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  • Laros Laros j.f.j.laros
  • Mihai Lefter Mihai Lefter mlefter
  • git mirror git mirror gitmirror
  • wgallard wgallard wgallard
4 authors
  1. Dec 13, 2013
  3. Mar 26, 2013
  5. Oct 29, 2012
  7. Nov 04, 2011
  9. Sep 07, 2011
  11. Apr 11, 2011
  13. Apr 07, 2011
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  23. Mar 28, 2011
  25. Mar 23, 2011
  27. Dec 20, 2010
  29. Aug 31, 2010
  31. Jul 19, 2010
    • Gerben Stouten's avatar
      TODO: · 7e91c366
      Gerben Stouten authored 
      		- update errorcodes.txt
		- rewrite some webservice.py functions
		- File.py ods files are not read in correctly. Temp file deleted before it
			can be used

    
CHANGES:
		- mutalyzer.conf
				Added pidfile reference
				Added Output Headers for the Batch Jobs

		- Db.txt
				Updated the Db.txt file so that it reflects the database changes
					* BatchJob now contains an Arg1 attribute, which is used by the
						Conversion Batch to store the build version. This could be
						changed to use the Filter Field.
					* Dropped the Var table
					* BatchQueue -> AccNo, Gene, Variant are dropped and replaced by
						single column input. This fields contains a single full
						mutalyzer variant description.

		- Install.txt
				Added the python-daemon dependency

		- handler.py
				Added a downloads handler for the old and new batch files
				Other handlers are changed so the filter for extensions now matches the
				trailing characters

		- webservice.py
				Made the functions compatible with the new Mapper.Converter class
				*** This webservice.py can use a bit more structure ***

		- index.py
				Moved a lot of logic from the index file to the Mapper.py module
				Implemented the batch handler, which has multiple entry points
				positionConverter now uses the Mapper.Converter class

		- BatchChecker.py
				Fixed the multiprocessing bugs. Now uses python-daemon to spawn a
				process and uses the var/batch.pid as a lockfile for the process

		---- Modules

		- Ouput.py
				Added getSoapMessages, which returns Soap compatible Messages for over
				the wire
				Added getBatchMessages, which returns messages above %level and filters
				the ParseError to one line
		
		- LRGparser.py
				Included the usage of transcription.translate and transcribe for the
				main transcript

		- Config.py
				Added the Batch Headers to the configfile
				Added a Batch Config object for the PID file

		- Scheduler.py
				Added the SyntaxCheck Batch
				Added the Conversion Batch
				Have the BatchProcesser read the Argument from the Batch
				Changed outputfile format to csv

		- File.py
				Changed the csv sniffer to drop the ":" delimiter in batch entries
				Updated some Job logic to detect all lines with basic errors

		- Mapper.py
				Practically a complete refactor of the module
				Added the Converter class for chromosome to c and back conversions
				Added a SoapMessage class which instances can be send over the wire
				Updated the Mapper.Mapping class to use SoapMessage messages
				Basically create correct mappings between c 2 chrom 2 c [tested]
				Reduced the number of Database calls needed significantly

		- Db.py
				Implemented getAllFields to retrieve complete dataset of Fields of
				intereset, this reduced the number of database calls
				Updated the Db logic to encompass the new Batch Job logic:
						Input entries are 1 field
						Jobs have a type
						Jobs can have arguments (1 at the moment, use BITFLAGS)


		---- Templates

		REMOVED 
				- batchCheck.html				-> All Batch jobs are united in batch.html
				- batch_convert.html		->  								"
				- convert.html					-> Replaced by converter.html

		CHANGED
				- batch.html
						Included big file type help
						Made template compatible with the three different batchTypes

				- gbupload.html & menu.html
						Fixed an onload javascript bug which caused a stream of javascript
						errors on pages other than gbupload
		
				- interface.js
						Added the changeBatch and toggle_visibility functions

		ADDED
				- downloads
						Added example download files for old & new batchfiles


NOTES:
		- change permission on var/batch.pid to have apache read/write it
		- 



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@67 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      7e91c366
  33. Jun 14, 2010
    • Laros's avatar
      Commit to do a merge with web_dev. This version is not suitable for · 48bb332d
      Laros authored 
      distribution as it is under heavy development.

Most modules will have minor changes because of a difference in set up of both
the Db and Config module.

install.sh:
- Added functionality to enable the cron restart of the Batch Checker.
- Added the auto-generation of a .htaccess file.
- Added permission settings.

mutalyzer.conf:
- Added configuration options for the Scheduler, File and GenRecord modules.

Db.txt:
- Described how to make the new ChrName tables for hg18 and hg19.

errorcodes.txt:
- Added classifications to the messages.

doc:
- Made a set up for the documentation.
  TechnicalReference:
  - This will be a technical document that describes the internals of the
    project. It is only meant for developers.
  API:
  - This is a description of the API, it is auto generated by the mkapidoc.sh
    script. Also only meant for developers.

