markerpositiontype prop?

[bradfordcondon]

marker_position_type is loaded as "start".

However the other featureposprops are

3.5     start position
1.1     start position
0       start position
50.9    stop position
50.8    stop position

does this really make sense? Do we still use the marker_position_type = start prop? Or is it a remnant of our previous way of doing things?

[bradfordcondon]

 select * from tripal_map_qtl_and_mtl_mview;
map_name        map_id  map_type        linkage_group   linkage_group_id        marker_locus_name       map_unit_type   marker_type     marker_pos_type marker_pos      organism_id     genus   species common_name     feature_id
      featurepos_id
QTL MAP 89      genetic L       4787    CmSNP00856      bin_unit        QTL     50.9    50.6    1       Fraxinus        excelsior       F. excelsior miniature  3880    2608
QTL MAP 89      genetic L       4787    CmSNP00856      bin_unit        QTL     50.6    50.6    1       Fraxinus        excelsior       F. excelsior miniature  3880    2608
QTL MAP 89      genetic L       4787    CmSNP00856      bin_unit        QTL     start   50.6    1       Fraxinus        excelsior       F. excelsior miniature  3880    2608
hkjhjkh 87      genetic L       4787    CmSNP00856      bin_unit        QTL     50.9    50.6    2       apis    melifera        bee     3880    1433
hkjhjkh 87      genetic L       4787    CmSNP00856      bin_unit        QTL     50.6    50.6    2       apis    melifera        bee     3880    1433
hkjhjkh 87      genetic L       4787    CmSNP00856      bin_unit        QTL     start   50.6    2       apis    melifera        bee     3880    1433
QTL MAP 89      genetic L       4787    CmSNP00284      bin_unit        QTL     50.8    50.6    1       Fraxinus        excelsior       F. excelsior miniature  3878    2607
QTL MAP 89      genetic L       4787    CmSNP00284      bin_unit        QTL     50.6    50.6    1       Fraxinus        excelsior       F. excelsior miniature  3878    2607
QTL MAP 89      genetic L       4787    CmSNP00284      bin_unit        QTL     start   50.6    1       Fraxinus        excelsior       F. excelsior miniature  3878    2607
hkjhjkh 87      genetic L       4787    CmSNP00284      bin_unit        QTL     50.8    50.6    2       apis    melifera        bee     3878    1432

if we look at how the mview is populating, it looks like "start" is the only one that IS loading properly with the mview...

[bradfordcondon]

marker_pos_type in the mview.

FPP.value as marker_pos_type . so we actually want to get FPP's type name for marker_pos_type instead.

SELECT FM.name as map_name,
FM.featuremap_id as map_id,
 FMP.value as map_type,
  F3.name as linkage_group,
F3.feature_id as linkage_group_id,
F.uniquename as marker_locus_name,
C1.name as map_unit_type,
C2.name as marker_type,
C4.name as marker_pos_type,
FP.mappos as marker_pos,
O.organism_id as organism_id, O.genus as genus, O.species as species, O.common_name as common_name,
F.feature_id as feature_id, FPP.featurepos_id as featurepos_id
FROM {feature} F
--F is the biological_region or parent marker locus
INNER JOIN {feature_relationship} FR 	ON FR.subject_id = F.feature_id AND
 F.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE name = 'biological_region' AND
 cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))
  AND
 FR.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE cvterm.name = 'instance_of' AND
 cv_id = (SELECT cv_id FROM cv WHERE name = 'OBO_REL'))

-- F2 is the marker feature itself
INNER JOIN {feature} F2               	ON FR.object_id = F2.feature_id
-- This mview is just for QTLs
INNER JOIN {cvterm} C ON F2.type_id = C.cvterm_id AND (C.name = 'QTL' OR C.name = 'heritable_phenotypic_marker')
INNER JOIN {featurepos} FP            	ON F2.feature_id = FP.feature_id
INNER JOIN {featuremap} FM    		ON FM.featuremap_id = FP.featuremap_id
INNER JOIN {cvterm} C1                ON C1.cvterm_id = FM.unittype_id
-- C2 is the marker type term
 INNER JOIN {cvterm} C2 ON C2.cvterm_id = F2.type_id
INNER JOIN {featuremapprop} FMP       ON FMP.featuremap_id = FP.featuremap_id AND
FMP.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'featuremap_type' AND
cv_id = (SELECT cv_id FROM cv WHERE name = 'local'))
INNER JOIN {featuremap_organism} FMO 	ON FMO.featuremap_id = FM.featuremap_id
--F3 is the parent feature of the map ie the linkage group
INNER JOIN {feature} F3 				ON FP.map_feature_id = F3.feature_id
INNER JOIN {featureposprop} FPP 		ON FPP.featurepos_id = FP.featurepos_id
INNER JOIN {organism} O 				ON FMO.organism_id = O.organism_id
INNER JOIN {cvterm} C4  ON FPP.type_id = C4.cvterm_id

so this instead. however, we have to deal with taht "extra" prop

[bradfordcondon]

need to fix both mviews.

