[API] New directory for jupyter notebooks #6854

spell00 · 2020-07-21T04:14:50Z

Brief summary of changes

New Jupyter notebooks to display how the api works.

xlecours

Can you provide markdown files as well?

docs/notebooks/LORIS-API_Part1-HTTP.ipynb

xlecours · 2020-09-01T15:31:53Z

@spell00 Remove the outputs of the notebooks before sending to github please.

spell00 · 2020-09-04T19:25:27Z

@xlecours I provided the markdowns, but now that I cleared the outputs from the notebooks before sending to Github, the content of the notebooks that I see is very similar to the markdowns. I wonder if it is still necessary? Before clearing the output, I could not see part2 as a notebook in Github, so I understood the necessity of the markdowns, but it seems redundant now. Does it serve another purpose I am not seeing?

xlecours · 2020-09-08T13:21:01Z

@xlecours I provided the markdowns, but now that I cleared the outputs from the notebooks before sending to Github, the content of the notebooks that I see is very similar to the markdowns. I wonder if it is still necessary? Before clearing the output, I could not see part2 as a notebook in Github, so I understood the necessity of the markdowns, but it seems redundant now. Does it serve another purpose I am not seeing?

Maybe @christinerogers can clarify if the markdown can be useful in our readthedoc. Otherwise, it can be removed so we don't have to make sure it is synchronized whit the actual notebook.

spell00 · 2020-09-21T15:44:29Z

@xlecours @christinerogers I think everyone agrees the markdowns are redundant, so I removed them. If anyone thinks of a good reason to include them, it can be added again very easily. I added links to the notebooks in Google colab, so that it can be tried directly in the browser. This way, anyone can test the notebooks even if they don't have Jupyter or Loris installed.

docs/notebooks/LORIS-API_Part1-HTTP.ipynb

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

docs/notebooks/LORIS-API_Part1-HTTP.ipynb

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

spell00 · 2020-10-26T21:33:23Z

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "colab": {},
+ "colab_type": "code",
+ "id": "ZJhfo1iB_PqE"
+ },
+ "outputs": [],
+ "source": [
+ "# The flag is used to break the loops once an example that contains a \n",
+ "# Dicom file is found\n",
+ "flag = 0\n",
+ "\n",
+ "for candidate in allCandidates['Candidates']:\n",
+ " candid = candidate['CandID']\n",
+ " visit_labels = GET('/'.join([baseurl, 'candidates', candid]))['Visits']\n",
+ " if flag == 1:\n",
+ " break\n",
+ " candid = candidate['CandID']\n",
+ " visit_labels = GET('/'.join([baseurl, 'candidates', candid]))['Visits']\n",
+ " for visit_label in visit_labels:\n",
+ " dicoms = GET('/'.join([baseurl, 'candidates', candid, \n",
+ " visit_label, 'dicoms']))\n",
+ " # We only want to get a single valid example of a candidate and visit that\n",
+ " # has Dicom files that can be used to test the Dicoms endpoints \n",
+ " if len(dicoms['DicomTars']) > 0:\n",
+ " flag = 1\n",
+ " break\n"
+ ]
+ },


This block won't be necessary when PR #6775 will be merged. It will add an endpoint listing all Dicoms in a project. It will then be possible to get a complete list of candidates and for which visits there is a Dicom file for a given project. For the moment, it is the only way to get these informations without hardcoding them in the notebook, which is problematic when not executed with raisinbread...

spell00 · 2020-10-26T22:05:27Z

docs/notebooks/LORIS-API_Part1-HTTP.ipynb

+ "source": [
+ "### Scripting and parsing json \n",
+ " \n",
+ "see: [part2 - Python script](https://github.com/aces/Loris/blob/main/docs/notebooks/LORIS-API_Part2-Python-script.ipynb)"


This link will be valid when the PR is merged to aces/main

spell00 · 2020-10-26T23:51:20Z

Some commands will fail until PR #6780 is merged. I tested using the branch containing the changes and there is no error.

xlecours · 2020-10-30T16:00:44Z

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

+ "source": [
+ "url = '/'.join([baseurl, 'projects', projectNames[0]])\n",
+ "project = GET(url)\n",
+ "prettyPrint(projects)"


Suggested change

"prettyPrint(projects)"

"prettyPrint(project)"

xlecours · 2020-10-30T16:03:18Z

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

+ " \"PSCID\" : PSCID, # only if config is set to prompt \n",
+ " \"EDC\" : \"YYYY-MM-DD\", # optional\n",
+ " \"DoB\" : \"YYYY-MM-DD\",\n",
+ " \"Gender\" : \"Male|Female\",\n",


Suggested change

" \"Gender\" : \"Male|Female\",\n",

" \"Sex\" : \"Male|Female\",\n",

xlecours · 2020-10-30T16:05:59Z

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

+ },
+ "outputs": [],
+ "source": [
+ "battery = candidateVisits['Meta']['Battery']\n",


This variable is not used

xlecours · 2020-10-30T16:07:52Z

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "V0Clu1dSCHvJ"
+ },
+ "source": []
+ },


This shows as Type Markdown and LaTeX: 𝛼2

christinerogers · 2020-11-02T20:09:55Z

@driusan requesting final review - this is our last stretch in which @spell00 can readily make changes. thank you!

spell00 · 2020-11-05T01:06:12Z

docs/notebooks/LORIS-API_Part1-HTTP.ipynb

+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#LORIS API Tour 1/2\nThis tutorial is also available as a Google colab notebook so you can run it directly from your browser. To access it, click on the button below: <a href=\"https://colab.research.google.com/github/aces/Loris/blob/main/docs/notebooks/LORIS-API_Part1-HTTP.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"