Mutalyzer.py:
- Added a new roll function that will always find both boundaries.
- Implemented a new protein naming scheme.
- Fixed the trimming of a delins.
- Rewrote the processing of a variant. 
  - Moved post processing of the GenBank record to the GenRecord module.
  - Moved the crossmapper instance to the GenBank module, to make one instance
    per transcript variant.
  - Moved the naming of a variant to the GenBank module, as is strongly
    interacts with the crossmapper instance.
- Moved the constructCDS function to the GenRecord module.

handler.py:
- Added functionality for the batch checker (retrieve results).
- Added functionality for the genbank uploader (retrieve GenBank files).

webservice.py:
- Modified to work with the new Db module.

UCSC_update.py:
- Modified to work with the new Db module.

GenRecord.py:
- Replaced the dictionary structure with a nested list structure to make
  iteration more convenient.
- Added names to the Locus and Gene objects.
- Added all information needed to do a crossmapping in the Locus object.
- Wrote functions to find Loci and Genes.
- Wrote a function that expands a description of a variant (coupled to a Locus).

Mutator.py:
- Added documentation.

Parser.py:
- Added documentation.

Web.py:
- Added documentation.
- Added a function that checks whether a string is an e-mail address.

Scheduler.py:
- Implemented a batch scheduler that uses a MySQL database for queueing.

File.py:
- Implemented a CSV, XLS and ODS parser for use in the Scheduler module.

Output.py:
- Added documentation.

Mapper.py:
- Modified the complex object initialisation.

Config.py:
- Made subclasses to configure the separate modules.

Db.py:
- Added documentation.
- Split the Db modules into different classes, according to functionality, they
  all inherit the query function from the Db base class.
- Added chromosome accession number to name conversion functions and vice versa.
- Added functionality for the batch checker.

Crossmap.py:
- Added documentation.

Retriever.py:
- Added documentation.
- Added fall back functionality when searching for a gene.

index.py:
- Added a batch submit interface.

batch.html:
- The layout of the batch submit interface.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@30 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      48bb332d
  35. May 18, 2010
    • Laros's avatar
      Altered the Output module in such a way that all messages are stored in a · 4a8a9986
      Laros authored 
      list with priorities, and all output is stored in a dictionary. This dictionary
can be read at a later time.
The Retriever module is changed to accommodate for uploaded GenBank files and
slices of a chromosome.
A Scheduler was added for batch checking.

mutalyzer.conf:
- Added variables for the Retriever module:
  - maxDldSize, minDldSize ; Maximum and minimum sizes for slices and uploaded 
    GenBank files.
- Added variables for the Output module:
  - loglevel, outputlevel ; Specify default verbosity levels for logging and 
    output.
- Added variables for the Scheduler module:
  - processName ; Name of the running scheduler.

Db.txt:
- Added information on how to create the newly used tables GbInfo, BatchQueue
  and BatchJob.

errorcodes.txt:
- Short description of the error codes used in the Output module.

webservice.py:
- Added a Complex class to test more complicated return types (see the web_dev
  branch).
- Modified the code to work with the new Output module.

index.py:
- Made a first upload page.

Mutalyzer.py:
- Modified the code to work with the new Output module.

UCSC_update.py:
- Modified the code to work with the new Output module.

Variant_info.py:
- Modified the code to work with the new Output module.

GenRecord.py:
- Added documentation.

Mutator.py:
- Modified the code to work with the new Output module.

Misc.py:
- New file, used for generating unique IDs.

Parser.py:
- Made a change to the definition of an UD accession number.
- Modified the code to work with the new Output module.

Scheduler.py:
- Made a batch checker scheduler.
  - isDaemonRunning() ; See if we need to be started.
  - process() ; Start the batch checker.
  - addJob() ; Add jobs to a queue in the database.

Output.py:
- Added a Message class to store all debug, info, warning, error and fatal
  messages.
  - If a message is given that exceeds the configured log level, it will be
    logged immediately.
- A function is added to the Output class to read all messages that exceed a 
  certain verbosity level.
- A function is added to create a named list as an output node.
- With the getOutput function the content of this list can be retrieved.

Config.py:
- Several sub-classes were added for each configurable module.

Db.py:
- Added documentation.
- Added functionality that is used by the Retriever module.
- Added functionality that is used by the Scheduler module.

Retriever.py:
- Added functionality to be able to use custom GenBank files and chromosome
  slices.
  - Information on these created files are stored in a database to be able to
    re-create them when the cache is cleaned.
  - The hash of each file is stored for error detection.

BatchChecker.py:
- A wrapper that is called either from the addJob() function from the Scheduler
  module, or from cron. It dispatches a background process that processes the
  batch jobs.

gbupload.html:
- Test template for uploading files (copied from Mutalyzer 1.0.4).

sp.py:
- Some test with a complex return type.

download.html:
- Did some first tests with a METAL template.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@26 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      4a8a9986