Pipelet is a free framework allowing for the creation, execution and
browsing of scientific data processing pipelines. It provides:

+ 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

The pipeline mechanism allows you to apply a sequence of processing
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

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
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

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


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

+ Running the Pipelet engine requires Python >= 2.6.

+ The web interface of Pipelet requires the installation of the
  cherrypy3 Python module (debian aptitude install python-cherrypy3).

You may find usefull to install some generic scientific tools that nicely interact with Pipelet: 
+ numpy
+ matplotlib
+ latex 

**** Getting Pipelet

There is not any published stable release of pipelet right now.

git clone git://gitorious.org/pipelet/pipelet.git

**** Installing Pipelet

sudo python setup.py install

*** Running a simple test pipeline

1. Run the test pipeline

cd test
python main.py

2. Add this pipeline to the web interface

pipeweb track test ./.sqlstatus

3. Set the access control and launch the web server

pipeutils -a username -l 2 .sqlstatus
pipeweb start

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

*** Getting a new pipe framework

To get a new pipeline framework, with example main and segment scripts : 

pipeutils -c pipename

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. 

The next section describes those two files in more details. 


** Writing Pipes
*** 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
graphviz dot language (http://www.graphviz.org). For exemple the string:

"""
a -> b -> d;
c -> d;
c -> e;
"""

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
of "a" will be feeded as input for "b". In the given example, the node
"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.

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
(this mecanism is useful to write generic segment and is completed by
the hooking system, described in the advanced usage section). The code
is then executed in a specific namespace (see below The execution
environment).

*** The Pipeline object

Practically, the creation of a Pipeline object needs 3 arguments:

P = Pipeline(pipedot, codedir=, prefix=)

- pipedot is the string description of the pipeline
- codedir is the path where the segment scripts can be found
- prefix  is the path to the data repository (see below Hierarchical data storage)

It is possible to output the graphviz representation of the pipeline. 
First, save the graph string into a .dot file with the pipelet function: 

P.to_dot('pipeline.dot')

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

dot -Tpng -o pipeline.png pipeline.dot

*** Dependencies between segments

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
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
default behaviour of the engine is to form the Cartesian product of
the output list of its parent.

To illustrate this behaviour let us consider the following pipeline,
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']

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

Four instances of segment "melt" will thus be run, each one receving
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')].


TODO : describe input data type : disctionnary , ... ? 

*** Multiplex directive

This 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.

- #multiplex : activate the default behaviour

- #multiplex cross_prod group by 0 : The input set contains one tuple of all the ouputs.

- #multiplex cross_prod group by ... : compute the cross_product and group the task
  that are identical. To make use of group, elements of the output set
  have to be hashable.

*** Orphan segments

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:

P.push (segname=seg_input)


*** 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 an 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 mecanism 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.

*** Hierarchical data storage

This system provides versionning 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
versionning which proves to be quite convenient.

The storage is organized as follows:

- 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
  to an unique match of the segment code.
      /prefix/segname_YFLJ65/
- 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
  	/prefix/segname_YFLJ65/data/1/
- if there is a single segment instance, then data are stored in
       /prefix/segname_YFLJ65/data/
- If a segment has at least one parent, its root will be located below
  one of its parent's one : 
       /prefix/segname_YFLJ65/segname2_PLMBH9/
- etc...
  



*** The segment environment

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

1. access to the segment input and output
   - seg_input:  this variable is a dictionnary containing the input of the segment
   - seg_output: this variable has to be a list. 

2. Functionnalities to use the automated hierarchical data storage system.
   - get_data_fn(basename): complete the filename with the path to the working directory. 
   - glob_seg(seg, regexp): return the list of filename matching regexp from segment seg
   - get_tmp_fn(): return a temporary filename.

3. Functionnalities to use the automated parameters handling
   - lst_par: list of parameter names of the segment 
   - lst_tag: list of parameter names which will be made visible from the web interface
   - load_param(seg, globals(), lst_par)

4. Various convenient functionalities
   - save_products(filename=', lst_par='*'): use pickle to save a
     part of a given namespace.
   - load_products(filename, lst_par): update the namespace by
     unpickling requested object from the file.
   - 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

5. Hooking support 
   Pipelet enables you to write reusable generic
   segments by providing a hooking system via the hook function.
   hook (hookname, globals()): execute Python script ‘segname_hookname.py’ and update the namespace.


*** The exemple pipelines
**** fft

***** 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. 





 





**** cmb

***** Highlights
***** Running the pipe

** Running Pipes

*** The sample main file

A sample main file is made available when creating a new pipelet
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). 


*** 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

All logging messages are saved in the differents pipelet log files,
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. 







*** The interactive mode
This mode has been designed to ease debugging. If P is an instance of
the pipeline object, the syntax reads :

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



*** The process mode
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)

*** The batch mode
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))

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.



** Browsing Pipes
*** 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

To remove a pipeline from the tracked list, use : 

pipeweb untrack <shortname>

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

To remove a user from the user list: 

pipeutils -d <username> sqlfile

Start the web server using : 

pipeweb start

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

To stop the web server : 

pipeweb stop

*** The web application

In order to ease the comparison of different processings, the web
interface displays various views of the pipeline data : 

**** The index page 

The index page displays a tree view of all pipeline instances. Each
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. 

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

The filter panel allows to display the segment instances wrt 2
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

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




* Advanced usage
** Database reconstruction

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)

All information will be retrieve, but with new identifiers. 

** The hooking system

As described in the 'segment environment' section, pipelet supports
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()) 

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

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




** Writing custom environments

The pipelet software provides a set of default utilities available
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
Environment. It is possible to add new functionnalities by using the
python heritage mechanism: 

File : myenvironment.py

   from pipelet.environment import *

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


The pipelet engine objects (segments, tasks, pipeline) are available
from the worker attribut self._worker. See section "The pipelet
actors" for more details about the pipelet machinery.


*** 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']

From the base environment, the basic functionnalities for getting file
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
from the worker attribut self._worker. See section "The pipelet
actors" for more details about the pipelet machinery.


*** Loading another environment

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

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

** Writing custom main files
** 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.


* The pipelet actors
  
This section document the code for developpers.

** The Repository object
** The Pipeline object
** The Task object
** The Scheduler object
** The Tracker object
** The Worker object
** The Environment object