

[Found at but copied here in case that server ever goes down - JG]

DESIGN NOTES for the LIGO ELabs Analysis Tool

Eric Myers <>

- General -

The purpose of the analysis tool (it doesn't yet have a formal name) is to provide web access to LIGO data channels to allow high school students and their teachers to use LIGO environmental data from sensors such as seismometers, magnetometers, tilt-meters and weather stations for investigative exercises called e-Labs. This is part of LIGO's contribution to "Interactions in Understanding the Universe" (I2U2) [//]

Since the tool does not yet have a name the letters TLA are used as a placeholder. Just about every other LIGO tool has a name that gets turned into a three letter acronym (DMT, DTT, GDS, etc) so TLA stands for "three letter acronym". If you don't like that and are willing to use military-style jargon, you can also think that it stands for "Tool, LIGO Analysis". This is so bad that we will be forced at some point to create a better name, perhaps even one that is not a three letter acronym. I've tried to minimize the use of TLA or any other name or identifier for the package so that it can easily be changed.

If you are reading the code and you find something that looks incomplete then it probably is. This tool was put together first as proof of concept and then as a quickly built tool for the first LIGO e-Lab, with the idea that it would be refined as further development proceeded. There is a lot more that needs to be done. I have tried to anticipate future developments in the design, where possible.

- Server Side Scripting -

Server: The tool runs on an Apache web server with server side scripting using PHP. (Any other web server which supports PHP would probably also work, but Apache is the best.) The continuous dialog between the user and the server is maintained using PHP's session management features. The server keeps track of the session variables between web page visits by using a web 'cookie' to identify the session. That means that the user's browser must have cookies enabled, at least to exchange cookies between the same site that sets them. This is the way just about every web commerce site (eg. Amazon, e-Bay, mySpace) works, so it should present no problems.

Cookies: It is recommended that the users only allow cookies to only be sent back to the pages that set them. That presents a problem if we use multiple servers to interact with the user, which we hope to do. More on the complications of that later when we deal with the issue of single-sign-on.

- Script Structure -

Each interactive web page is an HTML form which always submits the form variables back to itself. Because of this, each PHP file for a page has a definite structure. First there is some "setup" and authentication, then the "action" part of the form, based on any inputs, then the "display" part of the form, which shows any results or to update the output, and finally the "closing" part of the form which saves any state for the next iteration and finishes the page output.

Be careful not to deviate too much from this structure. The "setup" or "action" parts of the script may want to transfer control to a different script, using an HTTP location header (a 'redirect'), or HTTP refresh header, but you cannot send such headers if output has begun. Therefore, we always write output to the web page after any such processing and decision making.

Another thing to watch out for is any output at all before the headers are to be sent. Each file must begin with "<?php" as the very first line. Otherwise anything in front of that is sent as output, and since output has begun you cannot send headers. Remember, PHP is a 'pre-processor', and anything not between is just echoed to the browser. Which can be useful. This is a general issue with PHP, not something specific to our project.

Debugging: The functions in debug.php support the display of debugging messages based on a global variable called $debug_level, which generally ranges from 0 to 10. The higher the level, the more verbose the output. Messages with levels under 5 are for warnings or errors and are shown in red, while higher levels are for information or tracing and are shown in orange. Use higher levels inside loops, lower levels outside, and you can easily control the level of verbosity. The display of PHP warnings or errors is also controlled by the debug level, but this is only turned on for selected IP addresses so that only the developers will see these errors, not our 'customers'. There is a "pi" link at the bottom of pages where debugging is enabled. This will show the contents of _SESSION variables and other useful information.

As a general rule I try to use single quotes in HTML so that it can then be enclosed by double quotes in PHP without having to worry about escaping all the quotation marks.

- Data Flows -

The analysis dataflows are to be evaluated by an Execution Engine, which may or may not be based on the Grid tool VDS (Virtual Data System) using VDL (the Virtual Data Language). Regardless of the implementation, the idea is that each analysis flow is a transformation of input data into output data, and each transformation may itself composed of an arrangement of several smaller data transformations. Right now we just run one ROOT script, but in the future we can run just about anything in its place (including a program or script which runs a ROOT script.)

