Merge discvr-21.3 to develop

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics/.qview.xml

@@ -9,6 +9,7 @@
        <column name="readset" />
        <column name="analysis_id" />
        <column name="runid" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="dataid/Name"/>

SequenceAnalysis/resources/queries/sequenceanalysis/readData/.qview.xml

@@ -19,7 +19,7 @@
            </properties>
        </column>
        <column name="created" />
-       <column name="readset/workbook" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="readset" />

SequenceAnalysis/resources/queries/sequenceanalysis/readData/File Details.qview.xml

@@ -15,7 +15,7 @@
        <column name="archived" />
 
        <column name="created" />
-       <column name="readset/workbook" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="readset" />

SequenceAnalysis/resources/queries/sequenceanalysis/readData/With Filepath.qview.xml

@@ -15,7 +15,7 @@
        <column name="archived" />
 
        <column name="created" />
-       <column name="readset/workbook" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="readset" />

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.325-12.326.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column codon type VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.326-12.327.sql

@@ -0,0 +1,5 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column ref_aa type VARCHAR(4000);
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column q_aa type VARCHAR(4000);
+
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column ref_nt type VARCHAR(4000);
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column q_nt type VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.327-12.328.sql

@@ -0,0 +1,4 @@
+ALTER TABLE sequenceanalysis.alignment_summary_junction ADD container ENTITYID;
+
+UPDATE sequenceanalysis.alignment_summary_junction
+SET container = (SELECT s.container FROM sequenceanalysis.alignment_summary s WHERE s.rowid = alignment_id);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.325-12.326.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column codon VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.326-12.327.sql

@@ -0,0 +1,6 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column ref_aa VARCHAR(4000);
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column q_aa VARCHAR(4000);
+
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column ref_nt VARCHAR(4000);
+ALTER TABLE sequenceanalysis.nt_snps_by_pos ALTER column q_nt VARCHAR(4000);
+

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.327-12.328.sql

@@ -0,0 +1,4 @@
+ALTER TABLE sequenceanalysis.alignment_summary_junction ADD container ENTITYID;
+GO
+UPDATE sequenceanalysis.alignment_summary_junction
+SET container = (SELECT s.container FROM sequenceanalysis.alignment_summary s WHERE s.rowid = alignment_id);