Mercurial > repos > rmarenco > hubarchivecreator

comparison todo.md @ 20:40469b265ddb draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
author yating-l
date Fri, 20 Jan 2017 17:12:03 -0500
parents 3233451a3bd6
children
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19:0152500d9acd 20:40469b265ddb
1 ### TEMP St Louis ###
2 - How to manage messages to user and debugging:
3 - User should receive INFO / WARN / ERROR / CRITICAL:
4 - User summary informations in stdout
5 - Full error in stderr
6 - Developer should receive all Logging stack:
7 - Not the user summary in stdout
8 - Full stack in stdout and stderr directly
9
10 - HOWTO:
11 - Manage (at least) two type of Logging types:
12 - The user one => When Debug mode is not set or disabled
13 - The dev one => When Debug mode is enabled
14 - User:
15 - Two Handlers: stdout and stderr
16 - STDOUT:
17 - Filter stdout:
18 - NO ERROR and CRITICAL here
19 - (Warn)
20 - Formatter:
21 - Only show %(message) for clarity
22 - STDERR:
23 - Filter stderr => WARN / ERRROR / CRITICAL
24 - Formatter:
25 - Show message
26 - Show traceback
27 - Dev:
28 - One Handler:
29 - To both stdout and stderr
30 - Filter:
31 - Nope?
32 - Formatter:
33 - Show traceback in both
34
35 # HubArchiveCreator's TODO 1 # HubArchiveCreator's TODO
36 2
37 *TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613* 3 *TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613*
38 4
39 ### TO COMPLETE 5 ### TO COMPLETE
40 6
41 7
8 - [ ] Parse the [JSON received from Galaxy inputs](hubArchiveCreator.xml#L47-L137) in a class instead of doing [this spaghetti code](hubArchiveCreator.py#L137-L149)
42 - [ ] Don't let the Tool Classes manage the archive (add or remove files / folders) => Everything should pass through TrackHub or another class dedicated to that 9 - [ ] Don't let the Tool Classes manage the archive (add or remove files / folders) => Everything should pass through TrackHub or another class dedicated to that
43 - [ ] Move the class and others program related files, into separated folders 10 - [ ] Move the class and others program related files, into separated folders
44 - [ ] Take into account the name of the reference genome / the change: 11 - [ ] Take into account the name of the reference genome / the change:
45 - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated 12 - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated
46 - [ ] Add TDD => First add the test. It should not pass. Implement. It should now pass :) 13 - [ ] Replace Gff3/GTF by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
47 - [ ] Replace Gff3 by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
48 - [ ] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
49 - [ ] Manage the error when a user is selecting Generic Bed instead of Bed Simple Repeats. Two options: a. Output a better error message ("Check with the other Bed options") b. Identify internally this is not a regular BED but a specific one 14 - [ ] Manage the error when a user is selecting Generic Bed instead of Bed Simple Repeats. Two options: a. Output a better error message ("Check with the other Bed options") b. Identify internally this is not a regular BED but a specific one
50 - [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point 15 - [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point
51 - [ ] Rename all occurences of `extension` which `datatype` 16 - [ ] Rename all occurences of `extension` with `datatype`
52 - [ ] Follow https://google.github.io/styleguide/pyguide.html 17 - [ ] Follow https://google.github.io/styleguide/pyguide.html
53 - [ ] Move to Python 3 18 - [ ] Migrate to Python 3
54 - [ ] Remove the repetition of the extension if it already exists 19 - [ ] Remove the repetition of the extension file if it already exists
55 - [ ] Better thinking about the tool_directory management / Classes path refactoring 20 - [ ] Better thinking about the tool_directory management / Classes path refactoring
56 - [ ] Add a debug mode to have more outputs
57 - [ ] Improve the standard output of HAC
58 - [ ] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
59 - [ ] Sort the order of the HTML directories/files
60 21
61 ### DONE 22 ### DONE
62 23
63 24
25 - [x] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
26 - [x] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
27 - [x] Add a debug mode to have more outputs
28 - [x] Improve the standard output of HAC
64 - [x] Each time a file is added => Print it in the output with the full path (or relative path to root) 29 - [x] Each time a file is added => Print it in the output with the full path (or relative path to root)
30 - [x] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
31 - [x] Sort the order of the HTML directories/files
65 - [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py 32 - [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py
66 - [x] Add sorting BED if not sorted (Use the output of bedToBigBed) 33 - [x] Add sorting BED if not sorted (Use the output of bedToBigBed)
67 - [x] Add a script to install the huba datatype 34 - [x] Add a script to install the huba datatype
68 - [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py 35 - [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py
69 - [x] Fix the errors for the stdio regexp not properly processed in error case (always green) => Used `detect_errors` in galaxy wrapper and raise Exception in Python 36 - [x] Fix the errors for the stdio regexp not properly processed in error case (always green) => Used `detect_errors` in galaxy wrapper and raise Exception in Python