LabView: Many physicists and physics students are already familiar with another data flow tool called LabView (a commercial product of National Instruments, which works with hardware they also sell). Or they should be. I have modeled the data flow block diagrams on those used by LabView so that (1) anybody already familiar with LabView will know how our tool is supposed to work, or (2) anybody who uses our tool will then also quickly understand how to use LabView. I hope that this does not cause patent, trademark or copyright problems with National Instruments, and I've tried to avoid anything that would clearly cause be an infringement. If there is a question of a conflict we might ask them for permission. Since they already have a graphical editor for creating data flows (they call them VI's -- Virtual Instruments) it might be easy/useful to be able to use their software for our dataflows.

ROOT: The graphics are produced using the ROOT software package from CERN. This is the best tool for the job, since this is also used in the LIGO Control Room tools, but there is nothing specific in the tool that requires ROOT. You could also use gnuplot or octave/matlab or grace/xmgr for plotting.

dmtroot: The ROOT scripts make use of 'dmtroot', a collection of ROOT macros and ROOT enabled dynamic libraries which come from the LIGO Data Monitoring Tool (DMT) software, which is now a a part of the LIGO Global Diagnostic Software (GDS). I had to do a lot to get GDS to build on Linux and to get ROOT to use the libraries and macros. There are (or will be) separate notes on this.

- Transformations and DMT Monitors -

Data Monitors are daemon processes which run in the LIGO control room and generate both plots on the main display and digested data products. So, for example, we use the output frames from one of these to get bandwidth filtered seismic data. There is a software framework in DMT which lets the scientists write a new monitor by only writing a few key routines that are specific to that monitor, not all the other common stuff to get it working within DMT. I'd like to modify or add to that framework so that we can use existing monitor code, but in an off-line mode as a part of the data flow for this tool. Thus, for example, we could use the current seismic filter code, but feed it data from the magnetometer channels, obtaining bandwidth filtered data from those sensors. We could also use the earthquake monitor code to search for isolated electromagnetic events in the magnetometer channels. So this approach would very quickly open up a whole new set of possible e-Labs using the magnetometers.

In the long run it could also run the other way. If someone develops an interesting transformation using the Analysis Tool it would then be possible and relatively easy to bring it into the control room as a new DMT monitor. I don't know if that will ever happen with student created analyses, but I would like to make it a possibility. It certainly would be a sure sign of success for the students involved, and something like this did happen in the earlier Gladstone project.

Keep in mind that if we set up our Execution Engine to use the (modified?) DMT Monitor Framework and to be compatible with VDS then the transformations we build could be used much more widely than just in this tool.

- Browsers and Client Side Scripting -

Browser: Development was mainly done using Mozilla Firefox but it is a design goal that this work with all 'major' browsers (see below). So it needs to be tested from time to time to verify that it is not browser dependent. I have not done this. It also needs to be tested to see that it works on large screens, small screens, and with and without scripting. I have not done this (or at least not enough).

JavaScript: JavaScript is used to make the web pages easier to use, but we also recognize that some users may want to turn JavaScript off. Some schools may require that it be turned off. JavaScript is not as secure as Java for client side procedures, though it is more common. JavaScript flaws in some browsers have presented dangerous security holes. For example, scripts run on Internet Explorer can change the status bar at the bottom of the screen to present a fake URL, which is used as a part of 'phishing' scams. (Firefox lets you turn this off, and you should.) Given the security problems with scripting, some users may choose or even require that scripting be turned off in the browser. Therefore, it is a design goal that the web site should work correctly with JavaScript turned off, even if it is a little more complicated or if added bonus features do not work. Be sure to test this whenever the software is updated or released.

Browser Features: If you do need a feature from JavaScript that may not be available in all browsers, do not try to figure out if it is available via browser detection. That is complicated and doomed to failure, if not now then in the future. Instead, always test directly for the feature. If the feature isn't available (or you cannot detect it) then have a viable alternative action. This simpler approach avoids a lot of problems associated with 'browser detection' based on what the browser reports as the User Agent string.

DOM: If you do try to use special features with JavaScript, please try to conform to the W3C Document Object Model (DOM) as much as possible. If you need a feature that does not conform to the DOM, you really need to have a good reason to use it. Using the DOM means that it will work on all current and future browsers (well, IE 7 is headed that way, even if it's not fully DOM compliant). Supporting older browsers, if possible, is a good reason, but not a requirement.

Pull-down menus: I've just learned how to do pull-down menus in CSS, which does not require JavaScript. This is implemented in the e-Lab documentation part of the site (html/ligo), and I will later try to add this to the Analysis Tool itself. But this does not work for IE6, which does not do CSS correctly. So there is a supporting JavaScript module to fix the CSS hover capability in IE6. That could be turned on just via browser detection. IE7 supposedly does CSS correct (or more correct) and so we may not need the extra JavaScripting. But this should all be tested, and so far it has not.

