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The Pipelet Readme

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Pipelet is a free framework allowing for the creation, execution and
browsing of scientific data processing pipelines. It provides:
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+ easy chaining of interdependent elementary tasks,
+ web access to data products,
+ branch handling,
+ automated distribution of computational tasks.

Both engine and web interface are written in Python.

* Tutorial
** Introduction
*** Why using pipelines

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The pipeline mechanism allows you to apply a sequence of processing
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steps to your data, in a way that the input of each process is the
output of the previous one. Making visible these different processing
steps, in the right order, is essential in data analysis to keep track
of what you did, and make sure that the whole processing remains
consistent.

*** How it works

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Pipelet is based on the possibility to save on disk every intermediate
input or output of your pipeline, which is usually not a strong
constraint but offers a lot of benefits. It means that you can stop
the processing whenever you want, and begin it again without
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recomputing the whole thing: you just take the last products you have
on disk, and continue the processing where it stopped. This logic is
interesting when the computation cost is higher than the cost of disk
space required by intermediate products.

*** The Pipelet functionalities

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Pipelet is a free framework which helps you : 
+ to write and manipulate pipelines with any dependency scheme, 
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+ to dispatch the computational tasks on parallel architectures, 
+ to keep track of what processing has been applied to your data and perform comparisons.

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** Getting started
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*** Pipelet installation 
**** Dependencies 

+ Running the Pipelet engine requires Python >= 2.6.

+ The web interface of Pipelet requires the installation of the
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  cherrypy3 Python module (on Debian: aptitude install python-cherrypy3).
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You may find useful to install some generic scientific tools that nicely interact with Pipelet: 
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+ numpy
+ matplotlib
+ latex 
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**** Getting Pipelet
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There is not any published stable release of Pipelet right now.
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=git clone git://gitorious.org/pipelet/pipelet.git=
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**** Installing Pipelet
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sudo python setup.py install

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*** Running a simple test pipeline
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1. Run the test pipeline

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=cd test/first_test=

=python main.py=
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2. Add this pipeline to the web interface

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=pipeweb track test ./.sqlstatus=
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3. Set the access control and launch the web server

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=pipeutils -a username -l 2 .sqlstatus=

=pipeweb start=
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4. You should be able to browse the result on the web page
   http://localhost:8080

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*** Getting a new pipe framework

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To get a new pipeline framework, with example main and segment scripts : 
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=pipeutils -c pipename=
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This command ends up with the creation of directory named pipename wich contains: 
+ a main script (named main.py) providing functionnalities to execute
  your pipeline in various modes (debug, parallel, batch mode, ...)
+ an example of segment script (seg_default_code.py) which illustrates
  the pipelet utilities with comments. 
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The next section describes those two files in more details. 
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** Writing Pipes
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*** Pipeline architecture

The definition of a data processing pipeline consists in :
+ a succession of python scripts, called segments, coding each step
  of the actual processing.
+ a main script that defines the dependency scheme between segments,
  and launch the processing.

The dependencies between segments must form a directed acyclic
graph. This graph is described by a char string using a subset of the
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graphviz dot language (http://www.graphviz.org). For example the string:
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"""
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=a -> b -> d;=

=c -> d;=

=c -> e;=
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"""

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defines a pipeline with 5 segments {"a", "b", "c", "d", "e"}. The
relation "a->b" ensures that the processing of the segment "a" will be
done before the processing of its child segment "b". Also the output
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of "a" will be fed as input for "b". In the given example, the node
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"d" has two parents "b" and "c". Both will be executed before "d". As
their is no relation between "b" and "c" which of the two will be
executed first is not defined.

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When executing the segment "seg", the engine looks for a python script
named seg.py. If not found, it looks iteratively for script files
named "se.py" and "s.py". This way, different segments of the pipeline
can share the same code, if they are given a name with a common root
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(this mechanism is useful to write generic segment and is completed by
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the hooking system, described in the advanced usage section). The code
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is then executed in a specific namespace (see below [[*The%20segment%20environment][The execution
environment]]).
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*** The Pipeline object

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Practically, the creation of a Pipeline object needs 3 arguments:
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P = Pipeline(pipedot, codedir=, prefix=)
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- pipedot is the string description of the pipeline
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- codedir is the path where the segment scripts can be found
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- prefix  is the path to the data repository (see below [[*Hierarchical%20data%20storage][Hierarchical data storage]])
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It is possible to output the graphviz representation of the pipeline
(needs graphviz installed). First, save the graph string into a .dot
file with the pipelet function:
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P.to_dot('pipeline.dot')

Then, convert it to an image file with the dot command: 

dot -Tpng -o pipeline.png pipeline.dot

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*** Dependencies between segments

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The modification of the code of one segment will trigger its
recalculation and the recalculation of all the segments which
depend on it.

