mutation datasource doesn't work

[Gallì Anna]

Dear cBioPortal team,

I'm an academic researcher and I've been using cBio Portal for some time.

The mutation datasource doesn't work for several days. As usual, I'm using Google Chrome.

Please, can you help me?

Thank you and kind regards,

Anna Gallì

--

Dr.ssa Anna Gallì

Department of Hematology Oncology,

Fondazione IRCCS Policlinico San Matteo,

& Department of Molecular Medicine,

University of Pavia,

P.le Golgi 2, 27100 Pavia, Italy

Phone: +39-0382-501597

Fax: +39-0382-502250

E-mail: anna....@unipv.it

[Sjoerd van Hagen]

Hi Anna,

Could you describe exactly what is not working, preferably with some screenshots or links to pages that do not work? The mutation mapper seems to work fine for me.

Thanks,

Sjoerd.

---

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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[Gallì Anna]

Dear Sjoerd,

first of all many thanks for your very prompt response.

When I connect to your website (https://genie.cbioportal.org/), I'm able to query by gene, but after entering the gene name anck clicking "query", the portal doesn't open (please, see attached slide).

The last query was https://genie.cbioportal.org/results/cancerTypesSummary?cancer_study_list=brca_akt1_genie_2019%2Cglioma_dfci_2020%2Cgenie_public_6_1%2Cgenie_public%2Cmbc_genie_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&profileFilter=0&case_set_id=all&gene_list=TET2&geneset_list=%20&tab_index=tab_visualize&Action=Submit

I have tried many times to log out and log in again without solving the problem.

Thank you again,

Anna

[Sjoerd van Hagen]

Hi Anna,

Ah I see, it is on the genie portal.

For me it also seems to hang with a couple of requests to the server not returning. I am CCing Ino, who maintains this server. He is based in the US so it will take some time for him to respond.

Ino, can you have a look at this? There is a call that does not seem to finish and ends with a 504, to https://genie.cbioportal.org/api/mutations/fetch?projection=DETAILED, but other calls are also very slow.

Best,

Sjoerd.

---

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

[Gallì Anna]

Ok, thank you all very much.

Don't worry about the time required.

For me it's essential to solve the issue, I hope you can do it since cBioportal is very useful for variant classisìfication (I'm an NGS worker).

So, I take this opportunity to congratulate you for the website!

Anna

[de Bruijn, Ino/Sloan Kettering Institute]

Thanks for reporting Anna and Sjoerd!

 

I couldn’t immediately resolve the issue, but we will look into it further. You can follow updates here:

 

https://github.com/cBioPortal/cbioportal/issues/8468

 

Will keep you updated

 

Best wishes,

Ino

 

From: Gallì Anna <anna....@unipv.it>
Date: Tuesday, March 30, 2021 at 5:12 AM
To: Sjoerd van Hagen <sjo...@thehyve.nl>
Cc: "de Bruijn, Ino/Sloan Kettering Institute" <debr...@mskcc.org>, cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] Re: [cbioportal] mutation datasource doesn't work

 

Ok, thank you all very much.

 

Don't worry about the time required.

For me it's essential to solve the issue, I hope you can do it since cBioportal is very useful for variant classisìfication (I'm an NGS worker).

 

So, I take this opportunity to congratulate you for the website!

 

Anna

 

Il giorno mar 30 mar 2021 alle ore 10:56 Sjoerd van Hagen <sjo...@thehyve.nl> ha scritto:

Hi Anna,

 

Ah I see, it is on the genie portal.

 

For me it also seems to hang with a couple of requests to the server not returning. I am CCing Ino, who maintains this server. He is based in the US so it will take some time for him to respond.

 

Ino, can you have a look at this? There is a call that does not seem to finish and ends with a 504, to https://genie.cbioportal.org/api/mutations/fetch?projection=DETAILED, but other calls are also very slow.

 

Best,

 

Sjoerd.

