> > All the XML functionality is implemented in the new mxml.c/h library
> 
> mxml.c/h ... I separated it's CVS tree.
>
> The midas Makefile has been adjusted accordingly.

Looks like the midas mxml Makefile bits did not make it to CVS. Current Makefile
revision 1.67 does not have them and building midas from cvs sources fails because it
does not find mxml.h and mxml.c

K.O.

> Looks like the midas mxml Makefile bits did not make it to CVS. Current Makefile
> revision 1.67 does not have them and building midas from cvs sources fails because it
> does not find mxml.h and mxml.c

I forgot to commit the new Makefile, thanks for reminding me. Now it should be fine.

> Hi. Is it currently possible to automatically save the MIDAS ODB as a JSON file?
> I can do it manually in odbedit, but it looks like the only option for the
> automatic ODB save for each run is the standard .ODB format. Is there a way to
> change this?

I have the reverse question: Once we have a json file, can it be loaded again in the odb? We also use the odb as our analysis config. I don`t like .odb files in our repo, so we currently load settings in shell scripts (e.g. run dependent detector calibrations)

Hi. Is it currently possible to automatically save the MIDAS ODB as a JSON file?
I can do it manually in odbedit, but it looks like the only option for the
automatic ODB save for each run is the standard .ODB format. Is there a way to
change this?

> Hi. Is it currently possible to automatically save the MIDAS ODB as a JSON file?
> I can do it manually in odbedit, but it looks like the only option for the
> automatic ODB save for each run is the standard .ODB format. Is there a way to
> change this?

You mean you like an ODB dump at the end of every run in JSON format?

Sure this can be implemented. But I wonder for what purpose you need that. Can you elaborate a 
bit, maybe it's a useful feature also other people should be aware of. I'm also thinking if we should 
offer a CouchDB interface, so ODB data is written directly to that database.

Stefan

Hi,
We do generate a .json odb at the end of run in order to extract some of its info for our CouchDB.
This is done using the "/program/Execute on stop run" script command. This method decouples the necessity 
to describe completely the info extraction within the ODB/Logger/"CouchDB" and provides possibly better 
flexibility. But including a CouchDB support in the logger as well (like SQL) would be nice too.

Pierre-André


> > Hi. Is it currently possible to automatically save the MIDAS ODB as a JSON file?
> > I can do it manually in odbedit, but it looks like the only option for the
> > automatic ODB save for each run is the standard .ODB format. Is there a way to
> > change this?
> 
> You mean you like an ODB dump at the end of every run in JSON format?
> 
> Sure this can be implemented. But I wonder for what purpose you need that. Can you elaborate a 
> bit, maybe it's a useful feature also other people should be aware of. I'm also thinking if we should 
> offer a CouchDB interface, so ODB data is written directly to that database.
> 
> Stefan

> Hi. Is it currently possible to automatically save the MIDAS ODB as a JSON file?
> I can do it manually in odbedit, but it looks like the only option for the
> automatic ODB save for each run is the standard .ODB format. Is there a way to
> change this?

I think today it makes sense to make all ODB dump in the JSON format - in my experience it is much 
easier to work with JSON data compared to XML data.

To write the ODB dump file in JSON format, set "/logger/ODB Dump File" to "run%05d.json".

In the midas data files, the ODB dump made into the begin-of-run and end-of-run events is presently 
unconditionally done in XML format.

Perhaps the data file dump should match the format of the odb dump file (both XML or both JSON or 
both ODB).

But at the moment our standard analyzer ROOTANA does not have the code to process JSON ODB 
dumps, so I am hesitant to make this change today, Maybe tomorrow when there is a VirtualODB 
JsonOdb class in ROOTANA. The requires JSON parser is already part of MIDAS (mjson.h/mjson.cxx).

K.O.

Hi all,
for my experiment we ended up with the need of changing lot of parameters (~9000 values) in the ODB at once by the sequencer.
The very first solution was to use a sequencer function with a ton of ODBSET calls, however a more elegant solution may be to provide an "ODBLoad" command which mimics the "load" command of odbedit.
I already have a working modification to the sequencer for this, if you agree I will commit it to a dedicated brach.
Let me know if you think this is a good approach.

Marco F

> Hi all,
> for my experiment we ended up with the need of changing lot of parameters (~9000 values) in the ODB at once by the sequencer.
> The very first solution was to use a sequencer function with a ton of ODBSET calls, however a more elegant solution may be to provide an "ODBLoad" command which mimics the "load" command of odbedit.
> I already have a working modification to the sequencer for this, if you agree I will commit it to a dedicated brach.
> Let me know if you think this is a good approach.
> 
> Marco F

How can people judge your modification if they cannot see it? Why don't you make a pull request, so it can be properly reviewed.