The output of a segment is a list of python objects. If a segment as
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no particular output this list can be empty and do not need to be
specified. Elements of the list are allowed to be any kind of
pickleable python objects. However, a good practice is to fill the
list with the minimal set of characteristics relevant to describe the
output of the segment and to defer the storage of the data to
appropriate structures and file formats. For example, a segment which
performs computation on large images could virtually pass the results
of its computation to the following segment using the output list. It
is a better practice to store the resulting image in a dedicated file
and to pass in the list only the information allowing a non ambiguous
identification of this file (like its name or part of it) for the
following segments.

The input of a child segment is taken in a set build from the output
lists of its parents. The content of the input set is actually tunable
using the multiplex directive (see below). However the simplest and
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default behavior of the engine is to form the Cartesian product of
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the output list of its parent.

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To illustrate this behavior let us consider the following pipeline,
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build from three segments:

 knights -> melt;
 quality -> melt;

and assume that the respective output lists of segments knights and
quality are:

 ["Lancelot", "Galahad"]
and:
 ['the Brave', 'the Pure']

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The Cartesian product of the previous set is:
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 [('Lancelot','the Brave'), ('Lancelot,'the Pure'), ('Galahad','the Brave'), ('Galahad','the
Pure')]

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Four instances of segment "melt" will thus be run, each one receiving
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as input one of the four 2-tuples.

At the end of the execution of all the instances of a segment, their
output lists are concatenated. If the action of segment "melt" is to
concatenate the two strings he receives separated by a space, the
final output set of segment "melt" will be: 

 [('Lancelot the Brave'), ('Lancelot the Pure'), ('Galahad the Brave'), ('Galahad the Pure')].
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This default behavior can be altered by specifying a #multiplex
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directive in the commentary of the segment code. See section [[*Multiplex%20directive][Multiplex
directive]] for more details.
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As the segment execution order is not uniquely determined by the pipe
scheme (several path may exists), it is not possible to retrieve an
ordered input tuple. To overcome this issue, segment inputs are
dictionaries, with keywords matching parent segment names.  In the
above example, one can read "melt" inputs using:
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k = seg_input["knights"]
q = seg_input["quality"]

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See section [[*The%20segment%20environment]['The segment environment']] for more details.
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*** Orphan segments
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By default, orphan segments have no input argument (an empty list),
and therefore are executed once. 
The possibility is offer to push an input list to an orphan segment.  
If P is an instance of the pipeline object:

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P.push (segname=[1,2,3])

From the segment environment, inputs can be retrieve from the
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usual dictionary, using the keyword 'segnamephantom'. 
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id = seg_input['segnamephantom']
or
id = seg_input.values()[0]

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See section [[*The%20segment%20environment][The segment environment]] for more details.
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*** Hierarchical data storage

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The framework provides versioning of your data and easy access
through the web interface. It is also used to keep track of the code,
of the execution logs, and various meta-data of the processing. Of
course, you remain able to bypass the hierarchical storage and store
your actual data elsewhere, but you will loose the benefit of
automated versioning which proves to be quite convenient.
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The storage is organized as follows:
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- all pipeline instances are stored below a root which corresponds to
  the prefix parameter of the Pipeline object. 
      /prefix/
- all segment meta data are stored below a root which name corresponds
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  to a unique hash of the segment code.
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      /prefix/segname_YFLJ65/
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- Segment's meta data are: 
  - a copy of the segment python script
  - a copy of all segment hook scripts
  - a parameter file (.args) which contains segment parameters value
  - a meta data file (.meta) which contains some extra meta data
- all segment instances data and meta data are stored in a specific subdirectory
  which name corresponds to a string representation of its input
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  	/prefix/segname_YFLJ65/data/1/
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- if there is a single segment instance, then data are stored in
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       /prefix/segname_YFLJ65/data/
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- If a segment has at least one parent, its root will be located below
  one of its parent's one : 
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       /prefix/segname_YFLJ65/segname2_PLMBH9/
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- etc...
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*** The segment environment

The segment code is executed in a specific environment that provides:

1. access to the segment input and output
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   - seg_input:  this variable is a dictionary containing the input of the segment.

