Open Sigfried opened 2 years ago
I haven't looked at this in detail yet but I am guessing based on what you're describing that it may be possible to extract the who is auth text that you are mentioning using beautifulsoup4.
Basically with beautifulsoup, you can take the HTML string returned from a requests using the requests library, and it parses it into a object oriented structure that you can work with easily. You can drill down, iterate, find the ID of the HTML element that contains the auth text you need, and extract that text.
Oh, I already said this on Teams, but it's not web scraping. VSAC has a real API, but we need to figure out how to use it vis-a-vis authentication.
True that. I mean just using web scraping to extract the authentication, assuming that is like some code that constantly changes and is only accessible via the browser. If so, extracting that can be automated with web scraping. And then with that auth code, the rest can just be direct requests using the REST API.
Oh, whoops. I got mixed up. This issue isn't about VSAC, it's about OMOP. And it's OHDSI that has the real API (WebAPI), but, yeah, I haven't figured out how to log in to it except through ATLAS in a web browser, but I know it's possible.
We need a generic JHU BIDS "user" account. Can Siggie or Joe request that? Make one of you the eMail address for the generic account until we figure out an alternative. Then we can use those credentials for this development / API access
Best,
Davera Gabriel, RN Senior Research Terminologist
Johns Hopkins University Biomedical Informatics & Data Science 2024 E Monument St, Suite I-200 Baltimore, MD 21287 +1 (919) 561-8911 @.**@.>
From: Joe Flack @.> Sent: Wednesday, January 12, 2022 9:28 AM To: HOT-Ecosystem/ValueSet-Tools @.> Cc: Davera Gabriel @.>; Mention @.> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
True that. I mean just using web scraping to extract the authentication, assuming that is like some code that constantly changes and is only accessible via the browser. If so, extracting that can be automated with web scraping. And then with that auth code, the rest can just be direct requests using the REST API.
- Reply to this email directly, view it on GitHubhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHOT-Ecosystem%2FValueSet-Tools%2Fissues%2F14%23issuecomment-1011100980&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=BpkYr1kuBVLv45AwetilLYaRAlWWzQ27ZsSj5f1WvqQ%3D&reserved=0, or unsubscribehttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALQXTQLXMNAWH5Z3TUXCJBTUVWFYXANCNFSM5LWMYHQA&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0p58FZFkfZzNX9MdbRvFeC0SVletqKcx46mVuUxaQ58%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=a9h8q%2FiRqXeAsNPQf6WTMPuNguuyOifXF3jerOAE92A%3D&reserved=0 or Androidhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2FCB1yR7iqW6kV%2FxP0LJlHuW96DnoQJfI9SQYCOq6rvA%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.**@.>>
I can request this, but I don't know who to request this from / how to submit such a request. Do you have any idea?
Best wishes,
Joe Flack
From: Davera Gabriel @.> Sent: Wednesday, January 12, 2022 9:52 AM To: HOT-Ecosystem/ValueSet-Tools @.> Cc: Joe Flack @.>; Mention @.> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
We need a generic JHU BIDS "user" account. Can Siggie or Joe request that? Make one of you the eMail address for the generic account until we figure out an alternative. Then we can use those credentials for this development / API access
Best,
Davera Gabriel, RN Senior Research Terminologist
Johns Hopkins University Biomedical Informatics & Data Science 2024 E Monument St, Suite I-200 Baltimore, MD 21287 +1 (919) 561-8911 @.**@.>
From: Joe Flack @.> Sent: Wednesday, January 12, 2022 9:28 AM To: HOT-Ecosystem/ValueSet-Tools @.> Cc: Davera Gabriel @.>; Mention @.> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
True that. I mean just using web scraping to extract the authentication, assuming that is like some code that constantly changes and is only accessible via the browser. If so, extracting that can be automated with web scraping. And then with that auth code, the rest can just be direct requests using the REST API.
- Reply to this email directly, view it on GitHubhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHOT-Ecosystem%2FValueSet-Tools%2Fissues%2F14%23issuecomment-1011100980&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=BpkYr1kuBVLv45AwetilLYaRAlWWzQ27ZsSj5f1WvqQ%3D&reserved=0, or unsubscribehttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALQXTQLXMNAWH5Z3TUXCJBTUVWFYXANCNFSM5LWMYHQA&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0p58FZFkfZzNX9MdbRvFeC0SVletqKcx46mVuUxaQ58%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=a9h8q%2FiRqXeAsNPQf6WTMPuNguuyOifXF3jerOAE92A%3D&reserved=0 or Androidhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cdgabrie4%40jhmi.edu%7C79a756d3ceac4c87b00e08d9d5d7cd61%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637775945113194508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2FCB1yR7iqW6kV%2FxP0LJlHuW96DnoQJfI9SQYCOq6rvA%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.**@.>>
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It's a UMLS liscense. Like the one I presume you requested to access the VSAC
Best,
Davera Gabriel, RN Senior Research Terminologist
Johns Hopkins University Biomedical Informatics & Data Science 2024 E Monument St, Suite I-200 Baltimore, MD 21287 +1 (919) 561-8911 @.**@.>
From: Joe Flack @.> Sent: Wednesday, January 12, 2022 11:28 AM To: HOT-Ecosystem/ValueSet-Tools @.> Cc: Davera Gabriel @.>; Mention @.> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
I can request this, but I don't know who to request this from / how to submit such a request. Do you have any idea?
