Opened 13 years ago

Closed 13 years ago

#688 closed (fixed)

Support Mascot 2.3 server

Reported by: Fredrik Levander Owned by: Gregory Vincic
Milestone: Proteios 2.13.0 Keywords:
Cc:

Description (last modified by Fredrik Levander)

The current implementation does not permit searches in Mascot 2.3 server. Changes from Mascot 2.2 are that multiple databases can be selected, and the form is different for selecting modifications, which means that Proteios fails to retrieve the list of available modifications.

Change History (19)

comment:1 Changed 13 years ago by Fredrik Levander

(In [3698]) Refs #688. Changed parsing of results filename to cover 2.2 and 2.3. Non-optimal solution since 2.3 has to be specified in the config file as well.

comment:2 Changed 13 years ago by Fredrik Levander

Description: modified (diff)

comment:3 Changed 13 years ago by Gregory Vincic

Status: new → assigned

comment:4 Changed 13 years ago by Gregory Vincic

(In [3701]) Refs #688. Removing unused code, mostly log.debug statemts that where commented out

comment:5 Changed 13 years ago by Gregory Vincic

(In [3703]) Refs #688. Removing some less informative comments

comment:6 Changed 13 years ago by Gregory Vincic

(In [3704]) Refs #688. Initial revision of MascotServerIO class. It's purpose is to generate an easy to parse xml file, with valid input parameters, from the html interface.

comment:7 Changed 13 years ago by Gregory Vincic

(In [3705]) Refs #688. search_form.pl output is now converted into a static html that could be used as input to the current parser. Not testet yet though.

comment:8 Changed 13 years ago by Gregory Vincic

(In [3706]) Refs #688. Parsing new mascot results now work for modifications. Not sure if all other fields work, though they seem to. Also only one database may be selected as previously.

comment:9 Changed 13 years ago by Gregory Vincic

(In [3707]) Refs #688. Parsing of modifications now works for both mascot 2.2 and 2.3.

comment:10 Changed 13 years ago by Gregory Vincic

(In [3708]) Refs #688. Documenting MascotServerIO. Refactoring variable names. Removing private method close and renaming method getXML into getParsedHTML as it does not produce valid xml.

comment:11 Changed 13 years ago by Gregory Vincic

(In [3719]) Refs #688. Refactoring variables in mascot search plugin

comment:12 Changed 13 years ago by Gregory Vincic

(In [3720]) Refs #688. Added method addStringPart(...) making parts buildup code easier to read.

comment:13 Changed 13 years ago by Gregory Vincic

(In [3721]) Refs #688. Refactoring more variables on-top in method mascotSearchViaWebInterface(...)

comment:14 Changed 13 years ago by Gregory Vincic

(In [3722]) Refs #688. Tidying up couple debug statements

comment:15 Changed 13 years ago by Gregory Vincic

Resolution: → fixed
Status: assigned → closed

Searching now works with both mascot 2.2 and 2.3 though configuration in mascot.properties is needed. We still do not support multiple databases, this will be a new ticket. Also the error message from failing mascot searches could be improved if a upploaded file does not contain any searchable data.

comment:16 Changed 13 years ago by Fredrik Levander

Resolution: fixed
Status: closed → reopened

it seems like the Data format options are no longer parsed correctly. It is not possible to select 'mzML (.mzML)' from Proteios.

comment:17 Changed 13 years ago by Gregory Vincic

(In [3737]) Refs #688. Fixing problem with file format selection not parsed out correctly.

comment:18 Changed 13 years ago by Fredrik Levander

(In [3763]) Refs #688. Removed results script name from mascot parameters, since it is not stable. Updated parsing of results date and filename. Removed unused code.

comment:19 Changed 13 years ago by Fredrik Levander

Resolution: → fixed
Status: reopened → closed

Seems to be functional now

Note: See TracTickets for help on using tickets.