Stefan

> Hi all,
> for my experiment we ended up with the need of changing lot of parameters (~9000 values) in the ODB at once by the sequencer.
> The very first solution was to use a sequencer function with a ton of ODBSET calls, however a more elegant solution may be to provide an "ODBLoad" command which mimics the "load" command of odbedit.
> I already have a working modification to the sequencer for this, if you agree I will commit it to a dedicated brach.
> Let me know if you think this is a good approach.
> 

Sounds like a good idea. I trust you are using the data in json format? Perhaps the command
should be named "ODBLoadJSON" to be clear about this.

(JSON is preferred over .odb and .xml for many reasons (ask me))

K.O.

> > Hi all,
> > for my experiment we ended up with the need of changing lot of parameters (~9000 values) in the ODB at once by the sequencer.
> > The very first solution was to use a sequencer function with a ton of ODBSET calls, however a more elegant solution may be to provide an "ODBLoad" command which mimics the "load" command of odbedit.
> > I already have a working modification to the sequencer for this, if you agree I will commit it to a dedicated brach.
> > Let me know if you think this is a good approach.
> > 
> 
> Sounds like a good idea. I trust you are using the data in json format? Perhaps the command
> should be named "ODBLoadJSON" to be clear about this.
> 
> (JSON is preferred over .odb and .xml for many reasons (ask me))

What if some experiment keep some files in .xml format (ask me!). The routine should check for the extension and support all three formats.

Stefan

> > > Hi all,
> > > for my experiment we ended up with the need of changing lot of parameters (~9000 values) in the ODB at once by the sequencer.
> > > The very first solution was to use a sequencer function with a ton of ODBSET calls, however a more elegant solution may be to provide an "ODBLoad" command which mimics the "load" command of odbedit.
> > > I already have a working modification to the sequencer for this, if you agree I will commit it to a dedicated brach.
> > > Let me know if you think this is a good approach.
> > > 
> > 
> > Sounds like a good idea. I trust you are using the data in json format? Perhaps the command
> > should be named "ODBLoadJSON" to be clear about this.
> > 
> > (JSON is preferred over .odb and .xml for many reasons (ask me))
> 
> What if some experiment keep some files in .xml format (ask me!). The routine should check for the extension and support all three formats.
> 

Yes, hard to tell without seeing his full proposal, including the code. If it is load from file,
sure we look at the file extension, I think the existing code already would do this and support all 3 formats.

But if he wants to load ODB data from a text literal or from a string,
we might as well stick to json. I guess we could support the other formats, but I do not see anybody
using anything other than json for new code like this.

ODBPasteJSON("/foo/bar/baz", '{"var1":1, "var2":"somestr"}');

K.O.

> > > > Hi all,
> > > > for my experiment we ended up with the need of changing lot of parameters (~9000 values) in the ODB at once by the sequencer.
> > > > The very first solution was to use a sequencer function with a ton of ODBSET calls, however a more elegant solution may be to provide an "ODBLoad" command which mimics the "load" command of odbedit.
> > > > I already have a working modification to the sequencer for this, if you agree I will commit it to a dedicated brach.
> > > > Let me know if you think this is a good approach.
> > > > 
> > > 
> > > Sounds like a good idea. I trust you are using the data in json format? Perhaps the command
> > > should be named "ODBLoadJSON" to be clear about this.
> > > 
> > > (JSON is preferred over .odb and .xml for many reasons (ask me))
> > 
> > What if some experiment keep some files in .xml format (ask me!). The routine should check for the extension and support all three formats.
> > 
> 
> Yes, hard to tell without seeing his full proposal, including the code. If it is load from file,
> sure we look at the file extension, I think the existing code already would do this and support all 3 formats.
> 
> But if he wants to load ODB data from a text literal or from a string,
> we might as well stick to json. I guess we could support the other formats, but I do not see anybody
> using anything other than json for new code like this.
> 
> ODBPasteJSON("/foo/bar/baz", '{"var1":1, "var2":"somestr"}');

I agree that if one would paste a string to the ODB, then JSON would be best.

But at MEG, we keep hundreds of XML files for configuration. Mostly historical, but that's how it is.

Stefan

> ... at MEG, we keep hundreds of XML files for configuration. Mostly historical, but that's how it is.

same here, lots of historical .odb and .xml files.

I think the .odb and .xml support is here to stay. Best I remember, latest things I fixed in both
was support for unlimited string length (and removal of associated buffer overflows). Right now,
I am not sure if both are UTF-8 clean and if they properly escape all control characters,
something to fix as we go or as we bump into problems.

K.O.

My idea was to collect some feedback instead of blindly submitting code for a pull request.

Currently I'm just calling db_load() with a given file, so it is only supporting .odb formatting.
It is pretty easy to extend to json by calling the db_load_json() depending on the file extension.
I do not see a similar call for the .xml format, maybe I can study tomorrow how it is implemented in odbedit and port it to the sequencer.