Best wishes,
Joe Flack
From: Davera Gabriel @.<mailto:@.>> Sent: Wednesday, January 12, 2022 9:52 AM To: HOT-Ecosystem/ValueSet-Tools @.<mailto:@.>> Cc: Joe Flack @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
We need a generic JHU BIDS "user" account. Can Siggie or Joe request that? Make one of you the eMail address for the generic account until we figure out an alternative. Then we can use those credentials for this development / API access
Best,
Davera Gabriel, RN Senior Research Terminologist
Johns Hopkins University Biomedical Informatics & Data Science 2024 E Monument St, Suite I-200 Baltimore, MD 21287 +1 (919) 561-8911 @.**@.mailto:***@***.******@***.***>
From: Joe Flack @.<mailto:@.>> Sent: Wednesday, January 12, 2022 9:28 AM To: HOT-Ecosystem/ValueSet-Tools @.<mailto:@.>> Cc: Davera Gabriel @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
True that. I mean just using web scraping to extract the authentication, assuming that is like some code that constantly changes and is only accessible via the browser. If so, extracting that can be automated with web scraping. And then with that auth code, the rest can just be direct requests using the REST API.
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Ohh, I see.
That makes sense. An API_Key that we can share within BIDS.
I think I can just create a new gmail account and then request a UMLS account using that.
Best wishes,
Joe Flack
Sr. Programmer Analyst
Biomedical Informatics & Data Science Grouphttp://dhsi.med.jhmi.edu/
Johns Hopkins University School of Medicinehttps://www.hopkinsmedicine.org/som/index.html
2024 E Monument St, Baltimore, MD 21205
850-982-7871 || github.com/joeflack4https://github.com/joeflack4
From: Davera Gabriel @.> Sent: Wednesday, January 12, 2022 11:29 AM To: HOT-Ecosystem/ValueSet-Tools @.> Cc: Joe Flack @.>; Mention @.> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
It's a UMLS liscense. Like the one I presume you requested to access the VSAC
Best,
Davera Gabriel, RN Senior Research Terminologist
Johns Hopkins University Biomedical Informatics & Data Science 2024 E Monument St, Suite I-200 Baltimore, MD 21287 +1 (919) 561-8911 @.**@.>
From: Joe Flack @.> Sent: Wednesday, January 12, 2022 11:28 AM To: HOT-Ecosystem/ValueSet-Tools @.> Cc: Davera Gabriel @.>; Mention @.> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
I can request this, but I don't know who to request this from / how to submit such a request. Do you have any idea?
Best wishes,
Joe Flack
From: Davera Gabriel @.<mailto:@.>> Sent: Wednesday, January 12, 2022 9:52 AM To: HOT-Ecosystem/ValueSet-Tools @.<mailto:@.>> Cc: Joe Flack @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
We need a generic JHU BIDS "user" account. Can Siggie or Joe request that? Make one of you the eMail address for the generic account until we figure out an alternative. Then we can use those credentials for this development / API access
Best,
Davera Gabriel, RN Senior Research Terminologist
Johns Hopkins University Biomedical Informatics & Data Science 2024 E Monument St, Suite I-200 Baltimore, MD 21287 +1 (919) 561-8911 @.**@.mailto:***@***.******@***.***>
From: Joe Flack @.<mailto:@.>> Sent: Wednesday, January 12, 2022 9:28 AM To: HOT-Ecosystem/ValueSet-Tools @.<mailto:@.>> Cc: Davera Gabriel @.<mailto:@.>>; Mention @.<mailto:@.>> Subject: Re: [HOT-Ecosystem/ValueSet-Tools] Need to figure out how to handle authentication for automated REST calls on JHU ATLAS/OMOP instance (Issue #14)
External Email - Use Caution
True that. I mean just using web scraping to extract the authentication, assuming that is like some code that constantly changes and is only accessible via the browser. If so, extracting that can be automated with web scraping. And then with that auth code, the rest can just be direct requests using the REST API.
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Oh, @DaveraGabriel, you're talking about VSAC access, not JHU OMOP access. We should move that to a different issue. I already made the mistake of confusing the two in this thread.
I created a test file (see https://github.com/HOT-Ecosystem/ValueSet-Tools/issues/5#issuecomment-1009957921) to get search data from our ATLAS instance (actually, WebAPI). These calls require ATLAS authentication. There is probably a way to do that programmatically, but I did it like:
https://github.com/HOT-Ecosystem/ValueSet-Tools/blob/30d665b5e49a5b70afe799f58a18d8a49b8cd0a6/vsac_wrangler/test-webapi-call.py#L15-L25
I don't know how long the auth value I got will last, but it lasted long enough to run some queries. We'll want to figure out a less cumbersome way to do this in the future -- and a way that doesn't end up with sensitive data getting committed to github. Have others besides me and Joe gotten any of this code working yet? That requires that you set up a local /env folder for yourself. I have one on my home machine, but not on my SAFE Desktop yet.
Anyway, I'm assigning this to @richard1933 because I think he may be the person who understands the SAFE Desktop environment and our OMOP/ATLAS instance the best so far. (Will also tag @stephanieshong, @DaveraGabriel, @joeflack4, @tannerzhang.)