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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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synonyms and other CLI simplification & rationalization #38

Open noblem opened 7 years ago

noblem commented 7 years ago

Data type names (and other names & metadata) at the GDC can be long, cumbersome to type and somewhat fragile to use (e.g. by containing spaces). Two examples are

   "DNA Methylation"
   "Copy Number Variation"

which we download to "DNA_Methylation" and "Copy_Number_Variation," respectively.

It would be helpful to users if GDCtools would support simple synonyms like

     CN
     meth

(case-insensitively). Since March 2017 (see email snippet below) I've had a branch on my laptop with the beginnings of these changes, so this is just a placeholder issue to help remember to complete the work.

_MIME-Version: 1.0 Received: by 10.103.42.199 with HTTP; Wed, 29 Mar 2017 15:16:41 -0700 (PDT) Date: Wed, 29 Mar 2017 18:16:41 -0400 Subject: GDCtools GIT stash of cli args work From: Michael Noble mnoble@broadinstitute.org To: Michael Noble mnoble@broadinstitute.org Content-Type: multipart/alternative; boundary=001a114eb0f64ccd83054be5eeda --001a114eb0f64ccd83054be5eeda Content-Type: text/plain; charset=UTF-8

On my laptop:

% pwd /Users/mnoble/src/gdctools

% git stash show gdctools/GDCcli.py | 23 ++++++++++++----------- gdctools/gdc_mirror.py | 6 +++--- tests/Makefile | 2 +- 3 files changed, 16 insertions(+), 15 deletions(-)

% git stash list stash@{0}: On cliflags: first step of CLI arg rationalization

gsaksena commented 7 years ago

It would probably be adequate to be able to list what the actual codes are, to make them more easily discoverable.

noblem commented 7 years ago

Yep, that's been on the radar for a while too:

https://github.com/broadinstitute/gdctools/issues/26

On Wed, Apr 12, 2017 at 3:01 PM, Gordon Saksena notifications@github.com wrote:

It would probably be adequate to be able to list what the actual codes are, to make them more easily discoverable.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/gdctools/issues/38#issuecomment-293675924, or mute the thread https://github.com/notifications/unsubscribe-auth/ADtAh2mVWiMN7QiIZ8Z9Dp7QPDGAe_cjks5rvR-TgaJpZM4M705t .