Comments (8)
That sounds like a good way to start. Yes I'm the mentor for this project, so happy to help with any issues.
from intermine-data-browser-tool.
Hi @AdrianBZG, I'm an Outreachy applicant and would love a shot at this issue.
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Hi @JM-Mendez ,
Great! Let me know if you have any questions, I'll assign this to you 😄
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Awesome! I'll start getting familiar with the codebase and the linked issues to better understand the requirements, and then get back to you.
Are you the mentor for this issue/project that I need to report to? Not sure how this process works.
from intermine-data-browser-tool.
So I came across 2 issues so far with setting up the project. I'm not familiar with coffeescript, so I just traced my way through the compiled node modules package.
- The only test case hangs indefinitely.
I was able to console.log
the following error:
TypeError [ERR_INVALID_PROTOCOL]: Protocol "https:" not supported. Expected "http:"
in the https module of imjs. I'm not sure why it wasn't propagated up the promise chain. But changing the protocol to http
succeeded.
Yet, the test still hanged. I was only able to trace it as far as the service module authorise method. I'm not entirely sure, but it looks like fetchVersion
isn't resolving the promise?
EDIT: Just found this existing issue, so I will disregard this concern.
#71
npm run dev
does not work. The script dictates that there should be a webpack config, but I do not see one. I searched the commit history for the file but could not find it in any commit. I also do not see agulp watch
task to run on changes.
I doubt these 2 issues would prevent me from troubleshooting the main issue. Although without webpack or a gulp watch task, I'd have to restart the project on each change.
Would you like me to at the very least open an issue to address issue 2? I have experience setting up a dev environment using webpack and gulp, so can do it either way.
from intermine-data-browser-tool.
@JM-Mendez It would be very nice if you could set-up the dev environment, and this issue was opened to try to address that: #67.
Happy if you give it a try 😄
After that we can take a look at what happens with the other issue.
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EDIT: Crossposted to Draft PR #82 so that I can keep track of my contributions for Outreachy.
Hi @AdrianBZG, I've managed to add multiple lists to the query using window.imTable.query.addConstraints
which allows me to pass in an array of contraints.
I stepped through the debugger and for the most part it returns a result from the server, until it tries to parse the xml. Then I run into the error below. I truncated the view
and constraintLogic
so the code fits without scrolling
"Error: XML is not well formatted. Got
<query model="genomic" view="Gene.symbol Gene.name..." constraintLogic="(A OR B..." >
<constraint path="Gene" op="IN" value="PL_BHF_UCL_cardiovascGenes" code="N" />
<constraint path="Gene" op="IN" value="PL_DiabesityGWAS_pval-4" code="N" />
</query>
Yet when I try running the query on the humanMine website, I get this xml structure:
<query model="genomic" view="Gene.name Gene.symbol..." constraintLogic="A and B">
<constraint path="Gene" op="IN" value="PL_BHF_UCL_cardiovascGenes" code="B" />
<constraint path="Gene" op="IN" value="PL_DiabesityGWAS_pval-4" code="A"/>
</query>
This seems well formatted to me, so I'm at a loss as to what the error means.
The stack trace throws inside the es6-promise
package used by imTables
. The last method called that belongs to the imTables
library is Service.prototype.authorise
(I'm tracing through the compiled package).
I have no idea where to go from here. Any thoughts?
Here's a screenshot of the stack trace:
from intermine-data-browser-tool.
Hi @JM-Mendez ,
In this query:
<query model="genomic" view="Gene.symbol Gene.name..." constraintLogic="(A OR B..." > <constraint path="Gene" op="IN" value="PL_BHF_UCL_cardiovascGenes" code="N" /> <constraint path="Gene" op="IN" value="PL_DiabesityGWAS_pval-4" code="N" /> </query>
You see that in the two constraints, you have the same code (N). Can you try to change that to A for the first one and B for the second one and see if the query works? If I remember correctly, it's required to add an unique code to each constraints (A,B,C,D,E...).
PS: Let's discuss that in your draft PR.
from intermine-data-browser-tool.
Related Issues (20)
- Value Duplication when using filters. HOT 1
- Make the app fully responsive HOT 22
- Unwanted grey color background and extra row in the header HOT 2
- Server Started message on console HOT 2
- dev server of browser tool HOT 9
- Write new tests from scratch that query using im.js HOT 13
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- Modularize the project using React components or Vue for better scalability HOT 7
- Update screenshots in the readme to reflect latest version (1.2) look HOT 6
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- Background-color for button not visible enough in the menu bar. HOT 5
- Point University of Cambridge to their website HOT 1
- The checkboxes are showing over the Names in the Dataset name part HOT 1
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- The X button is not clearing the input text when the user click on HOT 2
- [missing] `cross-env` module is missing for setting up environment variables HOT 1
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