Viewing missing methods/software, part III: Table views

Repeat of the design goals for viewing missing methods/software: 

1. Allow users to see on a tree (using branch coloring) which questions don't have methods, which methods aren't in software, etc.
2. Allow users to arrange the order in which things are displayed: question->criterion->method, or question->character type 1 -> tree type -> branch length type -> data format -> software
3. Allow users to filter by option (only show methods relating to DNA data, for example)
4. Make it fast, intuitive, etc.

I think a way to address these is to create table views; one has all the available methods ("actualmethods"), one has all the available methods and software ("actualsoftware"), and one could have all the imaginable combinations of all options ("biggie"). That way, all the database logic for combining the primitive tables (method->methodtotreetypetobranchlengthtype->treetype, for example) is taken care of at the view creation step, rather than requiring it all to be created on the fly when a user re-orders options. [Aha: so this is a reason for using MVC]. To draw the tree of methods/software based on user choice, one gets the tree structure by looking in the [actually hypothetical] "biggie" table; combinations (edges on the display tree) present in the "actualsoftware" table are shown in the "+methods +software" color (purple?), combinations not present there but in the "actualmethods" table get the "+methods -software" color (black?), and others get the "-methods -software" color (gray?). The only problem with this is the size of the "biggie" table view: except for built-in relations between general and posed questions and posed questions and relevant combinations of characters (see schema), it's basically a massive cross join. That means that if there are 2 data formats, 6 tree formats, and 7 platforms, the table has 2 x 6 x 7 = 84 rows.  The actual "biggie" table, having info on all the imaginable options (input formats, tree types, character types, criteria, etc.) would currently have 1,361,817,600 (1.3 billion) distinct rows. Instead of creating such a huge table, I will have a view ("generaltoposedtochartype") containing the essential relations between general question, posed question, and character combinations (only 2,480 rows currently) and then just have the program returning possible branches for the tree know that all the other options can essentially be cross joined.

I had a bit of trouble creating the initial "actualmethods" view efficiently; Hilmar Lapp, an IT guru here at NESCent (codes for BioPerl, organizes hackathons, organizes people) edited the query to make it more efficient and eliminate return of duplicate rows (without using "distinct"). Below I've posted the sql statement used to make these views in case it's useful for others (or for me in the future).

-- All actual methods

CREATE VIEW 

actualmethods

(

actualmethods_generalquestion,

actualmethods_posedquestion,

actualmethods_char1,

actualmethods_char2,

actualmethods_char3,

actualmethods_treetype,

actualmethods_branchlengthtype,

actualmethods_criterion,

actualmethods_method

)

AS

SELECT

pq.posedquestion_generalquestion,

pq.posedquestion_id,

  cc.charactercombination_char1, 

cc.charactercombination_char2, 

cc.charactercombination_char3,

mttblt.methodtotreetypetobranchlengthtype_treetype,

mttblt.methodtotreetypetobranchlengthtype_branchlengthtype,

   mc.methodtocriterion_criterion,

mttblt.methodtotreetypetobranchlengthtype_method

FROM

methodtotreetypetobranchlengthtype mttblt,

methodtocriterion mc,

methodtocharactercombination mcc,

methodtoposedquestion mpq,

posedquestion pq,

charactercombination cc,

posedquestiontocharactercombination pqcc

WHERE

methodtocriterion_method=methodtotreetypetobranchlengthtype_method

AND  

methodtocharactercombination_method=methodtotreetypetobranchlengthtype_method

AND  

methodtocharactercombination_charactercombination=charactercombination_id

AND  

methodtoposedquestion_method=methodtotreetypetobranchlengthtype_method

AND

methodtoposedquestion_posedquestion=posedquestion_id

AND

posedquestiontocharactercombination_posedquestion=posedquestion_id

AND  

posedquestiontocharactercombination_charactercombination=charactercombination_id

;

