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  1. IGB
  2. IGBF-1379

Investigate why bookmark data set not loading

        Details

        • Story Points:
          1
        • Sprint:
          Fall 2018 1, Fall 2018 Sprint 2

          Description

          The following IGB bookmark should cause two data sets to load - TAIR10 mRNA and an RNA-Seq data. However, only the RNA-Seq data set is loaded.

          Background:

          Recently, I updated the default data models for Arabidopsis from TAIR10 to Araport 11. Now, when user selects Arabidopsis on the home screen (green plant next to Mona Lisa painting), the Araport11 data load automatically. This is because the Araport11 data set has "load_hint" of "genome" in the annots.xml for this genome version. This means that if a user clicks a bookmark referencing that genome, the Araport11 data set gets loaded automatically, along with other data sets referenced in the bookmark. I made the bookmark below before updating the Araport data set. Only now am I noticing that the old TAIR data set is not getting loaded, even though the bookmark mentions it.

          http://localhost:7085/IGBControl?feature_url_1=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&start=10326314&feature_url_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&query_url=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&query_url=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&sym_bg_0=0xFFFFFF&sym_col_1=0x00FFFF&version=A_thaliana_Jun_2009&sym_bg_1=0xFFFFFF&sym_method_1=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&sym_method_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&sym_col_0=0x000000&sym_name_1=shoot+ERR274310&sym_name_0=TAIR10+mRNA&loadresidues=true&create=2018%2F07%2F15+09%3A03%3A24&modified=2018%2F07%2F15+09%3A03%3A24&modified=2018%2F08%2F03+16%3A46%3A48&modified=2018%2F08%2F03+16%3A52%3A18&end=10330564&sym_ypos_1=0&sym_ypos_0=0&sym_yheight_0=50&server_url=http%3A%2F%2Florainelab-quickload.scidas.org%2Fbar%2F&server_url=http%3A%2F%2Figbquickload.org%2Fquickload%2F&seqid=Chr2&sym_yheight_1=50

          Determine the root cause of this unexpected behavior and propose a fix.

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
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              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
              Description The following IGB bookmark should cause two data sets to load - TAIR10 mRNA and an RNA-Seq data. However, only the RNA-Seq data set is loaded.

              Background:

              Recently, I updated the default data models for Arabidopsis from TAIR10 to Araport 11. Now, when user selects Arabidopsis on the home screen (green plant next to Mona Lisa painting), the Araport11 data load automatically. This is because the Araport11 data set has "load_hint" of "genome" in the annots.xml for this genome version. This means that if a user clicks a bookmark referencing that genome, the Araport11 data set gets loaded automatically, along with other data sets referenced in the bookmark. I made the bookmark below before updating the Araport data set. Only now am I noticing that the old TAIR data set is not getting loaded, even though the bookmark mentions it.

              http://localhost:7085/IGBControl?feature_url_1=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&start=10326314&feature_url_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&query_url=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&query_url=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&sym_bg_0=0xFFFFFF&sym_col_1=0x00FFFF&version=A_thaliana_Jun_2009&sym_bg_1=0xFFFFFF&sym_method_1=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&sym_method_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&sym_col_0=0x000000&sym_name_1=shoot+ERR274310&sym_name_0=TAIR10+mRNA&loadresidues=true&create=2018%2F07%2F15+09%3A03%3A24&modified=2018%2F07%2F15+09%3A03%3A24&modified=2018%2F08%2F03+16%3A46%3A48&modified=2018%2F08%2F03+16%3A52%3A18&end=10330564&sym_ypos_1=0&sym_ypos_0=0&sym_yheight_0=50&server_url=http%3A%2F%2Florainelab-quickload.scidas.org%2Fbar%2F&server_url=http%3A%2F%2Figbquickload.org%2Fquickload%2F&seqid=Chr2&sym_yheight_1=50               		The following IGB bookmark should cause two data sets to load - TAIR10 mRNA and an RNA-Seq data. However, only the RNA-Seq data set is loaded.

              Background:

              Recently, I updated the default data models for Arabidopsis from TAIR10 to Araport 11. Now, when user selects Arabidopsis on the home screen (green plant next to Mona Lisa painting), the Araport11 data load automatically. This is because the Araport11 data set has "load_hint" of "genome" in the annots.xml for this genome version. This means that if a user clicks a bookmark referencing that genome, the Araport11 data set gets loaded automatically, along with other data sets referenced in the bookmark. I made the bookmark below before updating the Araport data set. Only now am I noticing that the old TAIR data set is not getting loaded, even though the bookmark mentions it.

              http://localhost:7085/IGBControl?feature_url_1=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&start=10326314&feature_url_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&query_url=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&query_url=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&sym_bg_0=0xFFFFFF&sym_col_1=0x00FFFF&version=A_thaliana_Jun_2009&sym_bg_1=0xFFFFFF&sym_method_1=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2Faerial%2FERR274310%2Faccepted_hits.bam&sym_method_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz&sym_col_0=0x000000&sym_name_1=shoot+ERR274310&sym_name_0=TAIR10+mRNA&loadresidues=true&create=2018%2F07%2F15+09%3A03%3A24&modified=2018%2F07%2F15+09%3A03%3A24&modified=2018%2F08%2F03+16%3A46%3A48&modified=2018%2F08%2F03+16%3A52%3A18&end=10330564&sym_ypos_1=0&sym_ypos_0=0&sym_yheight_0=50&server_url=http%3A%2F%2Florainelab-quickload.scidas.org%2Fbar%2F&server_url=http%3A%2F%2Figbquickload.org%2Fquickload%2F&seqid=Chr2&sym_yheight_1=50

              Determine the root cause of this unexpected behavior and propose a fix.
              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
              Summary Load all bookmark data sets Investigate why bookmark data set not loading
              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
              Assignee Kiran Korey [ kkorey ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 2018 1 [ 51 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Sprint Fall 2018 1 [ 51 ] Fall 2018 1, Fall 2018 Sprint 2 [ 51, 52 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              kkorey Kiran Korey (Inactive) made changes -
              Attachment TAIR10_loaded.png [ 14149 ]
              kkorey Kiran Korey (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Open [ 1 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 18080 ] Fall 2019 Workflow Update [ 19931 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 19931 ] Revised Fall 2019 Workflow Update [ 22051 ]

                People

                • Assignee:
                  kkorey Kiran Korey (Inactive)
                  Reporter:
                  ann.loraine Ann Loraine
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                  Dates

                  • Created:
                    Updated:
                    Resolved: