[IGBF-1479] Identify genome versions without HEADER.md files - JIRA UNCC

Details

Type: Story
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
- Beginner

Story Points:
0.5
Epic Link:
Improve IGB for users
Sprint:
Fall 4 Oct 26 - Nov 6

Description

Review all genome version directories in IGB Quickload. Identify directories where there is no HEADER.md available. Make note of any genomes that are lacking a HEADER.md in the comments here.

See: https://svn.bioviz.org/viewvc for easy way to browse the directories. Alternatively, could write a bash script to check them all at once. Describe process used here.

Attachments

Issue Links

relates to

IGBF-2582 Add HEADER.md to quickload directories

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Activity

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Ann Loraine created issue - 14/Dec/18 11:35 AM

Ann Loraine made changes - 14/Dec/18 11:35 AM

Field	Original Value	New Value
Epic Link		~~IGBF-1478~~ [ 17563 ]

Ann Loraine made changes - 14/Dec/18 11:35 AM

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Ann Loraine made changes - 14/Dec/18 11:36 AM

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Ann Loraine [ aloraine ]

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Jill Jenkins (Inactive) added a comment - 17/Jan/19 5:26 PM - edited

On a Mac:

find . -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort

./A_thaliana_Apr_2008
./A_thaliana_Jun_2009
./B_distachyon_Aug_2010
./C_albicans_SC5314_Jun_2014
./C_albicans_SC5314_Nov_2008
./C_albicans_WO-1_Dec_2013
./C_albicans_WO-1_Jul_2010
./C_papaya_Aug_2010
./C_reinhardtii_Nov_2010
./F_vesca_Sep_2011
./G_max_Aug_2010
./H_sapiens_Dec_2013/UCSCTracks
./M_truncatula_Mar_2009
./O_sativa_japonica_Jun_2009
./P_persica_Apr_2010
./P_trichocarpa_Jan_2010
./R_communis_May_2008
./S_bicolor_Jan_2009
./S_pombe_May_2012
./S_tuberosum_DM_Jul_2011
./T_castaneum_Mar_2008
./T_kodakaraensis_KOD1_May_2004
./V_carteri_Jul_2010
./Z_mays_B73_Mar_2010

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Jill Jenkins (Inactive) added a comment - 17/Jan/19 5:26 PM - edited On a Mac: find . -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort ./A_thaliana_Apr_2008 ./A_thaliana_Jun_2009 ./B_distachyon_Aug_2010 ./C_albicans_SC5314_Jun_2014 ./C_albicans_SC5314_Nov_2008 ./C_albicans_WO-1_Dec_2013 ./C_albicans_WO-1_Jul_2010 ./C_papaya_Aug_2010 ./C_reinhardtii_Nov_2010 ./F_vesca_Sep_2011 ./G_max_Aug_2010 ./H_sapiens_Dec_2013/UCSCTracks ./M_truncatula_Mar_2009 ./O_sativa_japonica_Jun_2009 ./P_persica_Apr_2010 ./P_trichocarpa_Jan_2010 ./R_communis_May_2008 ./S_bicolor_Jan_2009 ./S_pombe_May_2012 ./S_tuberosum_DM_Jul_2011 ./T_castaneum_Mar_2008 ./T_kodakaraensis_KOD1_May_2004 ./V_carteri_Jul_2010 ./Z_mays_B73_Mar_2010

Ann Loraine made changes - 27/Aug/19 4:58 PM

Workflow

Loraine Lab Workflow [ 18194 ]

Fall 2019 Workflow Update [ 18928 ]

Ann Loraine made changes - 16/Oct/19 5:48 PM

Workflow	Fall 2019 Workflow Update [ 18928 ]	Revised Fall 2019 Workflow Update [ 21054 ]
Status	Open [ 1 ]	To-Do [ 10305 ]

Ann Loraine made changes - 13/Jul/20 5:05 PM

Epic Link

~~IGBF-1478~~ [ 17563 ]

IGBF-1765 [ 17855 ]

