Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

2.1 #130

Merged
merged 137 commits into from
Oct 13, 2024
Merged

2.1 #130

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
137 commits
Select commit Hold shift + click to select a range
ab21096
Added versions plugin to build file and updated all dependencies
mephenor May 13, 2020
003328e
Added code for issue #97 (Subsystem information without model id)
mephenor May 13, 2020
91f3e6f
Simplified database contract classes for better readability
mephenor May 13, 2020
52f5403
Added functionality for model annotation with genome accession, if mo…
mephenor May 13, 2020
5f88a8a
Hopefully fixing travis Slack integration
mephenor May 13, 2020
17bcc81
Bumped version to 2.1. Fixed typo in accession_value. Updated travis …
mephenor May 13, 2020
469af05
Testing one of two remaining possibilities for the secret
mephenor May 13, 2020
eb29da1
Some cleanup in BiGGDB - all queries using contract class again and r…
mephenor May 14, 2020
e3aa18b
Removed some unused variables, fixed spelling and corrected one logic…
mephenor May 21, 2020
3f20fd0
Renamed mpMessageBundle to MESSAGES. Replaced nearly all occurrences …
mephenor May 21, 2020
b54e210
Moved code regarding annotation of model, compartments, species, reac…
mephenor May 25, 2020
4f6b480
Unified CVTerm annotation code for species and reaction, as they alre…
mephenor May 26, 2020
65d4ea3
Implemented code to deal with Issue#100 for now. Moved combine archiv…
mephenor Jun 1, 2020
3771f0c
Moved polishing tasks into own classes, analogously to how annotation…
mephenor Jun 2, 2020
ec59134
Added explicit check if both input and output parameter are provided,…
mephenor Jun 2, 2020
54814ad
Simplified code in some places. Changed handling when dealing with re…
mephenor Jun 2, 2020
c37185d
Moved majority of polishing on model level into ModelPolishing class
mephenor Jun 2, 2020
34d74f0
Restructuring of COBRAParser finished, just needs a pass to check whi…
mephenor Jun 8, 2020
cfafc05
Moved all logged strings to polisher resource bundle. JSONParser shou…
mephenor Jun 12, 2020
6db7f57
Somehow missed out on actually fixing the JSONParser strings and movi…
mephenor Jun 12, 2020
c2b9deb
Changed Boolean to boolean in parameter class, no need to carry boxin…
mephenor Aug 4, 2020
15d6fbc
Another try at travis integration. Will fail on testing, as new MIRIA…
mephenor Aug 4, 2020
61234d6
Finally fixed java.util.prefs issue waiting for lock delaying execution.
mephenor Aug 4, 2020
aa5893a
Nearly finished rewrite of MIRIAM/identifiers.org annotation Registry…
mephenor Oct 24, 2020
1590a43
Registry class should now be working as expected - some smaller issue…
mephenor Oct 29, 2020
2897111
Reverted fix for SBML: namespace tag issue, as removing this in neste…
mephenor Oct 29, 2020
1436777
Updated dependecies to current versions. Added 'Gradle License Report…
mephenor Nov 3, 2020
ef3612f
Almost functional version of JSON writing capabilities implemented. g…
mephenor Nov 15, 2020
8b4a52b
Converting GeneProductAssociation to string should work now. Added op…
mephenor Nov 16, 2020
2257624
Converting notes to JSON representation works now. Some cleanup and s…
mephenor Nov 18, 2020
c95207c
issue #114: fix gradle task and test namespace
Schmoho May 10, 2022
81618c5
issue #115: update README.md
Schmoho May 10, 2022
4a8242c
issue #116: add javadoc task in gradle config
Schmoho May 10, 2022
dfd86a6
issue #116: add built javadocs
Schmoho May 10, 2022
871c05b
gradle version bump
