annotate differences #18

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FreakyBytes opened this Issue Jan 30, 2017 · 0 comments

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FreakyBytes commented Jan 30, 2017

Trac Ticket #18

component: code
owner: martin
reporter: martin
created: 2015-10-02 09:46:14
milestone:
type: task
version:
keywords:

as soon as bives-core:#44 is done we should annotate our patches with terms from comodi (​http://purl.org/net/comodi)

comment 1

time: 2015-11-08 17:23:32
author: Martin Scharm martin@binfalse.de

In None:


start implementating annotations of changes using COMODI [see #18]

comment 2

time: 2015-11-08 17:23:44
author: Martin Scharm martin@binfalse.de

In None:


create test infrastructure for annotation tests [see #18]

infrastructure taken from bives-cellml:source:src/test/java/de/unirostock/sems/TestAnnotations.java

implemented first test for renaming variables

comment 3

time: 2015-11-08 17:23:51
author: Martin Scharm martin@binfalse.de

In None:


created anotation infrastructure [see #18]

cmp bives-cellml:wiki

comment 4

time: 2015-11-08 17:23:59
author: Martin Scharm martin@binfalse.de

In None:


fixed first test for renaming a species [see #18]

comment 5

time: 2015-11-08 17:24:07
author: Martin Scharm martin@binfalse.de

In None:


implemented annotations for changes on species plus corresponding tests tests [see #18]

that involves

* renaming/re-id-ing of species
* deletion
* changing values -> math affecting

comment 6

time: 2015-11-08 17:24:14
author: Martin Scharm martin@binfalse.de

In None:


add support for annotations of function changes [see #18]

ins/del as well as changes

comment 7

time: 2015-11-08 17:24:21
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in events [see #18]

comment 8

time: 2015-11-08 17:24:30
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in rules [see #18]

comment 9

time: 2015-11-08 17:24:36
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in spec changes [see #18]

detects changes of SBML level and version

comment 10

time: 2015-11-08 17:24:45
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes of model name/id [see #18]

comment 11

time: 2015-11-08 17:24:53
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in machine readable annotations [see #18]

comment 12

time: 2015-11-08 17:25:01
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in textual descriptions [see #18]

comment 13

time: 2015-11-08 17:25:08
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in reaction networks [see #18]

comment 14

time: 2015-11-08 17:25:18
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes of (local) parameters [see #18]

comment 15

time: 2015-11-08 17:25:25
author: Martin Scharm martin@binfalse.de

In None:


add support for annotating changes in unit definitions [see #18]

comment 16

time: 2015-11-08 17:25:36
author: Martin Scharm martin@binfalse.de

In None:


first release officially supporting COMODI annotations [fixes #18]

comment 17

time: 2015-11-08 17:25:36
author: Martin Scharm martin@binfalse.de

Updated resolution to fixed

comment 18

time: 2015-11-08 17:25:36
author: Martin Scharm martin@binfalse.de

Updated status to closed

comment 19

time: 2016-03-11 23:01:58
author: Martin Scharm martin@binfalse.de

In None:


update to latest bives version

this does not include annotations by default [see #18]

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