- Web Design -

I've tried to follow some important guiding principles while designing the web client part of the Analysis Tool. These are intended to make the pages easy to read, easy to navigate, and easy to use, with little or no formal training. The pages need to pass these tests (at a minimum):

* First Impressions: someone unfamiliar with the project should be able to figure out from the main page what the project is about, and what they should/could do next. And they should be able to get to the main page easily from any other page, usually from a link in the upper left corner (could be the logo, could be "Home", could be both).

* Menus are shortcuts, not primary links: The pull-down menus or sidebars are helpers. Primary links for the flow of the dialog should be in the body of the page, even if they are also in such menus. Here is the test: does the page work as intended even if these menus/sidebars are removed?

* JavaScript: the page should function correctly, albeit perhaps not as nicely, even with client side scripting (JavaScript) turned off. (See above.)

* Size and scaling: All screen measurements for the sizes of things (eg. widths of tables, indentations) should be relative not absolute. Use 5% instead of 100px, and use 1em instead of 10px, so that measurements will adjust to the user's browser preferences.

Here are the tests:

    1. Change the browser window sizes, to fill the screen, or to be tall and narrow, or a small square. The page should look okay. It should not have a forced fixed size.

    1. Widen the page, then narrow it until a horizontal scroll bar appears. Is this reasonable? You should not have to use this scroll bar under normal operation for a normal page layout.

    1. On windows (or X11 can do this too) change the screen resolution, from 800x600 to 1280x1024 and in between and maybe even higher res. The page should look okay, and not be small and isolated compared to other windows.

* Font sizes: users can change the default font size, and the pages should still have a reasonable look with no broken lines or other artifacts. Try viewing the page at several font sizes, larger and smaller than what you think is "normal" to verify.

* Browser independence: The page(s) should work on all 'major' browsers, and on all platforms. So the web pages should be tested on Windows, Mac, and Linux (and perhaps Sun) with Firefox, Internet Explorer (IE6/IE7), Safari, Opera, Netscape (newer versions, at least), and (what others?). Perhaps even AOL and Compuserve, as students may be using our pages via those from home.

Our user base of teachers and students is likely to use the Windows browsers almost exclusively, though there is currently pressure against adoption of IE7. Even if we develop on Firefox we need to be sure that our pages work with IE6 and IE7, and whatever follows. The best way to do that is to try always to use standard conventions and stay away from browser-specific "tricks".

* New windows: Do not create new windows with "target=_blank", which always creates yet another new window. Instead, if you must create a new window (and often it's likely you don't really need to) then make the target a named window which matches the function of the window. For example, to pop open a new window with instruction for the current window (so you don't loose that window) set "target=help", and then all "help" instructions are confined to the one new "help" window. This has it's own problems: if the "help" window is open but obscured, pressing the button which usually pops it up will appear to have no effect.

- Server Configuration -

Right now special care has to be taken to configure the server so that image files are not cached by the browser. Otherwise the user will sometimes see an old, stale version of a plot even though a new one has been created on the server. This is a bug. It happens mainly when the "undo" feature is uses, but other times as well, such as starting a new analysis. This requires the server have the mod_expires module, which also has to be turned on explicitly. You could configure this in the site config file or in a .htaccess file in the working (session) directory. I have used the latter. In the working directory sess/ I put a .htaccess file containing

ExpiresActive On ExpiresByType image/jpeg now ExpiresByType image/gif now ExpiresByType image/svg now ExpiresByType image/png now

# also for the web pages themselves and any .C ROOT files:

ExpiresByType text/plain now ExpiresByType text/html now

Note also that for this to work from a .htaccess file you have to have the server configured to allow the use of a .htaccess file for that directory and to allow an override of "Index" information. So in the apache config file you must have an "AllowOverride Indexes" which applies to the session directory.

I don't like this, and it also fails with some browsers which don't seem to be as smart as they could about using the Expires: headers. The 'right' way to do this is to give each image file it's own unique name, and to track that name even as the "undo" feature is used. I'm working toward that as I work on the code, but it's not all in place yet.

- Channel Names -

I have followed the LIGO channel naming scheme as much as possible, but with some parts made a little bit more understandable for beginners. The first part, which is something like H2: or L1: (or H0: for LHO PEM data) is called the "site" for beginners, though it is really the "device" which produces the data, or the "source" of the data. The label changes for higher user levels, and misleading students a little bit so that they understand what is going on is not a bad thing if you clear up the distinction later. When we only offer PEM or PEM-derived data then "site" and "device" are really the same thing. Students with more experience can understand the distinction between H0, H1 and H2.