Schmoho Jun 22, 2022
e71fbed
SBMLPolisher test
Schmoho Jun 22, 2022
ae635f1
gradle test workflow def
Schmoho Jun 28, 2022
0ec1ab1
ticket #117 #120: unit tests for unit polishing
Schmoho Jun 28, 2022
5d2e87b
issue #117, #120: introduce unit polishing class
Schmoho Jun 28, 2022
717f2b6
issues #117, #120: introduce dedicated test class
Schmoho Jun 28, 2022
0ad4c92
issues #170 #120 remove dead code + introduce static utils
Schmoho Jun 28, 2022
5e98bdb
issue #117 remove non-comments
Schmoho Jun 28, 2022
9b4937d
issue #119 unit test
Schmoho Jun 21, 2022
8bd3163
issue #119 bug fix in objective polishing
Schmoho Jun 21, 2022
81ad955
issue #121 species polishing unit test
Schmoho Jun 28, 2022
26736ad
issue #121: remove non-comments
Schmoho Jun 28, 2022
f0d8225
just deleting some code
Schmoho Jun 28, 2022
f5ba799
issue #121 remove non-comments + some laptop-friendly formatting
Schmoho Jun 28, 2022
793436b
issue #121: reaction polishing test suite
Schmoho Jul 5, 2022
5ab2fd5
issue #121: cleaning out tests
Schmoho Jul 5, 2022
4b01758
issue #121 fix missing port bug
Schmoho Jul 26, 2022
6b667d9
issue #121 introduce DB tests + preloaded test-container
Schmoho Jul 26, 2022
0ac38c9
issue #121 move tests to proper packages + remove non-test
Schmoho Jul 26, 2022
951b87f
issue #121: remove pointless FUD
Schmoho Jul 26, 2022
fda2edd
issue #121 annotation tests
Schmoho Jul 26, 2022
4a35021
issue #121, #89 - test questionable water annotations
Schmoho Jul 26, 2022
82c05b1
issue #121 fix broken test references
Schmoho Aug 2, 2022
f1b3565
issue #121 test issue #76
Schmoho Aug 2, 2022
9d813b5
issue #121 test #27
Schmoho Aug 2, 2022
51c81d3
issue #121 test #47
Schmoho Aug 2, 2022
9a8cfaf
issue #121 test #122
Schmoho Aug 2, 2022
29830fb
issue #121 test #20
Schmoho Aug 2, 2022
580418e
isse #121 test #20
Schmoho Aug 2, 2022
1538292
issue #121 test #20
Schmoho Aug 2, 2022
5c65c11
issue #121 deactivate broken tests
Schmoho Aug 2, 2022
b065019
sparser logging + fix container testing setup for gradle runs
Schmoho Aug 23, 2022
adca85f
issue #121 #8 - more elaborate unit tests for unit polishing
Schmoho Aug 23, 2022
7bf4408
llm-based documentation
Schmoho Jun 11, 2024
c8c8377
clean out build
Schmoho Jun 11, 2024
42144b0
clean out project files
Schmoho Jun 11, 2024
086a3db
dependency version bumps
Schmoho Jun 11, 2024
4ddb4c5
changes for javadoc
Schmoho Jun 11, 2024
1e88b8d
updated javadoc
Schmoho Jun 11, 2024
38b9978
unused imports
Schmoho Jun 11, 2024
2dd1f5f
aktuelle Doku
Schmoho Jun 12, 2024
92a6091
stuff related to fixing the docker setup (no database dumps)
Schmoho Jul 2, 2024
11865ea
typo in workflow
Schmoho Jul 2, 2024
3bcf2c5
add gradle-wrapper.properties
Schmoho Jul 2, 2024
8948f80
fix tests
Schmoho Jul 2, 2024
2a99a87
move entrypoint classes out of bigg package
Schmoho Jul 8, 2024
b9b9b4a
disentangle CLI mode and MP logic
Schmoho Jul 8, 2024
4cc304d
disentangle ModelPolisherCLILauncher
Schmoho Jul 9, 2024
9a62ea2
remove static read/write datastructures
Schmoho Jul 10, 2024
8e43616
remove static parameters
Schmoho Jul 10, 2024
976e96d
move code around
Schmoho Jul 10, 2024
76940d0
updated javadoc
Schmoho Jul 10, 2024
a2469e3
code consistency and strictness check implementation
Schmoho Jul 11, 2024
2fbc36f
code consistency
Schmoho Jul 14, 2024
6f4d3d7
IntelliJ code problems
Schmoho Jul 14, 2024
7a68415
prepare parameters for non CLI mode
Schmoho Jul 14, 2024
e205214
identifers.org rework
Schmoho Jul 19, 2024
6993237
decomplect bigg and adb
Schmoho Jul 22, 2024