FP.mappos as marker_pos, C.name as marker_pos_type,

we actually need marker_pos to be = the featureposprop value

like this:

SELECT F.uniquename as marker_locus_name, F.feature_id as marker_locus_id, F2.uniquename as genetic_marker_name,
  C1.name as map_unit_type, C2.name as marker_type, FM.name as map_name, FM.featuremap_id as map_id, FMP.value as map_type,
  F3.name as linkage_group, F3.feature_id as linkage_group_id, FPP.value as marker_pos, C.name as marker_pos_type,
  O.organism_id as organism_id, O.genus as genus, O.species as species, O.common_name as common_name
  FROM {feature} F
  INNER JOIN {feature_relationship} FR 	ON FR.subject_id = F.feature_id AND
    F.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE name = 'biological_region' AND
    cv_id = (SELECT cv_id FROM {cv} WHERE name = 'sequence'))
     AND
    FR.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE {cvterm}.name = 'instance_of' AND
    cv_id = (SELECT cv_id FROM {cv} WHERE name = 'OBO_REL'))

  INNER JOIN {feature} F2               	ON FR.object_id = F2.feature_id 
     AND
    FR.type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = 'instance_of' AND
    cv_id = (SELECT cv_id FROM {cv} WHERE name = 'OBO_REL'))
    
  INNER JOIN {featurepos} FP            	ON F2.feature_id = FP.feature_id
  
  INNER JOIN {featuremap} FM    		ON FM.featuremap_id = FP.featuremap_id
  INNER JOIN {cvterm} C1                ON C1.cvterm_id = FM.unittype_id
  	INNER JOIN {cvterm} C2 ON C2.cvterm_id = F2.type_id
  INNER JOIN {featuremapprop} FMP       ON FMP.featuremap_id = FP.featuremap_id AND
   FMP.type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = 'featuremap_type' AND
   cv_id = (SELECT cv_id FROM {cv} WHERE name = 'local'))
  INNER JOIN {featuremap_organism} FMO 	ON FMO.featuremap_id = FM.featuremap_id
  INNER JOIN {feature} F3 				ON FP.map_feature_id = F3.feature_id
  INNER JOIN {featureposprop} FPP 		ON FPP.featurepos_id = FP.featurepos_id
  INNER JOIN {cvterm} C 				ON C.cvterm_id = FPP.type_id
  INNER JOIN {organism} O 				ON FMO.organism_id = O.organism_id

  

and for hte QTL mview

SELECT FM.name as map_name,
FM.featuremap_id as map_id,
 FMP.value as map_type,
  F3.name as linkage_group,
F3.feature_id as linkage_group_id,
F.uniquename as marker_locus_name,
C1.name as map_unit_type,
C2.name as marker_type,
C4.name as marker_pos_type,
FPP.value as marker_pos,
O.organism_id as organism_id, O.genus as genus, O.species as species, O.common_name as common_name,
F.feature_id as feature_id, FPP.featurepos_id as featurepos_id
FROM {feature} F
--F is the biological_region or parent marker locus
INNER JOIN {feature_relationship} FR 	ON FR.subject_id = F.feature_id AND
 F.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE name = 'biological_region' AND
 cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))
  AND
 FR.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE cvterm.name = 'instance_of' AND
 cv_id = (SELECT cv_id FROM cv WHERE name = 'OBO_REL'))

-- F2 is the marker feature itself
INNER JOIN {feature} F2               	ON FR.object_id = F2.feature_id
-- This mview is just for QTLs
INNER JOIN {cvterm} C ON F2.type_id = C.cvterm_id AND (C.name = 'QTL' OR C.name = 'heritable_phenotypic_marker')
INNER JOIN {featurepos} FP            	ON F2.feature_id = FP.feature_id
INNER JOIN {featuremap} FM    		ON FM.featuremap_id = FP.featuremap_id
INNER JOIN {cvterm} C1                ON C1.cvterm_id = FM.unittype_id
-- C2 is the marker type term
 INNER JOIN {cvterm} C2 ON C2.cvterm_id = F2.type_id
INNER JOIN {featuremapprop} FMP       ON FMP.featuremap_id = FP.featuremap_id AND
FMP.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'featuremap_type' AND
cv_id = (SELECT cv_id FROM cv WHERE name = 'local'))
INNER JOIN {featuremap_organism} FMO 	ON FMO.featuremap_id = FM.featuremap_id
--F3 is the parent feature of the map ie the linkage group
INNER JOIN {feature} F3 				ON FP.map_feature_id = F3.feature_id
INNER JOIN {featureposprop} FPP 		ON FPP.featurepos_id = FP.featurepos_id
INNER JOIN {organism} O 				ON FMO.organism_id = O.organism_id
INNER JOIN {cvterm} C4  ON FPP.type_id = C4.cvterm_id

[bradfordcondon]

ACK! Need to update the module settings to use our start / stop terms which are start position instead of start

[bradfordcondon]

I think the QTL marker name abbreviation is what is breakng it. its not part of the mview. Unchecking hte box in settings doenst fix it. So instead i suggest we replace the JS with this:

this.name = markerData.genetic_marker_locus_name;
			this.nameAbbrev = markerData.marker_name_abbrev ? markerData.marker_name_abbrev : markerData.genetic_marker_locus_name;

so if tehres an abbreviation use it, otherwise, us the full name.

without this code-

with this code -

[bradfordcondon]

Stop term isnt working

[bradfordcondon]

our features appear to be well-formed. they have a start and stop key defined by tripalmap

however, when we get to the JS and constructing the QTLMarker, we no longer have a stop position: