Expanded arguments for Constraint Expressions

From OPeNDAP Documentation
Jump to: navigation, search

<< back

1 Use Cases

1.1 Pass in a Constraint Expression (CE) using POST

  1. The DAP client builds a CE using the existing syntax as a UTF-8 string
  2. The client binds the POST information (request document body) to the URL and dereferences the URL
  3. The server detects an inbound request using POST
  4. The server rejects the POST request if the size of the request document body is larger then some upper limit set in a configuration file, returning an HTTP error code to the client
  5. The server processes the request and returns a response
  6. The client reads the response

1.2 Pass in a CE using both POST and GET

This is a variant on the first use case; the DAP client must combine the request document body with the query string and use them both with POST.

1.3 Build an array as an argument for a server function

  1. The BES evaluates a server function
  2. If the server function takes an array as an argument, it should use a new function named make_array()
  3. The make_array() function takes 2 arguments, specifying the type and shape of the array, followed by M values that are the elements of that array in row major order.
    1. The type and shape arguments are all string arguments
    2. The type must be the name of a value DAP2 simple type (Byte, ..., Float64).
    3. The type name does not have to be quoted
    4. The shape will be a valid array shape subexpression of the form "[size0][size1]...[sizeN]" where the size0, etc. is an unsigned integer and size0 * size1 * ... * sizeN is M
    5. The shape expression will be quoted
    6. The element values will be strings that will convert into elements of type type
    7. The element values do not have to be quoted
  4. make_array will build a DAP2 Array with the values and return a BaseType* to that array
  5. The current expression evaluator will pass that Array * into the outer function.

2 Definitions

3 Background

This should be completed before 26 June 2013.

The MIIC project would like to be able to pass modest sized arguments into server functions they have defined. The arrays should be passed into the functions as single BaseType Array objects, not as collections of 100s ++ of BaseType objects.

4 Design

4.1 Constraints that are large

POST support in the OLFS and passing large XML documents back to the BES.

4.2 DAP Array arguments in CE functions

There are two ways to implement this: First using a function that takes a long series of BaseType objects that hold individual values and using those to build a single array, and second, to modify the CE evaluator so that a long string of constant values can be formed into a DAP Array without the intermediate step of storing each of the values in a BaseType object.

Implementation of the first design is strait forward.

Implementation of the second design is more complicated.

4.3 Client support

Modify getdap so that it will from a request using a document instead of a CE passed in on the comand line. For example, getdap -D <url> -c <string> will be extended so that getdap -D <url> -f <file> will make a dods request where the CE will be read from <file> and submitted to <url> using HTTP POST.

4.4 A note about using the query string

This was originally a Google doc (https://docs.google.com/a/opendap.org/document/d/1GWTt64As6q6O74Mg2EMXijSB9oybAR9P-4m6Ydn29_M/edit) describing the syntax developed by GDS that we supported in Hyrax in mid 2013. It includes a syntax that supports the same semantics but uses the query string. FWIW

The GDS/F-TDS/Hyrax Syntax:

http://<machine/<path>[_expr{#1}{#2}{#3}].<response_object>[?DAP2_constraint]

Where:

  1. A URL to be referenced in #2. This provides a way for a single call to use values from two (or more?) datasets. [NB: This same idea was represented in the original DAP2 syntax using as well but dropped because it was never used and presented some complex security issues. For those reasons we ignore anything here
  2. An expression, using the syntax of the underlying compute engine (Ferret or GDS). In GDS the result of the expression(s) is stored in a GDS variable named result while in F-TDS the expression itself names the variable using Ferret's LET reserved word. In Hyrax, this is one or more calls to a server function where the functions are responsible for naming the results and the expression evaluator stores the results in a DAP2 DDS object/response.
  3. This contains limits on the domain of the values used when evaluating the expression in #2. The limits are typically in terms of latitude, longitude, time, ...

This is used only be GDS; F-TDS uses its lazy evaluation to achieve the same goal and Hyrax uses a similar technique.

Some features of this syntax

Layering constraints onto previous requests

It is possible to provide an expression (using argument #2) and make several requests for both metadata and data. For example:

Invalid language.

