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Tabular files with a single row don't show up properly in data_sets 1 file browser #1463

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scottx611x opened this issue Oct 12, 2016 · 4 comments

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@scottx611x
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scottx611x commented Oct 12, 2016

  • Specific code commit: fad81a2
  • Version of the web browser and OS: Chrome Version 53.0.2785.143 (64-bit)
  • Environment where the error occurred (Vagrant VM and site conf mode or AWS instance): https://test.stemcellcommons.org

Steps to reproduce

  1. Upload this comma delimited file (or any other tabular file referencing a single data file) into Refinery: sample-comma.txt
  2. View the File Browser at https://test.stemcellcommons.org/data_sets/<uuid>:
    • See no files displayed (no console errors): screen shot 2016-10-11 at 9 43 28 pm
  3. View the File Browser at https://test.stemcellcommons.org/data_sets2/<uuid>:
    • See the proper behavior:
      screen shot 2016-10-11 at 9 43 45 pm

Observed behavior

  • I haven't exhausted all edge cases but it seems that tabular files that reference a single data file, regardless of delimiter type, aren't displayed properly in the data_sets file broswer, but are displayed properly in data_sets2 file browser

Expected behavior

  • For the data_sets file browser to be able to handle tabular files referencing a single data file.
@scottx611x
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scottx611x commented Oct 14, 2016

I'm currently not able to reproduce this issue locally in gdev mode.

See:
screen shot 2016-10-14 at 1 15 59 pm

@scottx611x
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But I am able to see the issue in prod mode

See:
screen shot 2016-10-14 at 1 17 25 pm

@scottx611x
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Relevant Apache log:

[Fri Oct 14 13:20:49.588615 2016] [:error] [pid 4970:tid 139776429516544] 2016-10-14 13:20:49 INFO     requests.packages.urllib3.connectionpool:203 _new_conn() - Starting new HTTP connection (1): localhost
[Fri Oct 14 13:20:49.592677 2016] [:error] [pid 4970:tid 139776429516544] 2016-10-14 13:20:49 DEBUG    requests.packages.urllib3.connectionpool:383 _make_request() - "GET /solr/data_set_manager/select?fq=%28study_uuid%3A8576a656-dd1e-4192-8e78-ebd14b0125c6+AND+assay_uuid%3Adb27bb7d-2859-49b8-a84f-a7fa59c7bfcb%29&fq=type%3A%28%22Raw+Data+File%22+OR+%22Derived+Data+File%22+OR+%22Array+Data+File%22+OR+%22Derived+Array+Data+File%22+OR+%22Array+Data+Matrix+File%22+OR+%22Derived+Array+Data+Matrix+File%22%29&fq=is_annotation%3Afalse&rows=1&json.wrf=jQuery21103308266235968844_1476465648551&q=django_ct%3Adata_set_manager.node&start=0&wt=json&_=1476465648552 HTTP/1.1" 200 None
[Fri Oct 14 13:20:49.604417 2016] [:error] [pid 4970:tid 139776513443584] 2016-10-14 13:20:49 INFO     requests.packages.urllib3.connectionpool:203 _new_conn() - Starting new HTTP connection (1): localhost
[Fri Oct 14 13:20:49.616089 2016] [:error] [pid 4970:tid 139776513443584] 2016-10-14 13:20:49 DEBUG    requests.packages.urllib3.connectionpool:383 _make_request() - "GET /solr/data_set_manager/select?fq=%28study_uuid%3A8576a656-dd1e-4192-8e78-ebd14b0125c6+AND+assay_uuid%3Adb27bb7d-2859-49b8-a84f-a7fa59c7bfcb%29&fq=type%3A%28%22Raw+Data+File%22+OR+%22Derived+Data+File%22+OR+%22Array+Data+File%22+OR+%22Derived+Array+Data+File%22+OR+%22Array+Data+Matrix+File%22+OR+%22Derived+Array+Data+Matrix+File%22%29&fq=is_annotation%3Atrue&rows=1&json.wrf=jQuery21103308266235968844_1476465648553&q=django_ct%3Adata_set_manager.node&start=0&wt=json&_=1476465648554 HTTP/1.1" 200 None
[Fri Oct 14 13:20:49.634091 2016] [:error] [pid 4970:tid 139776521836288] 2016-10-14 13:20:49 INFO     requests.packages.urllib3.connectionpool:203 _new_conn() - Starting new HTTP connection (1): localhost
[Fri Oct 14 13:20:49.730978 2016] [:error] [pid 4970:tid 139776513443584] 2016-10-14 13:20:49 INFO     requests.packages.urllib3.connectionpool:203 _new_conn() - Starting new HTTP connection (1): localhost
[Fri Oct 14 13:20:49.816207 2016] [:error] [pid 4970:tid 139776521836288] 2016-10-14 13:20:49 DEBUG    requests.packages.urllib3.connectionpool:383 _make_request() - "GET /solr/data_set_manager/select?sort=REFINERY_SUBANALYSIS_2257_953_s+asc&fq=%28study_uuid%3A8576a656-dd1e-4192-8e78-ebd14b0125c6+AND+assay_uuid%3Adb27bb7d-2859-49b8-a84f-a7fa59c7bfcb%29&fq=type%3A%28%22Raw+Data+File%22+OR+%22Derived+Data+File%22+OR+%22Array+Data+File%22+OR+%22Derived+Array+Data+File%22+OR+%22Array+Data+Matrix+File%22+OR+%22Derived+Array+Data+Matrix+File%22%29&fq=is_annotation%3Afalse&rows=20&facet.field=REFINERY_SUBANALYSIS_2257_953_s&facet.field=REFINERY_ANALYSIS_UUID_2257_953_s&facet.field=REFINERY_WORKFLOW_OUTPUT_2257_953_s&facet.limit=-1&facet.sort=count&facet=true&json.wrf=jQuery21103308266235968844_1476465648551&q=django_ct%3Adata_set_manager.node&start=0&wt=json&facet.pivot=%2C&fl=REFINERY_SUBANALYSIS_2257_953_s%2Cspecies_Characteristics_2257_953_s%2Cuuid%2Cname%2Cassay_uuid%2CREFINERY_TYPE_2257_953_s%2Cfile_uuid%2Curl_Characteristics_2257_953_s%2Cid_Characteristics_2257_953_s%2Cis_annotation%2Cstudy_uuid%2CREFINERY_FILETYPE_2257_953_s%2CREFINERY_ANALYSIS_UUID_2257_953_s%2Ctype%2CREFINERY_WORKFLOW_OUTPUT_2257_953_s%2CREFINERY_NAME_2257_953_s&_=1476465648555 HTTP/1.1" 400 None
[Fri Oct 14 13:20:49.817312 2016] [:error] [pid 4970:tid 139776521836288] 2016-10-14 13:20:49 ERROR    core.views:727 solr_select() - 400 Client Error: Bad Request

@scottx611x
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scottx611x commented Oct 17, 2016

Some Context: Solr sends back an additional 400 error in the data_sets 1 filebrowser when there is only one row defined in the metadata since full_response.content has no facet_fields. Handling
this one-off case for now seems sufficient in my eyes since the way data_sets 2 filebrowser interacts with Solr doesn't produce this extra 400 error.

Fixes are encapsulated within #1479

@jkmarx jkmarx removed this from the Next milestone Oct 20, 2016
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