     In the general case, seg_input is a python dictionary which
     contains as many keywords as parent segments. In the case of orphan
     segment, the keyword used is suffixed by the 'phantom' word. 
     One exception to this is coming from the use of the 'group_by'
     directive, which alters the origin of the inputs. In this case,
     seg_input contains the resulting class elements. 

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   - seg_output: this variable has to be a list. 
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2. Functionalities to use the automated hierarchical data storage system.
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   - get_data_fn(basename): complete the filename with the path to the working directory. 
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   - glob_seg(seg, regexp): return the list of filename in segment seg
     working directory matching regexp.
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   - get_tmp_fn(): return a temporary filename.

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3. Functionalities to use the automated parameters handling
   - lst_par: list of parameter names of the segment to save in the meta data.
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   - lst_tag: list of parameter names which will be made visible from the web interface
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   - load_param(seg, globals(), lst_par): retrieve parameters from the meta data.
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4. Various convenient functionalities
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   - save_products(filename, lst_par='*'): use pickle to save a
     part of the current namespace.
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   - load_products(filename, lst_par): update the namespace by
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     unpickling requested object from the file.
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   - logged_subprocess(lst_args): execute a subprocess and log its
     output in processname.log and processname.err.
   - logger is a standard logging.Logger object that can be used to
     log the processing
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5. Hooking support 
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   Pipelet enables you to write reusable generic
   segments by providing a hooking system via the hook function.
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   hook (hookname, globals()): execute Python script ‘segname_hookname.py’ and update the namespace.
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   See the section [[*the%20Hooking%20system][Hooking system]] for more details.
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*** The example pipelines
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**** fft
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***** Highlights

This example illustrates a very simple image processing use.
The problematic is the following : one wants to apply a Gaussian
filter in Fourier domain on several 2D images. 

The pipe scheme is: 

pipedot = """
mkgauss->convol;
fftimg->convol;
"""

where segment 'mkgauss' computes the Gaussian filter, 'fftimg' computes the
Fourier transforms of the input images, and 'convol' performs the
filtering in Fourier domain, and the inverse transform of the filtered
images. 

P = pipeline.Pipeline(pipedot, code_dir=op.abspath('./'), prefix=op.abspath('./'))
P.to_dot('pipeline.dot')

The pipe scheme is output as a .dot file, that can be converted to an
image file with the command line: 

dot -Tpng -o pipeline.png pipeline.dot

To apply this filter to several images (in our case 4 input images),
the pipe data parallelism is used. 
From the main script, a 4-element list is pushed to the 'fftimg'
segment. 

P.push(fftimg=[1,2,3,4]) 

At execution, 4 instances of the 'fftimg' segment will be
created, and each of them outputs one element of this list : 

img = seg_input.values()[0] #(fftimg.py - line 16)
seg_output = [img]          #(fftimg.py - line 41)

On the other side, a single instance of the 'mkgauss' segment will be
executed, as there is one filter to apply. 

The last segment 'convol', which depends on the two others, will be
executed with a number of instances that is the Cartesian product of
its 4+1 inputs (ie 4 instances)

The instance identifier which is set by the 'fftimg' output, can be
retrieve with the following instruction: 

img = seg_input['fftimg']   #(convol.py - line 12)

***** Running the pipe

Follow the same procedure than for the first example pipeline, to run
this pipe and browse the result. 


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**** cmb
***** Running the pipe
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This CMB pipeline depends on two external python modules: 
+ healpy   :  http://code.google.com/p/healpy/
+ spherelib:  http://gitorious.org/spherelib
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***** Problematic

This example illustrates a very simple CMB data processing use.  

The problematic is the following : one wants to characterize the
inverse noise weighting spectral estimator (as applied to the WMAP 1yr
data). A first demo pipeline is built to check that the algorithm
has correctly been implemented. Then, Monte Carlo simulations are used
to compute error bars estimates. 