You need to specify a language like this: <source lang="html4strict">...</source>

Supported languages for syntax highlighting:

4cs, 6502acme, 6502kickass, 6502tasm, 68000devpac, abap, actionscript, actionscript3, ada, algol68, apache, applescript, apt_sources, arm, asm, asp, asymptote, autoconf, autohotkey, autoit, avisynth, awk, bascomavr, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_loadrunner, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, coffeescript, cpp, cpp-qt, csharp, css, cuesheet, d, dcl, dcpu16, dcs, delphi, diff, div, dos, dot, e, ecmascript, eiffel, email, epc, erlang, euphoria, f1, falcon, fo, fortran, freebasic, freeswitch, fsharp, gambas, gdb, genero, genie, gettext, glsl, gml, gnuplot, go, groovy, gwbasic, haskell, haxe, hicest, hq9plus, html4strict, html5, icon, idl, ini, inno, intercal, io, j, java, java5, javascript, jquery, kixtart, klonec, klonecpp, latex, lb, ldif, lisp, llvm, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, mmix, modula2, modula3, mpasm, mxml, mysql, nagios, netrexx, newlisp, nsis, oberon2, objc, objeck, ocaml, ocaml-brief, octave, oobas, oorexx, oracle11, oracle8, oxygene, oz, parasail, parigp, pascal, pcre, per, perl, perl6, pf, php, php-brief, pic16, pike, pixelbender, pli, plsql, postgresql, povray, powerbuilder, powershell, proftpd, progress, prolog, properties, providex, purebasic, pycon, pys60, python, q, qbasic, rails, rebol, reg, rexx, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, spark, sparql, sql, stonescript, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, upc, urbi, uscript, vala, vb, vbnet, vedit, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, whois, winbatch, xbasic, xml, xorg_conf, xpp, yaml, z80, zxbasic


http://machine/dataset_expr{}{ugrid_subset(...)}{}.das;
http://machine/dataset_expr{}{ugrid_subset(...)}{}.dds; and then 
http://machine/dataset_expr{}{ugrid_subset(...)}{}.dods; or
http://machine/dataset_expr{}{ugrid_subset(...)}{}.dods?u,v,lat,lon

where it might be that dataset processed by ugrid_subset() has lots more variables. The first call gets them all while the second call gets only four.

The implication is that the web service can do this without running the function four times!

Domain restrictions

All of the compute engines have some way of limiting the extent of the domain over which the function is evaluated, where domain is meant both in the sense of Earth-Science domain like latitude and longitude and in the mathematical sense of a function being a mapping of a domain onto a range.

Another class of operations that are implied by this syntax are range restrictions (range in the mathematical sense).

A note about security

The feature provided by #1 opens servers to working with non-local data. This is a known vulnerability for several of the servers in question because they use libraries to read data files that have known problems. Avoid this.

A note about syntax

There are a number of different syntax choices that could be made to represent this. Weighing on this is the decision by the OPULS/DAP4 team to drop the non-standard syntax it uses for constraints. In DAP4, we will use much more of what the URL query-string can provide. One way to map this syntax onto that is to adopt:

http://machine/path.<response>[?[other=#1] & [expr=#2] & [limits=#3]]

where the []s indicate optional elements and the (somewhat broken) syntax indicates that other, expr and limits are all optional (and other is still a really bad idea ;-). This syntax could (would?) be augmented by the DAP4 constraint expression syntax that will use additional identifiers concatenated using the standard syntax element &. This will provide a way around issues like non-standard use of {} or & and will create an extension mechanism that that's easy to document. The syntax is extensible because, within the scope of the syntax/specification, other groups can add new keys. Upstream HTTP software 'knows' that things in the query-string follow a certain syntax that should otherwise be ignored and servers can be written to either ignore or return an error when presented with keys they do not recognize.

Suggestion

I have suggestions about a syntax from the perspective of DAP4:

Drop the explicit references to non-local data. As powerful an idea as that is, it's too hard to secure and will leave the resulting effort open to the criticism that it contains a 'structural' flaw. Combine the expr (#2) and limits (#3) into a single expr key where each key combines the notion of a projection that describes some value and some set of filters that may apply to either domain, range or both. Allow several functions to be run and return distinct values that will be 'packaged' into a single result-set that is returned. This could be accomplished by listing the key=param clauses one after another. Include in the name of the key a notion of the kind of expression it accepts. For example, http://... .dods?ferret_expr=<expr>. Then looking to see if a particular server accepts ferret_expr tells you quite a bit about what you can do. It is not hard to move from this notion of using GET to POST where the request document body contains these same key-param pairs (separated by newlines, e.g.)