-- all actual methods and software

CREATE VIEW 

actualsoftware

(

actualsoftware_generalquestion,

actualsoftware_posedquestion,

actualsoftware_char1,

actualsoftware_char2,

actualsoftware_char3,

actualsoftware_treetype,

actualsoftware_branchlengthtype,

actualsoftware_criterion,

actualsoftware_method,

actualsoftware_dataformat,

actualsoftware_treeformat,

actualsoftware_applicationkind,

actualsoftware_platform,

actualsoftware_program

)

AS

SELECT

pq.posedquestion_generalquestion,

pq.posedquestion_id,

cc.charactercombination_char1, 

cc.charactercombination_char2, 

cc.charactercombination_char3,

mttblt.methodtotreetypetobranchlengthtype_treetype,

mttblt.methodtotreetypetobranchlengthtype_branchlengthtype,

mc.methodtocriterion_criterion,

mttblt.methodtotreetypetobranchlengthtype_method,

pdf.programtodataformat_dataformat, 

ptf.programtotreeformat_treeformat, 

ppak.programtoplatformappkind_applicationkind, 

ppak.programtoplatformappkind_platform, 

  pmcc.programtomethodtocharactercombination_program

FROM

methodtotreetypetobranchlengthtype mttblt,

methodtocriterion mc,

methodtocharactercombination mcc,

methodtoposedquestion mpq,

posedquestion pq,

charactercombination cc,

posedquestiontocharactercombination pqcc,

programtodataformat pdf,

programtotreeformat ptf,

programtomethodtocharactercombination pmcc,

programtoplatformappkind ppak

WHERE

methodtocriterion_method=methodtotreetypetobranchlengthtype_method

AND  

methodtocharactercombination_method=methodtotreetypetobranchlengthtype_method

AND  

methodtocharactercombination_charactercombination=charactercombination_id

AND  

methodtoposedquestion_method=methodtotreetypetobranchlengthtype_method

AND 

methodtoposedquestion_posedquestion=posedquestion_id

AND 

posedquestiontocharactercombination_posedquestion=posedquestion_id

AND  

posedquestiontocharactercombination_charactercombination=charactercombination_id

AND 

programtomethodtocharactercombination_methodtocharactercombination=methodtocharactercombination_id

AND 

programtomethodtocharactercombination_program=programtodataformat_program

AND 

programtodataformat_program=programtotreeformat_program

AND 

programtotreeformat_program=programtoplatformappkind_program

;

-- all general+posedquestions+chartypes

CREATE VIEW

generaltoposedtochartype

(

generaltoposedtochartype_generalquestion,

generaltoposedtochartype_posedquestion,

generaltoposedtochartype_char1,

generaltoposedtochartype_char2,

generaltoposedtochartype_char3

)

AS

SELECT

generalquestion_id,

posedquestion_id, 

charactercombination.charactercombination_char1, 

charactercombination.charactercombination_char2, 

charactercombination.charactercombination_char3

FROM

charactercombination,

posedquestiontocharactercombination,

posedquestion,

generalquestion

WHERE

posedquestion_generalquestion=generalquestion_id

AND

posedquestiontocharactercombination_charactercombination=charactercombination_id

AND

posedquestiontocharactercombination_posedquestion=posedquestion_id

;

-- all conceivable combinations of parameters other than question and chartype (a massive cross join, probably not used)

CREATE VIEW

crossjoinoptions

(

crossjoinoptions_treetype,

crossjoinoptions_branchlengthtype,

crossjoinoptions_criterion,

crossjoinoptions_dataformat,

crossjoinoptions_treeformat,

crossjoinoptions_applicationkind,

crossjoinoptions_platform

)

AS

SELECT 

treetype_id, 

branchlengthtype_id, 

criterion_id,

dataformat_id,

treeformat_id,

applicationkind_id,

platform_id

FROM

treetype,

branchlengthtype,

criterion,

dataformat,

treeformat,

applicationkind,

platform

;