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ucscXena / XenaGoWidget

Xena Gene Set Viewer (demo: http://xenademo.berkeleybop.io/xena)
https://xenageneset.berkeleybop.io/xena/
BSD 3-Clause "New" or "Revised" License
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reloading after loading a sub-cohort fails to reselect the same sub-cohort #259

Closed nathandunn closed 5 years ago

nathandunn commented 5 years ago

I get 500 errors for 

(; sparseData
(fn [dataset samples genes]
    (let [getfield (fn [field]
                     (:id (car (query {:select [:field.id]
                                       :from [:dataset]
                                       :join [:field [:= :dataset.id :field.dataset_id]]
                                       :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))
          sampleID (getfield "sampleID")]
      {:samples (map :value (query {:select [:value]
                                    :from [:code]
                                    :where [:and [:in :value samples][:= :field_id sampleID]]}))
       :rows (xena-query {:select ["ref" "alt" "altGene" "effect" "dna-vaf" "rna-vaf" "amino-acid" "genes" "sampleID" "position"]
                          :from [dataset]
                          :where [:and [:in :any "genes" genes] [:in "sampleID" samples]]})}))
 "TCGA.OV.sampleMap/mutation_wustl" "OVCA.Differentiated" ["DLL1" "DTX1" "JAG1" "JAG2" "ADAM10" "PSEN1" "PSEN2" "PSENEN" "LATS2" "MOB1B" "MOB1A" "SAV1" "STK3" "STK4" "TAZ" "YAP1" "MST1" "WWTR1" "UNG" "SMUG1" "MBD4" "TDG" "OGG1" "MUTYH" "NTHL1" "MPG" "NEIL1" "NEIL2" "NEIL3" "APEX1" "APEX2" "LIG3" "XRCC1" "PNKP" "APLF" "PARP1" "PARP2" "PARP3" "MGMT" "ALKBH2" "ALKBH3" "T

and more importantly:

(; datasetFetch
(fn [dataset samples probes]
  (fetch [{:table dataset
           :columns probes
           :samples samples}]))
 "mutation_sampleEvent" "OVCA.Differentiated" ["event_K" "total_pop_N"])

and

(; datasetFetch
(fn [dataset samples probes]
  (fetch [{:table dataset
           :columns probes
           :samples samples}]))
 "cnv_sampleEvent" "OVCA.Differentiated" ["event_K" "total_pop_N"])

Should be:

(; datasetFetch
(fn [dataset samples probes]
  (fetch [{:table dataset
           :columns probes
           :samples samples}]))
 "mutation_sampleEvent" ["TCGA-04-1353-01" "TCGA-04-1516-01" "TCGA-04-1638-01" "TCGA-04-1644-01" "TCGA-04-1646-01" "TCGA-04-1648-01" "TCGA-04-1649-01" "TCGA-04-1651-01" "TCGA-04-1652-01" "TCGA-04-1655-01" "TCGA-09-1664-01" "TCGA-09-1670-01" "TCGA-09-1672-01" "TCGA-09-1673-01" "TCGA-09-1674-01" "TCGA-09-1675-01"  ... ] ["event_K" "total_pop_N"])

(identical for cnv_sampleEvent)

(; sparseData
(fn [dataset samples genes]
    (let [getfield (fn [field]
                     (:id (car (query {:select [:field.id]
                                       :from [:dataset]
                                       :join [:field [:= :dataset.id :field.dataset_id]]
                                       :where [:and [:= :field.name field] [:= :dataset.name dataset]]}))))
          sampleID (getfield "sampleID")]
      {:samples (map :value (query {:select [:value]
                                    :from [:code]
                                    :where [:and [:in :value samples][:= :field_id sampleID]]}))
       :rows (xena-query {:select ["ref" "alt" "altGene" "effect" "dna-vaf" "rna-vaf" "amino-acid" "genes" "sampleID" "position"]
                          :from [dataset]
                          :where [:and [:in :any "genes" genes] [:in "sampleID" samples]]})}))
 "TCGA.OV.sampleMap/mutation_wustl" ["TCGA-04-1353-01" "TCGA-04-1516-01" "TCGA-04-1638-01" "TCGA-04-1644-01" "TCGA-04-1646-01" "TCGA-04-1648-01" "TCGA-04-1649-01" "TCGA-04-1651-01" "TCGA-04-1652-01" "TCGA-04-1655-01" "TCGA-09-1664-01" "TCGA-09-1670")