 

---

 

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

 

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

 

    

 

 

On Tue, Mar 30, 2021 at 10:39 AM Gallì Anna <anna....@unipv.it> wrote:

Dear Sjoerd,

first of all many thanks for your very prompt response.

 

When I connect to your website (https://genie.cbioportal.org/), I'm able to query by gene, but after entering the gene name anck clicking "query", the portal doesn't open (please, see attached slide).

 

The last query was https://genie.cbioportal.org/results/cancerTypesSummary?cancer_study_list=brca_akt1_genie_2019%2Cglioma_dfci_2020%2Cgenie_public_6_1%2Cgenie_public%2Cmbc_genie_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&profileFilter=0&case_set_id=all&gene_list=TET2&geneset_list=%20&tab_index=tab_visualize&Action=Submit

 

I have tried many times to log out and log in again without solving the problem.

 

Thank you again,

Anna

 

Il giorno mar 30 mar 2021 alle ore 10:21 Sjoerd van Hagen <sjo...@thehyve.nl> ha scritto:

Hi Anna,

 

Could you describe exactly what is not working, preferably with some screenshots or links to pages that do not work? The mutation mapper seems to work fine for me.

 

Thanks,

 

Sjoerd.

 

---

 

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

 

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

 

    

 

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[Gallì Anna]

Dear all,

unfortunately cBioportal doesn't run yet.

Do you have an idea if you can fix the issue and when?

Many thanks,

Anna 

[de Bruijn, Ino/Sloan Kettering Institute]

Hi Anna,

 

Thanks for reaching out again

 

We are still trying to investigate the cause of the issue. We have some leads but aren’t entirely sure yet:

 

https://github.com/cBioPortal/cbioportal/issues/8468

 

We are actively working on it, so hopefully we are able to solve it this week

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On Tue, Mar 30, 2021 at 10:39 AM Gallì Anna <anna....@unipv.it> wrote:

Dear Sjoerd,

first of all many thanks for your very prompt response.

 

When I connect to your website (https://genie.cbioportal.org/), I'm able to query by gene, but after entering the gene name anck clicking "query", the portal doesn't open (please, see attached slide).

 

The last query was https://genie.cbioportal.org/results/cancerTypesSummary?cancer_study_list=brca_akt1_genie_2019%2Cglioma_dfci_2020%2Cgenie_public_6_1%2Cgenie_public%2Cmbc_genie_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&profileFilter=0&case_set_id=all&gene_list=TET2&geneset_list=%20&tab_index=tab_visualize&Action=Submit

 

I have tried many times to log out and log in again without solving the problem.

 

Thank you again,

Anna

 

Il giorno mar 30 mar 2021 alle ore 10:21 Sjoerd van Hagen <sjo...@thehyve.nl> ha scritto:

Hi Anna,

 

Could you describe exactly what is not working, preferably with some screenshots or links to pages that do not work? The mutation mapper seems to work fine for me.

 

Thanks,

 

Sjoerd.

 

---

 

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

 

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

 

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[Gallì Anna]

Many thanks again.

I'm following the link, but it's difficult for me to understand. Am I the only one that can't use your website?

I hope that everything works out!

Anna

[de Bruijn, Ino/Sloan Kettering Institute]

Sorry – yes the github issue link is indeed rather detailed. It’s more a way for you to see that people are working on it

 

That particular query is not working for anyone, but certain other queries are working e.g. https://bit.ly/3rBgaAO

[Ino de Bruijn]

Hi Anna,

We have deployed a fix. Let us know if you still have issues

Btw I noticed the previous example I shared was incorrect and should actually be: https://bit.ly/39TAZkZ

Best wishes,

Ino

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/84AE4767-6089-4A22-B7F1-3406B2510375%40mskcc.org.

[Gallì Anna]

Dear Ino and dear all,

thank you very much for the resolution.

cBioportal is running and I can look at mutation again, essential for variant classification.

Have a nice day,

Anna