Search GeneSets function not working

[mfmiles]

There is something seriously wrong with the Search GeneSets function in GeneWeaver. It is producing very few in any hits and those don't even have the query gene in them. I tried this with several different gene symbols and got the same results each time.

[bergsalex]

@mfmiles, could you provide some examples of the queries you tried? I need to reproduce the behavior before I can identify the issue and a fix.

[mfmiles]

Hi Alexander, Sure. But what is going on at Jackson. Seems that GeneWeaver and e.g. some web sites (QTL viewer) serving features of the Churchill laboratory have been broken, moved or discontinued? I log in to the usual GeneWeaver site at https://www.geneweaver.org and then just search for a gene – e.g. Car8 or Nin – and the search will come up with no genesets or maybe 1 geneset – when I know there are hundreds or >1000 for these genes. But this is intermittent problem. Late yesterday afternoon I tried to search for a gene and got nothing. Just now, I searched for Car8 and it seemed to work fine. So it just has been erratic it seems – like the search function is not working properly or is unable to access the geneset database. Anyway – this will likely be difficult to troubleshoot since it is intermittent. I will post another bug report when it recurs and provide details. BTW – I am using a Mac with OS 12.6 and a Safari browser (version 16). Thanks, Mike

…

------------- Michael F. Miles, M.D., Ph.D. Director, VCU Alcohol Research Center Professor, Departments of Pharmacology and Neurology Virginia Commonwealth University Tel: 804-827-4054 FAX: 804-828-6432 NOTE NEW EMAIL ADDRESS: ***@***.******@***.***> Web pages: https://pharmtox.vcu.edu/about/our-team/michael-f-miles-md-phd.html https://arc.vcu.edu/researchers/michael-f-miles-md-phd/

------------ Mailing Address: Virginia Commonwealth University P.O. Box 980613 Richmond, VA 23298-0599 ------------ Address for Express Mail: Virginia Commonwealth University Molecular Medicine Research Bldg, Rm 6034 1220 E. Broad Street Richmond, VA 23298 Tel: 804-827-4054 From: Alexander Berger ***@***.***> Date: Thursday, July 18, 2024 at 10:19 AM To: TheJacksonLaboratory/geneweaver-legacy ***@***.***> Cc: Michael Miles ***@***.***>, Mention ***@***.***> Subject: Re: [TheJacksonLaboratory/geneweaver-legacy] Search GeneSets function not working (Issue #11) @mfmiles, could you provide some examples of the queries you tried? I need to reproduce the behavior before I can identify the issue and a fix. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/JqxBPMk!m_OgzlxsfrMzNth2vzTPJJnHWcdk_pi1XF4p9Pn_EuJBXfVqjHZDMGCb6Ngj5n-d1_gOroexEOec_xgpCM-jwJM3vd67Pl36E_om2hCQ9Nlfr8jAVrGPnaoBwmY65IjBPG4$> Report Suspicious <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/JqxBPMk!m_OgzlxsfrMzNth2vzTPJJnHWcdk_pi1XF4p9Pn_EuJBXfVqjHZDMGCb6Ngj5n-d1_gOroexEOec_xgpCM-jwJM3vd67Pl36E_om2hCQ9Nlfr8jAVrGPnaoBwmY65IjBPG4$> ZjQcmQRYFpfptBannerEnd @mfmiles<https://urldefense.com/v3/__https:/github.com/mfmiles__;!!JqxBPMk!gXYgifuUJw8cbkHP7DdBElgmeXRc5XW_OjEw5bqrH-GA8-9Q2t9lPMDBwsra7OSxronCNz_YqmP_1oQFnskwvi4aucg$>, could you provide some examples of the queries you tried? I need to reproduce the behavior before I can identify the issue and a fix. — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/TheJacksonLaboratory/geneweaver-legacy/issues/11*issuecomment-2236658642__;Iw!!JqxBPMk!gXYgifuUJw8cbkHP7DdBElgmeXRc5XW_OjEw5bqrH-GA8-9Q2t9lPMDBwsra7OSxronCNz_YqmP_1oQFnskwm9Zmfkc$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ACCCHFOXH3QGA5B37ZWIHKTZM7FGVAVCNFSM6AAAAABKRSR54GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGY2TQNRUGI__;!!JqxBPMk!gXYgifuUJw8cbkHP7DdBElgmeXRc5XW_OjEw5bqrH-GA8-9Q2t9lPMDBwsra7OSxronCNz_YqmP_1oQFnskwGUASzqs$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[mfmiles]