I guess that the ODBPasteJSON can be a solution as well but I find it a bit too technical.
Anyway it is easy to implement just by calling db_paste_json(), I will keep this in mind.

I'll try to sort this out and make a commit soon.
Best,

Marco



> > ... at MEG, we keep hundreds of XML files for configuration. Mostly historical, but that's how it is.
> 
> same here, lots of historical .odb and .xml files.
> 
> I think the .odb and .xml support is here to stay. Best I remember, latest things I fixed in both
> was support for unlimited string length (and removal of associated buffer overflows). Right now,
> I am not sure if both are UTF-8 clean and if they properly escape all control characters,
> something to fix as we go or as we bump into problems.
> 
> K.O.

I just submitted a pull request for this feature, I did quite a lot of testing and it looks good to me.
Let me know if something is not clear.

I'll take care of adding the relevant informations to the wiki once it is merged.
Best,

Marco


> My idea was to collect some feedback instead of blindly submitting code for a pull request.
> 
> Currently I'm just calling db_load() with a given file, so it is only supporting .odb formatting.
> It is pretty easy to extend to json by calling the db_load_json() depending on the file extension.
> I do not see a similar call for the .xml format, maybe I can study tomorrow how it is implemented in odbedit and port it to the sequencer.
> 
> I guess that the ODBPasteJSON can be a solution as well but I find it a bit too technical.
> Anyway it is easy to implement just by calling db_paste_json(), I will keep this in mind.
> 
> I'll try to sort this out and make a commit soon.
> Best,
> 
> Marco
> 
> 
> 
> > > ... at MEG, we keep hundreds of XML files for configuration. Mostly historical, but that's how it is.
> > 
> > same here, lots of historical .odb and .xml files.
> > 
> > I think the .odb and .xml support is here to stay. Best I remember, latest things I fixed in both
> > was support for unlimited string length (and removal of associated buffer overflows). Right now,
> > I am not sure if both are UTF-8 clean and if they properly escape all control characters,
> > something to fix as we go or as we bump into problems.
> > 
> > K.O.

I quickly checked the pull request and could not find any obvious problem, so I merged it.

odbedit can now save ODB in JSON-formatted files. (JSON is a popular data encoding standard associated 
with Javascript). The intent is to eventually use the ODB JSON encoder in mhttpd to simplify passing of 
ODB data to custom web pages. In mhttpd I also intend to support the JSON-P variation of JSON (via the 
jQuery "callback=?" notation).

JSON encoding implementation follows specifications at:
http://json.org/
http://www.json-p.org/
http://api.jquery.com/jQuery.getJSON/  (seek to JSONP)

The result passes validation by:
http://jsonlint.com/

Added functions:
   INT EXPRT db_save_json(HNDLE hDB, HNDLE hKey, const char *file_name);
   INT EXPRT db_copy_json(HNDLE hDB, HNDLE hKey, char **buffer, int *buffer_size, int *buffer_end, int 
save_keys, int follow_links);

For example of using this code, see odbedit.c and odb.c::db_save_json().

Example json file:

Notes:
1) hex numbers are quoted "0x1234" - JSON does not permit "hex numbers", but Javascript will 
automatically convert strings containing hex numbers into proper integers.
2) "double" is encoded with full 15 digit precision, "float" with full 7 digit precision. If floating point values 
are actually integers, they are encoded as integers (10.0 -> "10" if (value == (int)value)).
3) in this example I deleted all the "name/key" entries except for "stringvalue" and "sbyte2". I use the 
"/key" notation for ODB KEY data because the "/" character cannot appear inside valid ODB entry names. 
Normally, depending on the setting of "save_keys" argument, KEY data is present or absent for all entries.

ladd03:midas$ odbedit
[local:testexpt:S]/>cd /test
[local:testexpt:S]/test>save test.js
[local:testexpt:S]/test>exit
ladd03:midas$ more test.js
# MIDAS ODB JSON
# FILE test.js
# PATH /test
{
  "test" : {
    "intarr" : [ 15, 0, 0, 3, 0, 0, 0, 0, 0, 9 ],
    "dblvalue" : 2.2199999999999999e+01,
    "fltvalue" : 1.1100000e+01,
    "dwordvalue" : "0x0000007d",
    "wordvalue" : "0x0141",
    "boolvalue" : true,
    "stringvalue" : [ "aaa123bbb", "", "", "", "", "", "", "", "", "" ],
    "stringvalue/key" : {
      "type" : 12,
      "num_values" : 10,
      "item_size" : 1024,
      "last_written" : 1288592982
    },
    "byte1" : 10,
    "byte2" : 241,
    "char1" : "1",
    "char2" : "-",
    "sbyte1" : 10,
    "sbyte2" : -15,
    "sbyte2/key" : {
      "type" : 2,
      "last_written" : 1365101364
    }
  }
}

svn rev 5356
K.O.