5 Deliverables

A new version of Hyrax on the trunk such that a special branch can be formed for the MIIC project to use. Once the feature is stable, make a Hyrax 1.9 branch which should include this feature.

5.1 OLFS

To configure the OLFS so that it will accept requests using POST, you first need to set the olfs.xml file in the content directory. Add the following to the end of the configuration file, after the closing of <HttpGetHandlers>:

<HttpPostHandlers>
    <Handler className="opendap.bes.dapResponders.DapDispatcher" >
        <AllowDirectDataSourceAccess />
        <MaxPostBodyLength>500</MaxPostBodyLength>
        <!-- UseDAP2ResourceUrlResponse / -->
     </Handler>
</HttpPostHandlers>

When a client sends a request using POST, the format of the request document body is a function of the value of the request's Content-Type header. If Content-Type is application/x-www-form-urlencoded, then the request body should start with the literal ce= (or dap:ce=) and then contain the constraint expression. If Content-Type is not set, do not include the ce= prefix. In both cases the syntax of the CE is unchanged.

Important: Make sure you configure the POST handler and the DAP Dispatch handler with the same optional values.

Note: If you are using curl to test this (or as a client), it will set Content-Type for you (to application/x-www-form-urlencoded) so you must use the ce= literal.

5.2 Constraints

There are two ways to make arrays that can be passed into DAP2 server functions. The first way, and the slower of the two, is to use a function called make_array() as an argument to another function. The faster of the two ways to pass an array of constant values into a server function is to use the new constant array special form.

5.2.1 The make_array() function

The make_array() function takes three or more arguments and returns a DAP2 Array with the values passed to the function.

make_array(<type>, <shape>, <values>, ...)
<type> is any of the DAP2 numeric types (Byte, Int16, UInt16, Int32, UInt32, Float32, Float64); <shape> is a string that indicates the size and number of the array's dimensions. Following those two arguments are N arguments that are the values of the array. The number of values must equal the product of the dimension sizes.

Example: make_array(Byte,"[4][4]",2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5) will return a DAP2 four by four Array of Bytes with the values 2, 3, ... . The Array will be named g<int> where <int> is 1, 2, ..., such that the name does not conflict with any existing variable in the dataset. Use bind_name() to change the name.

This function can build an array with 1024 X 1024 Int32 elements in about 4 seconds.

5.2.2 The array constant special forms

These special forms can build vectors with specific values and return them as DAP2 Arrays. The Array variables can be named using the bind_name() function and have their shape set using bind_shape().

$<type>(<size hint>
<values>, ...): The $<type> ($Byte, ...) literal starts the special form. The first argument <size_hint> provides a way to preallocate the memory needed to hold the vector of values. Following that, the values are listed. Unlike make_array(), it is not necessary to provide the exact size of the vector; the size hint is just that, a hint. If a size hint of zero is supplied, it will be ignored. Any of the DAP2 numeric types can be used with this special form. This is called a 'special form' because it invokes a custom parser that can process values very efficiently.

Example: $Byte(16:2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5) will return a one dimensional (i.e., a vector) Array of Bytes with values 2, 3, ... . The vector is named g<int> just like the array returned by make_array(). The vector can be turned in to a N-dimensional Array using bind_shape() using bind_shape("[4][4]",$Byte(16:2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5)).

The special forms can make a 1,047,572 element vector on Int32 in 0.4 seconds.

5.2.3 The bind_name() and bind_shape() functions

These functions take a BaseType* object and bind a name or shape to it (in the latter case the BaseType* must be an Array*). They are intended to be used with make_array() and the $type special forms, but they can be used with any variable in a dataset.

bind_name(<name>,<variable>)
The <name> must not exist in the dataset; <variable> may be the name of a variable in the dataset (so this function can rename an existing variable) or it can be a variable returned by another function or special form.
bind_shape(<shape expression>,<variable>)
The <shape expression> is a string that gives the number and size of the array's dimensions; the <variable> may be the name of a variable in the dataset (so this function can rename an existing variable) or it can be a variable returned by another function or special form.