Alex or whomever, I just tried GeneWeaver again – and now it gives “Your search returned 0 results” – several times with searching for Car8. This happens whether I log on as a guest of through my account ***@***.******@***.***>). A screenshot of the error message is below. Interestingly, the search space in the error message does not show “Car8” – which I had entered. Not sure if that means the system is just not reading the input or not. Thanks, Mike ***@***.***

…

------------- Michael F. Miles, M.D., Ph.D. Director, VCU Alcohol Research Center Professor, Departments of Pharmacology and Neurology Virginia Commonwealth University Tel: 804-827-4054 FAX: 804-828-6432 NOTE NEW EMAIL ADDRESS: ***@***.******@***.***> Web pages: https://pharmtox.vcu.edu/about/our-team/michael-f-miles-md-phd.html https://arc.vcu.edu/researchers/michael-f-miles-md-phd/

------------ Mailing Address: Virginia Commonwealth University P.O. Box 980613 Richmond, VA 23298-0599 ------------ Address for Express Mail: Virginia Commonwealth University Molecular Medicine Research Bldg, Rm 6034 1220 E. Broad Street Richmond, VA 23298 Tel: 804-827-4054 From: Michael Miles ***@***.***> Date: Thursday, July 18, 2024 at 10:57 AM To: TheJacksonLaboratory/geneweaver-legacy ***@***.***>, ***@***.*** ***@***.***> Subject: Re: [TheJacksonLaboratory/geneweaver-legacy] Search GeneSets function not working (Issue #11) Hi Alexander, Sure. But what is going on at Jackson. Seems that GeneWeaver and e.g. some web sites (QTL viewer) serving features of the Churchill laboratory have been broken, moved or discontinued? I log in to the usual GeneWeaver site at https://www.geneweaver.org and then just search for a gene – e.g. Car8 or Nin – and the search will come up with no genesets or maybe 1 geneset – when I know there are hundreds or >1000 for these genes. But this is intermittent problem. Late yesterday afternoon I tried to search for a gene and got nothing. Just now, I searched for Car8 and it seemed to work fine. So it just has been erratic it seems – like the search function is not working properly or is unable to access the geneset database. Anyway – this will likely be difficult to troubleshoot since it is intermittent. I will post another bug report when it recurs and provide details. BTW – I am using a Mac with OS 12.6 and a Safari browser (version 16). Thanks, Mike

------------- Michael F. Miles, M.D., Ph.D. Director, VCU Alcohol Research Center Professor, Departments of Pharmacology and Neurology Virginia Commonwealth University Tel: 804-827-4054 FAX: 804-828-6432 NOTE NEW EMAIL ADDRESS: ***@***.******@***.***> Web pages: https://pharmtox.vcu.edu/about/our-team/michael-f-miles-md-phd.html https://arc.vcu.edu/researchers/michael-f-miles-md-phd/

------------ Mailing Address: Virginia Commonwealth University P.O. Box 980613 Richmond, VA 23298-0599 ------------ Address for Express Mail: Virginia Commonwealth University Molecular Medicine Research Bldg, Rm 6034 1220 E. Broad Street Richmond, VA 23298 Tel: 804-827-4054 From: Alexander Berger ***@***.***> Date: Thursday, July 18, 2024 at 10:19 AM To: TheJacksonLaboratory/geneweaver-legacy ***@***.***> Cc: Michael Miles ***@***.***>, Mention ***@***.***> Subject: Re: [TheJacksonLaboratory/geneweaver-legacy] Search GeneSets function not working (Issue #11) @mfmiles, could you provide some examples of the queries you tried? I need to reproduce the behavior before I can identify the issue and a fix. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. Report Suspicious <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/JqxBPMk!m_OgzlxsfrMzNth2vzTPJJnHWcdk_pi1XF4p9Pn_EuJBXfVqjHZDMGCb6Ngj5n-d1_gOroexEOec_xgpCM-jwJM3vd67Pl36E_om2hCQ9Nlfr8jAVrGPnaoBwmY65IjBPG4$> ZjQcmQRYFpfptBannerEnd @mfmiles<https://urldefense.com/v3/__https:/github.com/mfmiles__;!!JqxBPMk!gXYgifuUJw8cbkHP7DdBElgmeXRc5XW_OjEw5bqrH-GA8-9Q2t9lPMDBwsra7OSxronCNz_YqmP_1oQFnskwvi4aucg$>, could you provide some examples of the queries you tried? I need to reproduce the behavior before I can identify the issue and a fix. — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/TheJacksonLaboratory/geneweaver-legacy/issues/11*issuecomment-2236658642__;Iw!!JqxBPMk!gXYgifuUJw8cbkHP7DdBElgmeXRc5XW_OjEw5bqrH-GA8-9Q2t9lPMDBwsra7OSxronCNz_YqmP_1oQFnskwm9Zmfkc$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ACCCHFOXH3QGA5B37ZWIHKTZM7FGVAVCNFSM6AAAAABKRSR54GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGY2TQNRUGI__;!!JqxBPMk!gXYgifuUJw8cbkHP7DdBElgmeXRc5XW_OjEw5bqrH-GA8-9Q2t9lPMDBwsra7OSxronCNz_YqmP_1oQFnskwGUASzqs$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[bergsalex]

