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annotate todo.md @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents fcff8e9146e7
children 3233451a3bd6
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25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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1 ### TEMP St Louis ###
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2 - How to manage messages to user and debugging:
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3 - User should receive INFO / WARN / ERROR / CRITICAL:
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4 - User summary informations in stdout
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5 - Full error in stderr
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6 - Developer should receive all Logging stack:
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7 - Not the user summary in stdout
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8 - Full stack in stdout and stderr directly
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9
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10 - HOWTO:
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11 - Manage (at least) two type of Logging types:
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12 - The user one => When Debug mode is not set or disabled
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13 - The dev one => When Debug mode is enabled
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14 - User:
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15 - Two Handlers: stdout and stderr
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16 - STDOUT:
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17 - Filter stdout:
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18 - NO ERROR and CRITICAL here
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19 - (Warn)
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20 - Formatter:
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21 - Only show %(message) for clarity
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22 - STDERR:
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23 - Filter stderr => WARN / ERRROR / CRITICAL
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24 - Formatter:
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25 - Show message
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26 - Show traceback
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27 - Dev:
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28 - One Handler:
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29 - To both stdout and stderr
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30 - Filter:
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31 - Nope?
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32 - Formatter:
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33 - Show traceback in both
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34
1
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35 # HubArchiveCreator's TODO
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36
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37 *TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613*
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38
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39 ### TO COMPLETE
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40
13
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41
1
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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
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43 - [ ] Move the class and others program related files, into separated folders
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44 - [ ] Take into account the name of the reference genome / the change:
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45 - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated
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46 - [ ] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
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47 - [ ] Replace Gff3 by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
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48 - [ ] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
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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
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50 - [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point
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51 - [ ] Rename all occurences of `extension` which `datatype`
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52 - [ ] Follow https://google.github.io/styleguide/pyguide.html
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53 - [ ] Move to Python 3
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54 - [ ] Remove the repetition of the extension if it already exists
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55 - [ ] Better thinking about the tool_directory management / Classes path refactoring
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56 - [ ] Add a debug mode to have more outputs
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57 - [ ] Improve the standard output of HAC
5
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58 - [ ] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
1
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59
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60 ### DONE
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62
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63 - [x] Each time a file is added => Print it in the output with the full path (or relative path to root)
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64 - [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py
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65 - [x] Add sorting BED if not sorted (Use the output of bedToBigBed)
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66 - [x] Add a script to install the huba datatype
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67 - [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py
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68 - [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
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69 - [x] Add a class named ~~TrfBigProcess~~ BedSimpleRepeats
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70 - [x] Add a class named TrackHub: Create the base TrackHub hierarchy
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71 - [x] Change the Name of the classes
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72 - [x] Add a class named AugustusProcess: Process the Augustus output to BigBed (and others needed in TrackHub) and (create folders + add the files into the right location => Process can be ported in a class responsible for that)
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73 - [x] Add a class named AugustusProcess
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74 - [x] Process the Augustus output to BigBed
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75 - [x] create folders + add the files into the right location
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76 - [x] Creation of folders to be ported into a separated class => In Datatype.py but should be into a dedicated to file manipulation class
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77 - [x] Refactoring of the AugustusProcess class to behave like a class and not like a procedural masked into a class
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78 - [x] Rename AugustusProcess into something more generic if the process is shared (gtf to BigBed) => Gff3.py
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79 - [x] Use gffToBed for Gtf instead of GtfToGenePred => Cancelled
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80 - [x] Clean the mess with the File handling (sometimes File, sometimes String, sometimes open File)
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81 - [x] Find a way to avoid repetitions in TrackDb and Track (I repeat myself atm) => Track instance has a TrackDb instance as attribute
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82 - [x] Refactor the creation of the structure to TrackHub: Access to paths via this Class, and creation of file through it