5.3 Performance measurements

Time to make 1,000,000 (actually 1,048,576) element Int32 array using the special form, where the argument vector<int> was preset to 1,048,576 elements. Times are for 50 repeats.

Summary: Using the special for $Int32(size_hint, values...) is about 10 times faster for a 1 million element vector than make_array(Int32,[1048576],values...). As part of the performance testing, the scanner and parser were run under a sampling runtime analyzer ('Instruments' on OS/X) and the code was optimized so that long sequences of numbers would scan and parse more efficiently. This benefited both the make_array() function and $type() special form.

5.3.1 Raw timing data

In all cases, a 1,048,576 element vector of Int32 was built 50 times. The values were serialized and written to /dev/null using the command time besstandalone -c bes.conf -i bescmd/fast_array_test_3.dods.bescmd -r 50 > /dev/null where the .bescmd file lists a massive constraint expression (a million values). The same values were used.

These values are using the ce_expr parser & scanner before it was optimized.


Runtimes for make_array() and $type, before scanner/parser optimization
Time in seconds
What Real User System
$type, with hint 37.975 37.415 0.426
$type, no hint 39.388 38.600 0.397
make_array() 212.697 206.894 5.771


The scanner was improved based on info from 'instruments', an OS/X profiling tool. Copying values and applying www2id escaping was moved from the scanner, where it was applied it to every token that matched SCAN_WORD, to the parser, where it was used only for non-numeric tokens. This performance tweak makes a big difference in this case since there are a million SCAN_WORD tokens that are not symbols.

Runtimes for make_array() and $type, scanner/parser optimized, two trials
Time in seconds
What Real (s) User System
$type, with hint 19.844 19.355 0.437
$type, with hint 19.817 19.369 0.427
$type, no hint 19.912 19.444 0.430
$type, no hint 19.988 19.444 0.428
make_array() 195.332 189.271 6.058
make_array() 197.900 191.628 6.254


5.4 Testing

Note: To test the #type special form using a browser, make sure to escape the # character. That is, type %23Byte(... instead of #Byte(.... The # character is reserved by RFC3986.

One of the issues with testing POST responses is having a client that will use the HTTP POST verb. I'll show how to use curl.

There are two ways to POST with curl: Using data from the command line and use data from a file.

To POST using data from the command line, use the --data switch. Here's an example:

Invalid language.

You need to specify a language like this: <source lang="html4strict">...</source>

Supported languages for syntax highlighting:

4cs, 6502acme, 6502kickass, 6502tasm, 68000devpac, abap, actionscript, actionscript3, ada, algol68, apache, applescript, apt_sources, arm, asm, asp, asymptote, autoconf, autohotkey, autoit, avisynth, awk, bascomavr, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_loadrunner, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, coffeescript, cpp, cpp-qt, csharp, css, cuesheet, d, dcl, dcpu16, dcs, delphi, diff, div, dos, dot, e, ecmascript, eiffel, email, epc, erlang, euphoria, f1, falcon, fo, fortran, freebasic, freeswitch, fsharp, gambas, gdb, genero, genie, gettext, glsl, gml, gnuplot, go, groovy, gwbasic, haskell, haxe, hicest, hq9plus, html4strict, html5, icon, idl, ini, inno, intercal, io, j, java, java5, javascript, jquery, kixtart, klonec, klonecpp, latex, lb, ldif, lisp, llvm, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, mmix, modula2, modula3, mpasm, mxml, mysql, nagios, netrexx, newlisp, nsis, oberon2, objc, objeck, ocaml, ocaml-brief, octave, oobas, oorexx, oracle11, oracle8, oxygene, oz, parasail, parigp, pascal, pcre, per, perl, perl6, pf, php, php-brief, pic16, pike, pixelbender, pli, plsql, postgresql, povray, powerbuilder, powershell, proftpd, progress, prolog, properties, providex, purebasic, pycon, pys60, python, q, qbasic, rails, rebol, reg, rexx, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, spark, sparql, sql, stonescript, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, upc, urbi, uscript, vala, vb, vbnet, vedit, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, whois, winbatch, xbasic, xml, xorg_conf, xpp, yaml, z80, zxbasic


curl --data "ce=#Byte(4:2,3,4,5)" http://localhost:8080/opendap/hyrax/data/nc/fnoc1.nc.ascii

Dataset: fnoc1.nc
g6, 2, 3, 4, 5

To POST using daa from a file, first store the data in a file:

Invalid language.

