diff todo.md @ 0:3e0c61b52a06 draft

planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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+### TEMP St Louis ###
+- How to manage messages to user and debugging:
+    - User should receive INFO / WARN / ERROR / CRITICAL:
+        - User summary informations in stdout
+        - Full error in stderr
+    - Developer should receive all Logging stack:
+        - Not the user summary in stdout
+        - Full stack in stdout and stderr directly
+
+    - HOWTO:
+        - Manage (at least) two type of Logging types:
+            - The user one => When Debug mode is not set or disabled
+            - The dev one => When Debug mode is enabled
+        - User:
+            - Two Handlers: stdout and stderr
+            - STDOUT:
+                - Filter stdout:
+                    - NO ERROR and CRITICAL here
+                    - (Warn)
+                - Formatter:
+                    - Only show %(message) for clarity
+            - STDERR:
+                - Filter stderr => WARN / ERRROR / CRITICAL
+                - Formatter:
+                    - Show message
+                    - Show traceback
+        - Dev:
+            - One Handler:
+                - To both stdout and stderr
+            - Filter:
+                - Nope?
+            - Formatter:
+                - Show traceback in both
+
+# HubArchiveCreator's TODO
+
+*TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613*
+
+### TO COMPLETE
+
+
+- [ ] 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
+- [ ] Move the class and others program related files, into separated folders
+- [ ] Take into account the name of the reference genome / the change:
+  - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated
+- [ ] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
+- [ ] Replace Gff3 by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
+- [ ] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
+- [ ] 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
+- [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point
+- [ ] Rename all occurences of `extension` which `datatype`
+- [ ] Follow https://google.github.io/styleguide/pyguide.html
+- [ ] Move to Python 3
+- [ ] Remove the repetition of the extension if it already exists
+- [ ] Better thinking about the tool_directory management / Classes path refactoring
+- [ ] Add a debug mode to have more outputs
+- [ ] Improve the standard output of HAC
+- [ ] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
+- [ ] Sort the order of the HTML directories/files
+
+### DONE
+
+
+- [x] Each time a file is added => Print it in the output with the full path (or relative path to root)
+- [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py
+- [x] Add sorting BED if not sorted (Use the output of bedToBigBed)
+- [x] Add a script to install the huba datatype
+- [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py
+- [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
+- [x] Add a class named ~~TrfBigProcess~~ BedSimpleRepeats
+- [x] Add a class named TrackHub: Create the base TrackHub hierarchy
+- [x] Change the Name of the classes
+- [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)
+ - [x] Add a class named AugustusProcess
+ - [x] Process the Augustus output to BigBed
+ - [x] create folders + add the files into the right location
+ - [x] Creation of folders to be ported into a separated class => In Datatype.py but should be into a dedicated to file manipulation class
+ - [x] Refactoring of the AugustusProcess class to behave like a class and not like a procedural masked into a class
+ - [x] Rename AugustusProcess into something more generic if the process is shared (gtf to BigBed) => Gff3.py
+- [x] Use gffToBed for Gtf instead of GtfToGenePred => Cancelled
+- [x] Clean the mess with the File handling (sometimes File, sometimes String, sometimes open File)
+- [x] Find a way to avoid repetitions in TrackDb and Track (I repeat myself atm) => Track instance has a TrackDb instance as attribute
+- [x] Refactor the creation of the structure to TrackHub: Access to paths via this Class, and creation of file through it