7b84b25
intellij issues fixed
Schmoho Jul 22, 2024
bc7151f
updated javadocs
Schmoho Jul 22, 2024
b5a658b
parameters rewrite and parser
Schmoho Jul 23, 2024
477bbab
updated javadoc
Schmoho Jul 23, 2024
5c8bdc4
parameter rework, logging and exception handling
Schmoho Jul 26, 2024
435261f
updated javadocs
Schmoho Jul 26, 2024
eeff80e
files moved according to classpath
Schmoho Jul 26, 2024
f294dbf
clean out repository
Schmoho Aug 7, 2024
8829f61
rampage
Schmoho Aug 14, 2024
1b8a125
rampage extended
Schmoho Aug 15, 2024
7d57fdd
potential NPE
Schmoho Aug 15, 2024
76077ff
static init biggdb
Schmoho Aug 15, 2024
91d8652
logging
Schmoho Aug 15, 2024
dfafe97
adb parameter name consistency
Schmoho Aug 15, 2024
294b3bc
toString on parameters
Schmoho Aug 15, 2024
9518897
fix resource removal in annotation polisher
Schmoho Aug 16, 2024
f433465
comments and minor code orga
Schmoho Aug 18, 2024
f7775cd
generate pom in the jar
Schmoho Aug 18, 2024
546261e
new config options for fixer
Schmoho Aug 18, 2024
47ece05
add compartment fixer
Schmoho Aug 18, 2024
9052b57
debugging adb
Schmoho Aug 18, 2024
6dc07e1
OCD and CLI mode debugging
Schmoho Aug 19, 2024
64e78f4
example configs + compose
Schmoho Aug 19, 2024
a4537cc
logging config + constructor on AbstractFixer
Schmoho Aug 19, 2024
49eeef4
fix docker setup
Schmoho Aug 20, 2024
334e5f3
fix pattern
Schmoho Aug 21, 2024
7ed5b33
fix patterns
Schmoho Aug 26, 2024
40c86aa
charge handling for iYS1720
Schmoho Aug 26, 2024
cb9180a
update readme
Schmoho Sep 1, 2024
9f35b28
restructure build
Schmoho Sep 6, 2024
8af30f5
adapt dockerfile
Schmoho Sep 16, 2024
e8026cf
remove build folders from vcs
Schmoho Sep 16, 2024
5bed11f
fix #106
Schmoho Sep 16, 2024
340fb9f
updated javadoc
Schmoho Sep 16, 2024
cd94618
fix whitespace in gradle file
Schmoho Sep 16, 2024
fe192dd
fix missing SBO annotations on reactions
Schmoho Sep 29, 2024
27b4e84
unit test for duplicate patterns issue 123
Schmoho Sep 29, 2024
d4b14a1
new entry in identifiers.org
Schmoho Sep 29, 2024
e30a4bc
duplicate patterns test + bugfix
Schmoho Sep 29, 2024
10ca970
move species SBO to polisher and fix it
Schmoho Oct 12, 2024
1e3d367
allow to set reaction compartment from bigg-style id
Schmoho Oct 12, 2024
0045b80
allow annotation of non-bigg models
Schmoho Oct 12, 2024
a0934bf
unit tests
Schmoho Oct 12, 2024
6692356
fix in CLI mode
Schmoho Oct 12, 2024
6968cf4
misc
Schmoho Oct 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
25 changes: 15 additions & 10 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,24 @@
*.class
*.dump
.classpath
.gradle/
.idea/
.settings/
.classpath
.project
/build/
/target/
src/main/resources/edu/ucsd/sbrg/miriam/IdentifiersOrg-Registry.json
/src/scripts/ModelPolisherTemplate.*
ModelPolisher.iml
jsbml.log
.settings/
/.DS_Store
/.vscode/
/bin
/build/
/minimalSysBio.xml
/model_polisher.log
/out
/src/main/resources/edu/ucsd/sbrg/example_models/output
/src/scripts/ModelPolisherTemplate.*
/src/test/resources/edu/ucsd/sbrg/bigg/e_coli_core.zip
*.class
/bin
/target/
ModelPolisher.iml
jsbml.log
src/main/resources/edu/ucsd/sbrg/identifiersOrgRegistry/IdentifiersOrg-Registry.json
/input/
/app/build/
/lib/build/
36 changes: 0 additions & 36 deletions .travis.yml
View file
Open in desktop

This file was deleted.

40 changes: 0 additions & 40 deletions BuildSBMLFix.xml
View file
Open in desktop

This file was deleted.

16 changes: 0 additions & 16 deletions Notes for contributors.md
View file
Open in desktop

This file was deleted.

Loading