Thank you Mike (@mfmiles),

I believe that's enough information to troubleshoot the error. I've reproduced it and we will start work on a fix. This appears to be related to our recent infrastructure migration. Looks like we missed it because it's intermittent.

I'll keep this issue up to date with any progress we make on resolving the issue.

Best,
Alex

[bergsalex]

Hi Mike (@mfmiles),

I wanted to let you know that we've taken action that we hope will mitigate this error and have a fix planned and scheduled. The mitigation has already been applied and should fully stabilize within the next 30 minutes.

Thank you again for bringing this to our attention. I'm going to keep this issue open until we've fully implemented the fix.

Best,
Alex

[mfmiles]

Hi Alex, Thanks very much. Seemed to work fine yesterday. I appreciate the help. Mike From: Alexander Berger ***@***.***> Date: Wednesday, July 24, 2024 at 10:42 AM To: TheJacksonLaboratory/geneweaver-legacy ***@***.***> Cc: Michael Miles ***@***.***>, Mention ***@***.***> Subject: Re: [TheJacksonLaboratory/geneweaver-legacy] Search GeneSets function not working (Issue #11) Hi Mike (@ mfmiles), I wanted to let you know that we've taken action that we hope will mitigate this error and have a fix planned and scheduled. The mitigation has already been applied and should fully stabilize within the next 30 minutes. Thank ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/JqxBPMk!m_OgzlxsfrMzNth2vzTPJJnHWcdk_pi1XF4p9Pn_EuJBXfVqjHZDMGCb6Ngj5n-d1_gOroex8Sd9fpnpSA-jwI0NSE-1iIWyw1H2RsbYj9H_p-hrjQ7edJ7lCd43LdS4bgs$> Report Suspicious <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/JqxBPMk!m_OgzlxsfrMzNth2vzTPJJnHWcdk_pi1XF4p9Pn_EuJBXfVqjHZDMGCb6Ngj5n-d1_gOroex8Sd9fpnpSA-jwI0NSE-1iIWyw1H2RsbYj9H_p-hrjQ7edJ7lCd43LdS4bgs$> ZjQcmQRYFpfptBannerEnd Hi Mike ***@***.***<https://urldefense.com/v3/__https:/github.com/mfmiles__;!!JqxBPMk!g0E1JvAb-Qz1GEahIp4kTxlLfwBDkUqNsE5gmXPhPE0xzVVZuozXf1vLckiswCwJkeUkoXx0JRlqsAdnl75wCssNiNY$>), I wanted to let you know that we've taken action that we hope will mitigate this error and have a fix planned and scheduled. The mitigation has already been applied and should fully stabilize within the next 30 minutes. Thank you again for bringing this to our attention. I'm going to keep this issue open until we've fully implemented the fix. Best, Alex — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/TheJacksonLaboratory/geneweaver-legacy/issues/11*issuecomment-2248194864__;Iw!!JqxBPMk!g0E1JvAb-Qz1GEahIp4kTxlLfwBDkUqNsE5gmXPhPE0xzVVZuozXf1vLckiswCwJkeUkoXx0JRlqsAdnl75wo1-P9WI$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ACCCHFN34C2CH53WHX7XDHLZN64LPAVCNFSM6AAAAABKRSR54GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBYGE4TIOBWGQ__;!!JqxBPMk!g0E1JvAb-Qz1GEahIp4kTxlLfwBDkUqNsE5gmXPhPE0xzVVZuozXf1vLckiswCwJkeUkoXx0JRlqsAdnl75wLgB0tAY$>. You are receiving this because you were mentioned.Message ID: ***@***.***>