***** A design pipeline

The design pipe scheme is: 

pipe_dot = """ 
cmb->clcmb->clplot;
noise->clcmb;
noise->clnoise->clplot;
"""

where: 
+ cmb: generate a CMB map from LCDM power spectrum. 
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+ noise: compute the mode coupling matrix from the input hit-count map
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+ clnoise: compute the empirical noise power spectrum from a noise
  realization. 
+ clcmb: generate two noise realizations, add them to the CMB map, to compute a
  first cross spectrum estimator. Then weighting mask and mode
  coupling matrix are applied to get the inverse noise weighting
  estimator
+ clplot: make a plot to compare pure cross spectrum vs inverse noise
  weighting estimators. 

As the two first orphan segments depends on a single shared parameter
which is the map resolution nside, this argument is pushed from the
main script. 

Another input argument of the cmb segment, is its simulation identifier,
which will be used for latter Monte Carlo. In order to push two
inputs to a single segment instance, we use python tuple data type.

P.push(cmb=[(nside, 1)])
P.push(noise=[nside])

From the segment, those inputs are retrieved with : 

nside  = seg_input.values()[0][0] ##(cmb.py line 13)
sim_id = seg_input.values()[0][1] ##(cmb.py line 14)

nside  = seg_input.values()[0]  ##(noise.py line 16)


The last segment produces a plot in which we compare: 
+ the input LCDM power spectrum
+ the binned cross spectrum of the noisy CMB maps
+ the binned cross spectrum of which we applied hitcount weight and
  mode coupling matrix. 
+ the noise power spectrum computed by clnoise segment. 

In this plot we check that both estimators are corrects, and that the
noise level is the expected one.

***** From the design pipeline to Monte Carlo

As a second step, Monte Carlo simulations are used to compute error
bars. 

The clnoise segment is no longer needed, so that the new pipe scheme
reads : 

pipe_dot = """ 
cmb->clcmb->clplot;
noise->clcmb;
"""

We now use the native data parallelization scheme of the pipe to build
many instances of the cmb and clcmb segments. 

cmbin = []
for sim_id in [1,2,3,4,5,6]:
    cmbin.append((nside, sim_id))
P.push(cmb=cmbin)
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** Running Pipes
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*** The sample main file

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A sample main file is made available when creating a new Pipelet
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framework. It is copied from the reference file: 

pipelet/pipelet/static/main.py

This script illustrates various ways of running pipes. It describes
the different parameters, and also, how to write a
main python script can be used as any binary from the command line
(including options parsing). 

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*** Common options
Some options are common to each running modes.
**** log level

The logging system is handle by the python logging facility module. 
This module defines the following log levels : 
+ DEBUG
+ INFO
+ WARNING
+ ERROR
+ CRITICAL

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All logging messages are saved in the different Pipelet log files,
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available from the web interface (rotating file logging).  It is also
possible to print those messages on the standard output (stream
logging), by setting the desired log level in the launchers options:
For example: 

import logging
launch_process(P, N,log_level=logging.DEBUG)

If set to 0, stream logging will be disable. 


**** matplotlib

The matplotlib documentation says: 

"Many users report initial problems trying to use maptlotlib in web
application servers, because by default matplotlib ships configured to
work with a graphical user interface which may require an X11
connection. Since many barebones application servers do not have X11
enabled, you may get errors if you don’t configure matplotlib for use
in these environments. Most importantly, you need to decide what kinds
of images you want to generate (PNG, PDF, SVG) and configure the
appropriate default backend. For 99% of users, this will be the Agg
backend, which uses the C++ antigrain rendering engine to make nice
PNGs. The Agg backend is also configured to recognize requests to
generate other output formats (PDF, PS, EPS, SVG). The easiest way to
configure matplotlib to use Agg is to call:

matplotlib.use('Agg')
"

The matplotlib and matplotlib_interactive options turn the matplotlib
backend to Agg in order to allow the execution in non-interactive
environment.

Those two options are set to True by default in the sample main
script.
TODO : explain why. 