The link https://colab.research.google.com/github/aces/Loris/blob/main/docs/notebooks/LORIS-API_Part1-HTTP.ipynb won't work until the PR is merged. For now, for testing purposes, one has to use the notebook in this Pr on this branch : https://colab.research.google.com/github/spell00/Loris/blob/2020-07-20-jupyterApiPart2/docs/notebooks/LORIS-API_Part1-HTTP.ipynb

spell00 · 2020-11-05T01:09:09Z

docs/notebooks/LORIS_API_Part2_Python-script.ipynb

+ "\n",
+ "This tutorial contains basic examples in Python to demonstrate how to interact with the API.\n",
+ "To run this tutorial, click on `Runtime -> Run all`",
+ "This tutorial is also available as a Google colab notebook so you can run it directly from your browser. To access it, click on the button below: <a href=\"https://colab.research.google.com/github/aces/Loris/blob/main/docs/notebooks/LORIS_API_Part2_Python-script.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"


the link https://colab.research.google.com/github/aces/Loris/blob/main/docs/notebooks/LORIS_API_Part2_Python-script.ipynb won't work until the PR is merged. For testing, use https://colab.research.google.com/github/spell00/Loris/blob/2020-07-20-jupyterApiPart2/docs/notebooks/LORIS_API_Part2_Python-script.ipynb

spell00 · 2020-11-05T05:33:06Z

@xlecours @driusan It is now passing Travis and ready for final review

driusan

I don't know enough about jupyter notebooks to really review this, I'll merge it based on @xlecours approval..

New Jupyter notebooks to demonstrate how the REST API works.

spell00 added API PR or issue introducing/requiring modifications to the API code Needs Work PR awaiting additional changes by the author or contains issues that the author needs to fix labels Jul 21, 2020

christinerogers added the Documentation PR or issue introducing/requiring modifications to the code documentation (test plans, wikis, docs) label Jul 21, 2020

spell00 changed the base branch from master to main July 23, 2020 14:20

spell00 requested a review from xlecours August 5, 2020 15:28

xlecours requested changes Aug 10, 2020

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spell00 requested a review from xlecours October 8, 2020 18:59

xlecours requested changes Oct 26, 2020

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spell00 commented Oct 26, 2020

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spell00 force-pushed the 2020-07-20-jupyterApiPart2 branch from f16c232 to d8a2de1 Compare October 26, 2020 21:58

spell00 commented Oct 26, 2020

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spell00 removed the Needs Work PR awaiting additional changes by the author or contains issues that the author needs to fix label Oct 26, 2020

spell00 requested a review from xlecours October 26, 2020 22:57

spell00 added the Blocked PR awaiting the merge, resolution or rejection of an other Pull Request label Oct 26, 2020

spell00 force-pushed the 2020-07-20-jupyterApiPart2 branch 2 times, most recently from 4526194 to 5dbe25b Compare October 29, 2020 15:54

spell00 requested a review from driusan October 29, 2020 17:35

spell00 removed the Blocked PR awaiting the merge, resolution or rejection of an other Pull Request label Oct 29, 2020

xlecours requested changes Nov 2, 2020

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spell00 requested a review from xlecours November 2, 2020 17:50

xlecours approved these changes Nov 2, 2020

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christinerogers requested review from driusan and removed request for driusan November 2, 2020 20:09

spell00 added the Blocked PR awaiting the merge, resolution or rejection of an other Pull Request label Nov 2, 2020

spell00 added 12 commits November 4, 2020 12:21

trying to solve travis packages problem

4448ef0

Remove changes to composer

c75955e

add link for colab to second notebook

267ff08

Changing colab button

21bfab6

adjusting message for colab button

321c19b

corrections

a4ac704

modifs

8cf766c

error in composer rollback

b5505a9

error in composer rollback

675e28f

still going back from rebase errors

c76417d

rebase

b499182

applying correct rollback

8fe4135

spell00 force-pushed the 2020-07-20-jupyterApiPart2 branch from a0dfa88 to 8fe4135 Compare November 4, 2020 17:30

spell00 added 8 commits November 4, 2020 13:08

Getting out of rebase hell

9910675

out of rebase hell

cb50d6d

get notebooks back

ec0dd62

remove stuff that is wrong

8bc16d5

repair link for colab button

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repair other link colab

ad3c43b

repair other link colab

5fa6843

Replace links for future links in colab

7190df5

spell00 commented Nov 5, 2020

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2020-07-20-jupyterApiPart2

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spell00 removed the Blocked PR awaiting the merge, resolution or rejection of an other Pull Request label Nov 5, 2020

driusan reviewed Nov 5, 2020

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driusan merged commit c1bb1da into aces:main Nov 5, 2020

ridz1208 added this to the 24.0.0 milestone Nov 27, 2020

AlexandraLivadas pushed a commit to AlexandraLivadas/Loris that referenced this pull request Jun 29, 2021

[API] New directory for jupyter notebooks (aces#6854)

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New Jupyter notebooks to demonstrate how the REST API works.

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[API] New directory for jupyter notebooks #6854

[API] New directory for jupyter notebooks #6854

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christinerogers commented Nov 2, 2020

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	" \"Gender\" : \"Male\|Female\",\n",
	" \"Sex\" : \"Male\|Female\",\n",

[API] New directory for jupyter notebooks #6854

[API] New directory for jupyter notebooks #6854

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spell00 commented Jul 21, 2020

Brief summary of changes

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