The LIGO channel naming scheme is device:subsystem_station_sensor.ttype. The "ttype" is absent for untrended data, and will be "mean" or "rms" or something else for trended channels. In general the "station" is the location of the sensor, such as EX, EY, LVEA, etc. DMT monitors which derive their data from a particular sensor then have the same "station" as the sensor. Some monitors, such as the GDS earthquake monitor, don't have a "station", so we use "monitor" to reserve the position and preserve the pattern.

Non-LIGO data can be made to fit into the same scheme. This is not hard, because any data source can be classified by some hierarchical scheme, so the only real question is how many level of hierarchy are we using? For non-LIGO sources we substitute something else for the "device", such as NOAA for buoys. Then we can use "BUOY" for the subsystem, the buoy number or name for the "station", and the particular sensor name on the buoy for the "sensor". Or for NOAA surface observations we can use "METAR" for the "subsystem" for surface observations, and the station ID (eg. KPOU or KRLD) for the "station" So with only minor wiggling everything seems to fit this naming scheme.

- Plot Options -

The way plot options and other controls are dealt with deserves explanation. For each "control" there is a function to display an input item (text field, pull-down or radio button), and there is another function to "handle" the input from that input item control (or maybe a set of them). Plot options are kept in an array of ROOT_Plot_Option objects, and any changes are recorded in the array as the explicit ROOT command which will make the appropriate change. When a plot is to be updated we run through this list of options and emit the ROOT commands for all options that have changed. Then we run ROOT, first with the file which produced the original (or previous plot), then with the file containing the commands to modify the plot, then a file to write both the new plot and the commands to produce it (for the next iteration).

- Authentication -

We want to allow the Analysis Tool to be accessible in two different ways, either as an anonymous 'guest' user or by authenticating as a previously registered user who has their own personal account on the logbook/discussion site. We require some kind of authentication so that we can limit use of the tool to only those who are participating in the program while it's being developed, and in anticipation of a need for authentication when the user base is larger. If we tie in authentication to the Analysis Tool with authentication to the logbook/discussion site then we can provide simpler single-sign on, and we can eventually allow users to save the results of their investigations in a "file locker" associated with their account.

However, we have observed from the way our teachers and their students have used the tool that it is much easier for beginners to get started without having to set up an account on the logbook/discussion site. A guest login will also let us demonstrate the Analysis Tool to people who are not directly involved in the program and not likely to need or want a personal account. So we really need to support both methods of access.

I have set up a somewhat clever way to use HTTP basic authentication for guest accounts on the machine on which the Analysis Tool is running. Normally this kind of authentication is not optional. You either require it or you don't use it. What I have done is direct guest logins to a sub-directory for which HTTP "basic" authentication is required. Once they successfully authenticate a script in that sub-directory saves the authentication information into the PHP session, and that in turn confers authentication to the whole Analysis Tool even though the server and browser only negotiated access for the subdirectory.

For authentication via a user account (not a guest account which uses HTTP basic authentication) we want to allow authentication on the logbook/discussion site to confer authentication to the Analysis Tool without the user having to stop and enter their password again. The way this is implemented is that on the discussion site we generate a long random hex number called a 'ticket'. (It's similar in principle to a Kerberos ticket in that it's a short-term token for authentication, but it's not the same implementation.) The user's name, IP address and authenticator are sent with the ticket number to the remote server via a secure back channel (currently SSH, could be a secure SQL connection), then the user's session is redirected to the remote server with the ticket number in the URL. If the ticket is not too old and the ticket number and IP address match then the user is automatically authenticated on the remote server. (If we use a database we could also mark the ticket as 'used'.)

The ticket generation and redirection are in relay.php. Acceptance of the ticket is in auth.php. An unauthenticated request is sent to auth_required.php. All guest logins are sent to tekoa to use the subdirectory trick described above for HTTP basic authentication. All user logins are sent to the discussion site for login or verification of authentication, then redirect to tekoa with a ticket via relay.php. This is all almost completely symmetric -- it should work almost same on both servers, or more than these if we add more servers.

A diagram of how a web request is shuttled between pages based on previous authentication and the user's choice of guest or user login is shown in cross-server-auth.dia (and img/cross-server-auth.png).

-- Main.JoelG - 2016-12-09


Topic revision: r2 - 2019-05-22, AdminUser
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