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*** The interactive mode
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This mode has been designed to ease debugging. If P is an instance of
the pipeline object, the syntax reads :
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from pipelet.launchers import launch_interactive
w, t = launch_interactive(P)
w.run()

In this mode, each tasks will be computed in a sequential way. 
Do not hesitate to invoque the Python debugger from IPython : %pdb

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To use the interactive mode, run: 
main.py -d
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*** The process mode
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In this mode, one can run simultaneous tasks (if the pipe scheme
allows to do so). 
The number of subprocess is set by the N parameter : 

from pipelet.launchers import launch_process
launch_process(P, N)

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To use the process mode, run: 
main.py 
or
main.py -p 4

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*** The batch mode
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In this mode, one can submit some batch jobs to execute the tasks. 
The number of job is set by the N parameter : 

from pipelet.launchers import launch_pbs
launch_pbs(P, N , address=(os.environ['HOST'],50000))
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It is possible to specify some job submission options like: 
+ job name 
+ job header: this string is prepend to the PBS job scripts. You may
  want to add some environment specific paths. Log and error files are
  automatically handled by the pipelet engine, and made available from
  the web interface. 
+ cpu time: syntax is: "hh:mm:ss"

The 'server' option can be disable to add some workers to an existing
scheduler.

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To use the batch mode, run: 
main.py -b

to start the server, and: 

main.py -a 4
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to add 4 workers. 
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** Browsing Pipes
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*** The pipelet webserver and ACL

The pipelet webserver allows the browsing of multiple pipelines. 
Each pipeline has to be register using : 

pipeweb track <shortname> sqlfile

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To remove a pipeline from the tracked list, use : 

pipeweb untrack <shortname>

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As the pipeline browsing implies a disk parsing, some basic security
has to be set also. All users have to be register with a specific access
level (1 for read-only access, and 2 for write access).  

pipeutils -a <username> -l 2 sqlfile
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To remove a user from the user list: 

pipeutils -d <username> sqlfile

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Start the web server using : 

pipeweb start

Then the web application will be available on the web page http://localhost:8080
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To stop the web server : 

pipeweb stop

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*** The web application
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In order to ease the comparison of different processing, the web
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interface displays various views of the pipeline data : 

**** The index page 

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The index page displays a tree view of all pipeline instances. Each
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segment may be expand or reduce via the +/- buttons.  

The parameters used in each segments are resumed and displayed with
the date of execution and the number of related tasks order by
status. 

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A check-box allows to performed operation on multiple segments :
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  - deletion : to clean unwanted data
  - tag : to tag remarkable data

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The filter panel allows to display the segment instances with respect to 2
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criterions :
  - tag
  - date of execution

**** The code page

Each segment names is a link to its code page. From this page the user
can view all python scripts code which have been applied to the data.

The tree view is reduced to the current segment and its related
parents.

The root path corresponding to the data storage is also displayed.


**** The product page

The number of related tasks, order by status, is a link to the product
pages, where the data can be directly displayed (if images, or text
files) or downloaded. 
From this page it is also possible to delete a specific product and
its dependencies. 


**** The log page

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The log page can be acceded via the log button of the filter panel.
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Logs are ordered by date. 



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* Advanced usage
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** Multiplex directive
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The default behavior can be altered by specifying a #multiplex
directive in the commentary of the segment code. If several multiplex
directives are present in the segment code the last one is retained.

The multiplex directive can be one of: 

+ #multiplex cross_prod : default behavior, return the Cartesian
  product. 
+ #multiplex union : make the union of the inputs

Moreover the #multiplex cross_prod directive admits filtering and
grouping by class similarly to SQL requests:

#multiplex cross_prod where "condition" group_by "class_function"

"condition" and "class_function" are python code evaluated for each element
of the product set. 

The argument of where is a condition. The element will be part of the
input set only if it evaluates to True.

The group_by directive groups elements into class according to the
result of the evaluation of the given class function. The input set
contains all the resulting class. For example, if the function is a
constant, the input set will contain only one element: the class
containing all elements.

During the evaluation, the values of the tuple elements are accessible
as variable wearing the name of the corresponding parents.

Following the previous example, one can use :

#multiplex cross_prod where "quality=='the Brave'" 
to get 2 instances of the "melt" segment : ('Lancelot','the Brave'), ('Galahad','the Brave')

#multiplex cross_prod group_by "knights"
to get 2 instances of the "melt" segment : ('Lancelot'), ('Galahad')

#multiplex cross_prod group_by "0"
to get 1 instance of the "melt" segment : (0)

Note that to make use of group, elements of the output set have to be
hashable.

