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genome-one / monarch

https://genome-one.github.io/monarch/#/redoctopus
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Free text window for CR #1

Open genome-one opened 7 years ago

genome-one commented 7 years ago

Add a copy paste window to the current tool so that users can paste in part of a PDF file that describes a patient

nguyen9301 commented 7 years ago

New design for Monarch to include free text window. I used the accordion to make it easier for the user to switch between upload and a free text window. 1) Upload tool: . I just make a small change for spinner style and layout for upload box. uploadwindow

2) Free text window tool demo: . Users can paste in part of a PDF file that describes a patient . At the moment, it just a demo for how it works and still waiting for back-end @genome-one. freetextwindow

jmcmurry commented 7 years ago

@nguyen9301 I'm super impressed you managed to do this with a gif; how did you record it, may I ask?

cmcnamara87 commented 7 years ago

@nguyen9301 looks great. Can you try how it looks with tabs instead of an accordion? Also, add an "Upload" button at the bottom of the text section.

nguyen9301 commented 7 years ago

@jmcmurry ah yeah.. i used http://recordit.co/ to make a gif! It really cool and easy to use :D ! @cmcnamara87 i plan to do that as well.. coming soon kk :p

nguyen9301 commented 7 years ago

Custom tab layout design:

tabwindow

cmcnamara87 commented 7 years ago

@nguyen9301 I meant horizontal tabs. I think both the accordion and the vertical tabs don't convey that you should Upload OR Add Text. It looks like you should Upload THEN Add Text.

nguyen9301 commented 7 years ago

@cmcnamara87 you are right! I changed it to horizontal tabs and when you click on add text, it will clean the upload window! horizontaltab

cmcnamara87 commented 7 years ago

@genome-one ready to go for the backend

genome-one commented 7 years ago

@nguyen9301 @cmcnamara87 - The backend is already there: POST to http://phenotyper.monarchinitiative.org:5555/cr/annotate with the payload the text from the free text window (in the example below "Flared, cupped and irregular metaphyses.") will give you this: [ { "start_offset": 19, "end_offset": 39, "length": 20, "original_text": "irregular metaphyses", "source": "HPO", "term": { "uri": "HP:0003025", "preferredLabel": "Metaphyseal irregularity", "synonyms": [ "Metaphyseal fraying", "Frayed, irregular metaphyses", "Frayed, irregular, metaphyses", "Metaphyseal irregularities", "Irregular wide portion of a long bone", "Irregular metaphyses" ] }, "negated": false } ]

nguyen9301 commented 7 years ago

My first approach for Free text window:

Copy paste text: copypastetext

Enter a phrase: enteraphrase

At the moment, It only shows the original text and preferred label. I also added a notification to show whether it's uploaded or not!

nguyen9301 commented 7 years ago

Updated 'Add text' window! uploadtextwindow

nguyen9301 commented 7 years ago

http://phenotyper.monarchinitiative.org/ is up!

cmcnamara87 commented 7 years ago

oh amazing! @nguyen9301

genome-one commented 7 years ago

perfect! Now all I have to do is to finalize the push to GitHub part.

genome-one commented 7 years ago

This can be closed BTW ...

cmcnamara87 commented 7 years ago

can you describe what was the process for getting it up on phenotyper.monarchinitiative.org just so we have it down somewhere

jmcmurry commented 7 years ago

ahhhmazing. Thanks all. Just to check, is the export to Phenopackets.org working or in progress? Should we break out into a separate ticket?

jmcmurry commented 7 years ago

cc: @doctorbud

genome-one commented 7 years ago

@jmcmurry - we can probably close this. The export is still in progress - I'm working on it.

cmcnamara87 commented 7 years ago

@genome-one add a ticket for the export

jmcmurry commented 7 years ago

as soon as export is done we can do a soft beta release to twitterverse. Until then, the button will mislead. Don't want anyone having their data fall on the floor without their realizing it. thanks :)