> odbedit can now save ODB in JSON-formatted files.
> 
> JSON encoding implementation follows specifications at:
> http://json.org/
> 
> The result passes validation by:
> http://jsonlint.com/
> 

A bug was reported in my JSON ODB encoder: NaN values are not encoded correctly. A quick review found this:

1) the authors of JSON smoked some bad mushrooms and specifically disallowed NaN and Inf values for floating point numbers: 
http://tools.ietf.org/html/rfc4627
2) most JSON encoders and decoders do reasonable and unreasonable things with NaN and Inf values. The worst ones encode them as zero. More bad 
mushrooms.

There is a quick survey at: http://lavag.org/topic/16217-cr-json-labview/?p=99058

<pre>
Some Javascript engines allow it since it is valid Javascript but not valid Json however there is no concensus.
cmj-JSON4Lua: raw tostring() output (invalid JSON).
dkjson: 'null' (like in the original JSON-implementation).
Fleece: NaN is 0.0000, freezes on +/-Inf.
jf-JSON: NaN is 'null', Inf is 1e+9999 (the encode_pretty function still outputs raw tostring()).
Lua-Yajl: NaN is -0, Inf is 1e+666.
mp-CJSON: raises invalid JSON error by default, but runtime configurable ('null' or Nan/Inf).
nm-luajsonlib: 'null' (like in the original JSON-implementation).
sb-Json: raw tostring() output (invalid JSON).
th-LuaJSON: JavaScript? constants: NaN is 'NaN', Inf is 'Infinity' (this is valid JavaScript?, but invalid JSON).
</pre>

For the MIDAS JSON encoder (and decoder) I have several choices:
a) encode NaN and Inf using the printf("%f") encoding (as strings, making it valid JSON)
b) encode NaN and Inf as strings using the Javascript special values: "NaN", "Infinity" and "-Infinity", see 
http://www.w3schools.com/jsref/jsref_positive_infinity.asp

I note that the Python JSON encoder does (b), see section 18.2.3.3 at http://docs.python.org/2/library/json.html

In either case, behaviour of the JSON decoder on the Javascript side needs to be tested. (Silent conversion to value of zero is not acceptable).

If anybody has an suggestion on this, please let me know.



P.S. If you do not know all about NaN, Inf, "-0" and other floating point funnies, please read:  https://www.ualberta.ca/~kbeach/phys420_580_2010/docs/ACM-Goldberg.pdf

P.P.S. If you ever used the type "float" or "double", used the "/" operator or the function "sqrt()" you also should read that reference.

K.O.

> > odbedit can now save ODB in JSON-formatted files.
> A bug was reported in my JSON ODB encoder: NaN values are not encoded correctly.

Tested the browser-builtin JSON.stringify() function in google-chrome, firefox, safari, opera:
everybody encodes numeric values NaN and Inf as JSON value [null].

To me, this clearly demonstrates a severe defect in the JSON standard and in it's Javascript implementation:
a) NaN, Inf and -Inf are valid, useful and commonly used numeric values defined by the IEEE754/854 standard (as opposed to the special value "-0", which is also defined by the standard, but is not nearly as useful)
b) they are all distinct numeric values, encoding them all into the same JSON value [null] is the same as encoding all even numbers into the JSON value [42].
c) on the decoding end, JSON value [null] is decoded into Javascript value [null], which works as 0 for numeric computation, so effectively NaN, Inf and -Inf are made equal to zero. A neat trick.

Note that (c) - NaN, Inf is same as 0 - eventually produces incorrect numerical results by breaking the IEEE754/854 standard specification that number+NaN->NaN, number+infinity->infinity, etc.

In MIDAS we have a requirement that results be numerically correct: if an ODB value is "infinity", the corresponding web page should not show "0".

In addition we have a requirement that JSON encoding should be lossess: i.e. ODB contents encoded by JSON should decode back into the same ODB contents.

To satisfy both requirements, I now encode NaN, Inf and -Inf as JSON string values "NaN", "Infinity" and "-Infinity". (Corresponding to the respective Javascript values).

Notes:
1) this is valid JSON
2) it survives decode/encode in the browser (ODBMCopy()/JSON.parse/modify some values/JSON.stringify/ODBMPaste() does not destroy these special values)
3) it is numerically correct for "NaN" values (Javascript [1+"NaN"] -> NaN)
4) it fails in an obvious way for Inf and -Inf values (Javascript [1+"Infinity"] is NaN instead of Infinity).

https://bitbucket.org/tmidas/midas/commits/82dd203cc95dacb6ec9c0a24bc97ffd45bb58427
K.O.