Another caution on the use of group: segment input data type is no
longer a dictionary in those cases as the original tuple is
transformed but simply the result of the class function.

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See section [[*The%20segment%20environment][The segment environment]] for more details.
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** Depend directive

As explained in the introduction section, Pipelet offers the
possibility to spare CPU time by saving intermediate products on disk.
We call intermediate products the input/output data files of the
different segments.  

Each segment repository is identified by a unique key which depends
on: 
- the segment processing code and parameters (segment and hook
  scripts)
- the input data (identified from the key of the parent segments)

Every change made on a segment (new parameter or new parent) will then
give a different key, and tell the Pipelet engine to compute a new
segment instance.

It is possible to add some external dependencies to the key
computation using the depend directive: 

#depend file1 file2

At the very beginning of the pipeline execution, all dependencies will
be stored, to prevent any change (code edition) between the key
computation and actual processing.

Note that this mechanism works only for segment and hook
scripts. External dependencies are also read as the beginning of the
pipeline execution, but only used for the key computation.

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** Database reconstruction

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In case of unfortunate lost of the pipeline sql data base, it is
possible to reconstruct it from the disk : 

import pipelet
pipelet.utils.rebuild_db_from_disk (prefix, sqlfile)
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All information will be retrieve, but with new identifiers. 

** The hooking system
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As described in the 'segment environment' section, Pipelet supports
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an hooking system which allows the use of generic processing code, and
code sectioning.

Let's consider a set of instructions that have to be systematically
applied at the end of a segment (post processing), one can put those
instruction in the separate script file named for example
'segname_postproc.py' and calls the hook function: 

hook('postproc', globals()) 

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A specific dictionary can be passed to the hook script to avoid
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confusion. 

The hook scripts are included into the hash key computation (see
advanced usage section). 



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** Writing custom environments

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The Pipelet software provides a set of default utilities available
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from the segment environment. It is possible to extend this default
environment or even re-write a completely new one.

*** Extending the default environment

The different environment utilities are actually methods of the class
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Environment. It is possible to add new functionalities by using the
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python heritage mechanism: 

File : myenvironment.py

   from pipelet.environment import *

   class MyEnvironment(Environment):
         def my_function (self):
            """ My function do nothing
	    """
	    return 


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The Pipelet engine objects (segments, tasks, pipeline) are available
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from the worker attribut self._worker. See section [[*the%20pipelet%20actors][The Pipelet actors]]
for more details about the Pipelet machinery.
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*** Writing new environment

In order to start with a completely new environment, extend the base
environment: 

File : myenvironment.py

   from pipelet.environment import *

   class MyEnvironment(EnvironmentBase):
         def my_get_data_fn (self, x):
            """ New name for get_data_fn
	    """
	    return self._get_data_fn(x)

         def _close(self, glo):
            """ Post processing code
            """	 
	    return glo['seg_output']

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From the base environment, the basic functionalities for getting file
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names and executing hook scripts are still available through: 
- self._get_data_fn 
- self._hook

The segment input argument is also stored in self._seg_input
The segment output argument has to be returned by the _close(self, glo)
method. 

The pipelet engine objects (segments, tasks, pipeline) are available
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from the worker attribut self._worker. See section [[*the%20pipelet%20actors][The Pipelet
actors]] for more details about the Pipelet machinery.
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*** Loading another environment

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To load another environment, set the pipeline environment attribute
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accordingly. 

Pipeline(pipedot, codedir=, prefix=, env=MyEnvironment)

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** Writing custom main files
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** Launching pipeweb behind apache

Pipeweb use the cherrypy web framework server and can be run behind an
apache webserver which brings essentially two advantages:
- https support.
- faster static files serving.
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See the [[http://www.cherrypy.org/wiki/TableOfContents][cherrypy]] documentation for hints about this.
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* The Pipelet actors
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This section document the code for developers.
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The code documentation can be built using the doxygen configuration
file

pipelet/doc/pipelet.dox
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** The Repository object
** The Pipeline object
** The Task object
** The Scheduler object
** The Tracker object
** The Worker object
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** The Environment object
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