You need to specify a language like this: <source lang="html4strict">...</source>

Supported languages for syntax highlighting:

4cs, 6502acme, 6502kickass, 6502tasm, 68000devpac, abap, actionscript, actionscript3, ada, algol68, apache, applescript, apt_sources, arm, asm, asp, asymptote, autoconf, autohotkey, autoit, avisynth, awk, bascomavr, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_loadrunner, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, coffeescript, cpp, cpp-qt, csharp, css, cuesheet, d, dcl, dcpu16, dcs, delphi, diff, div, dos, dot, e, ecmascript, eiffel, email, epc, erlang, euphoria, f1, falcon, fo, fortran, freebasic, freeswitch, fsharp, gambas, gdb, genero, genie, gettext, glsl, gml, gnuplot, go, groovy, gwbasic, haskell, haxe, hicest, hq9plus, html4strict, html5, icon, idl, ini, inno, intercal, io, j, java, java5, javascript, jquery, kixtart, klonec, klonecpp, latex, lb, ldif, lisp, llvm, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, mmix, modula2, modula3, mpasm, mxml, mysql, nagios, netrexx, newlisp, nsis, oberon2, objc, objeck, ocaml, ocaml-brief, octave, oobas, oorexx, oracle11, oracle8, oxygene, oz, parasail, parigp, pascal, pcre, per, perl, perl6, pf, php, php-brief, pic16, pike, pixelbender, pli, plsql, postgresql, povray, powerbuilder, powershell, proftpd, progress, prolog, properties, providex, purebasic, pycon, pys60, python, q, qbasic, rails, rebol, reg, rexx, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, spark, sparql, sql, stonescript, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, upc, urbi, uscript, vala, vb, vbnet, vedit, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, whois, winbatch, xbasic, xml, xorg_conf, xpp, yaml, z80, zxbasic


echo "ce=#Byte(4:2,3,4,5)" > POST.data.txt

and then use the -X and -d switches:

Invalid language.

You need to specify a language like this: <source lang="html4strict">...</source>

Supported languages for syntax highlighting:

4cs, 6502acme, 6502kickass, 6502tasm, 68000devpac, abap, actionscript, actionscript3, ada, algol68, apache, applescript, apt_sources, arm, asm, asp, asymptote, autoconf, autohotkey, autoit, avisynth, awk, bascomavr, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_loadrunner, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, coffeescript, cpp, cpp-qt, csharp, css, cuesheet, d, dcl, dcpu16, dcs, delphi, diff, div, dos, dot, e, ecmascript, eiffel, email, epc, erlang, euphoria, f1, falcon, fo, fortran, freebasic, freeswitch, fsharp, gambas, gdb, genero, genie, gettext, glsl, gml, gnuplot, go, groovy, gwbasic, haskell, haxe, hicest, hq9plus, html4strict, html5, icon, idl, ini, inno, intercal, io, j, java, java5, javascript, jquery, kixtart, klonec, klonecpp, latex, lb, ldif, lisp, llvm, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, mmix, modula2, modula3, mpasm, mxml, mysql, nagios, netrexx, newlisp, nsis, oberon2, objc, objeck, ocaml, ocaml-brief, octave, oobas, oorexx, oracle11, oracle8, oxygene, oz, parasail, parigp, pascal, pcre, per, perl, perl6, pf, php, php-brief, pic16, pike, pixelbender, pli, plsql, postgresql, povray, powerbuilder, powershell, proftpd, progress, prolog, properties, providex, purebasic, pycon, pys60, python, q, qbasic, rails, rebol, reg, rexx, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, spark, sparql, sql, stonescript, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, upc, urbi, uscript, vala, vb, vbnet, vedit, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, whois, winbatch, xbasic, xml, xorg_conf, xpp, yaml, z80, zxbasic


curl -X POST -d @POST.data.txt http://localhost:8080/opendap/hyrax/data/nc/fnoc1.nc.ascii

Dataset: fnoc1.nc
g5, 2, 3, 4, 5

6 Period of use

26 June 2013 onward