How can this be translated into postgresql? - sql

Question

I am fairly new to sql in general, and I am trying to work with a database which is extremely large. Now, on the website's examples, there is this query
SELECT m.chembl_id AS compound_chembl_id,
s.canonical_smiles,
r.compound_key,
NVL(TO_CHAR(d.pubmed_id),d.doi) AS pubmed_id_or_doi,
a.description AS assay_description, act.standard_type,
act.standard_relation,
act.standard_value,
act.standard_units,
act.activity_comment
FROM compound_structures s,
molecule_dictionary m,
compound_records r,
docs d,
activities act,
assays a,
target_dictionary t
WHERE s.molregno (+) = m.molregno
AND m.molregno = r.molregno
AND r.record_id = act.record_id
AND r.doc_id = d.doc_id
AND act.assay_id = a.assay_id
AND a.tid = t.tid
AND t.chembl_id = 'CHEMBL1827';
because of this (+) and this NVL I assumed it is Oracle. I am working on pgadmin4 and all my attempts at translating this after doing some research, resulted in errors. Example of my attempt and the error given bellow
SELECT m.chembl_id AS compound_chembl_id,
s.canonical_smiles,
r.compound_key,
COALESCE(CAST(d.pubmed_id AS varchar),d.doi) AS pubmed_id_or_doi,
a.description AS assay_description,
act.standard_type,
act.standard_relation,
act.standard_value,
act.standard_units,
act.activity_comment
FROM compound_structures s,
compound_records r,
docs d,
activities act,
assays a,
target_dictionary t
LEFT OUTER JOIN molecule_dictionary m ON s.molregno = m.molregno
WHERE m.molregno = r.molregno
AND r.record_id = act.record_id
AND r.doc_id = d.doc_id
AND act.assay_id = a.assay_id
AND a.tid = t.tid
AND t.chembl_id = 'CHEMBL1827';
ERROR: invalid reference to FROM-clause entry for table "s"
LINE 16: LEFT OUTER JOIN molecule_dictionary m ON s.molregno = m.molr...
^
HINT: There is an entry for table "s", but it cannot be referenced from this part of the
query.
SQL state: 42P01
Character: 492
Could someone help me?

Answer 1

Don't mix the old, ancient implicit joins and explicit JOIN operator:
SELECT m.chembl_id AS compound_chembl_id,
s.canonical_smiles,
r.compound_key,
COALESCE(CAST(d.pubmed_id AS varchar),d.doi) AS pubmed_id_or_doi,
a.description AS assay_description,
act.standard_type,
act.standard_relation,
act.standard_value,
act.standard_units,
act.activity_comment
FROM compound_structures s
LEFT JOIN molecule_dictionary m ON s.molregno = m.molregno
JOIN compound_records r ON m.molregno = r.molregno
JOIN docs d ON r.doc_id = d.doc_id
JOIN activities act ON r.record_id = act.record_id
JOIN assays a ON act.assay_id = a.assay_id
JOIN target_dictionary t ON a.tid = t.tid
WHERE t.chembl_id = 'CHEMBL1827';
I hope I got the direction of the outer join correct - I haven't used that Oracle syntax for decades (note that even Oracle recommends to stop using it).
But the inner join on the following tables effectively turns that outer join back into an inner join - I don't think the Oracle syntax changes that (meaning: I think that attempt on an outer join in the original query was wrong to begin with). So maybe you can simplify the LEFT JOIN to a JOIN. I am not sure if that outer join actually makes sense in the Oracle query.

Answer 2

Consider:
SELECT
m.chembl_id AS compound_chembl_id,
s.canonical_smiles,
r.compound_key,
COALESCE((d.pubmed_id)::text, d.doi) AS pubmed_id_or_doi,
a.description AS assay_description,
act.standard_type,
act.standard_relation,
act.standard_value,
act.standard_units,
act.activity_comment
FROM
compound_structures s
INNER JOIN molecule_dictionary m ON s.molregno = m.molregno
INNER JOIN compound_records r ON m.molregno = r.molregno
INNER JOIN docs d ON r.doc_id = d.doc_id
INNER JOIN activities act ON r.record_id = act.record_id
INNER JOIN assays a ON act.assay_id = a.assay_id
INNER JOIN target_dictionary t ON a.tid = t.tid AND t.chembl_id = 'CHEMBL1827'
Rationale:
use standard, explicit joins everywhere; old school joins have been deprecated 20 years ago!
COALESCE() is more standard than NVL()
a LEFT JOIN followed by INNER JOINs that relate to columns coming for the left table is actually equivalent to INNER JOIN