Ann Loraine made changes - 29/Oct/20 4:37 PM

Sprint

Fall 4 Oct 26 - Nov 6 [ 107 ]

Irvin Naylor (Inactive) made changes - 29/Oct/20 4:49 PM

Assignee

Irvin Naylor [ inaylor ]

Irvin Naylor (Inactive) made changes - 29/Oct/20 5:12 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Irvin Naylor (Inactive) added a comment - 30/Oct/20 2:54 PM

Command: find ./quickload -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort
Ran in directory integrated-genome-browser/core

./quickload
./quickload/src
./quickload/src/main
./quickload/src/main/java
./quickload/src/main/java/org
./quickload/src/main/java/org/lorainelab
./quickload/src/main/java/org/lorainelab/igb
./quickload/src/main/java/org/lorainelab/igb/quickload
./quickload/src/main/java/org/lorainelab/igb/quickload/model
./quickload/src/main/java/org/lorainelab/igb/quickload/model/annots
./quickload/src/main/java/org/lorainelab/igb/quickload/util
./quickload/src/main/resources
./quickload/src/test
./quickload/src/test/java
./quickload/src/test/java/org
./quickload/src/test/java/org/lorainelab
./quickload/src/test/java/org/lorainelab/igb
./quickload/src/test/java/org/lorainelab/igb/quickload
./quickload/src/test/java/org/lorainelab/igb/quickload/utils
./quickload/src/test/resources
./quickload/src/test/resources/A_thaliana_Jun_2009
./quickload/src/test/resources/quickload
./quickload/src/test/resources/quickload/A_thaliana_Jun_2009
./quickload/src/test/resources/quickload/H_sapiens_Dec_2013

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Irvin Naylor (Inactive) added a comment - 30/Oct/20 2:54 PM Command: find ./quickload -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort Ran in directory integrated-genome-browser/core ./quickload ./quickload/src ./quickload/src/main ./quickload/src/main/java ./quickload/src/main/java/org ./quickload/src/main/java/org/lorainelab ./quickload/src/main/java/org/lorainelab/igb ./quickload/src/main/java/org/lorainelab/igb/quickload ./quickload/src/main/java/org/lorainelab/igb/quickload/model ./quickload/src/main/java/org/lorainelab/igb/quickload/model/annots ./quickload/src/main/java/org/lorainelab/igb/quickload/util ./quickload/src/main/resources ./quickload/src/test ./quickload/src/test/java ./quickload/src/test/java/org ./quickload/src/test/java/org/lorainelab ./quickload/src/test/java/org/lorainelab/igb ./quickload/src/test/java/org/lorainelab/igb/quickload ./quickload/src/test/java/org/lorainelab/igb/quickload/utils ./quickload/src/test/resources ./quickload/src/test/resources/A_thaliana_Jun_2009 ./quickload/src/test/resources/quickload ./quickload/src/test/resources/quickload/A_thaliana_Jun_2009 ./quickload/src/test/resources/quickload/H_sapiens_Dec_2013

Irvin Naylor (Inactive) made changes - 30/Oct/20 2:54 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 01/Nov/20 5:59 AM

Comment

[ Run above command again and report output here. ]

Ann Loraine made changes - 01/Nov/20 5:59 AM

Comment

[ Nice one! ]

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Ann Loraine added a comment - 01/Nov/20 6:03 AM

Sorry, the description was not clear enough.
By "quickload," I meant the site that we use to distribute data to IGB, not the quickload module in the IGB bitbucket repository.
However I just now checked a few of the directories Jill listed in her comment and it looks like her output is correct.
The next step will be to add the header files. Making a new issue for that.

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Ann Loraine added a comment - 01/Nov/20 6:03 AM Sorry, the description was not clear enough. By "quickload," I meant the site that we use to distribute data to IGB, not the quickload module in the IGB bitbucket repository. However I just now checked a few of the directories Jill listed in her comment and it looks like her output is correct. The next step will be to add the header files. Making a new issue for that.