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DEIB-GECO / GMQL

GMQL - GenoMetric Query Language
http://www.bioinformatics.deib.polimi.it/geco/
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Metadata values with quotation mark #43

Closed acanakoglu closed 7 years ago

acanakoglu commented 7 years ago

Double(or single) quotation mark between the double(or single) quotation needs to be escaped by compiler. This could be applied to other string literal fields.

pp86 commented 7 years ago

Ok, Could you provide an example?

Doesn't:

work?

acanakoglu commented 7 years ago

Yes, this could resolve the problem however in the case of both type of quotation marks available as value? In HG19_ENCODE_BED public dataset, there are samples with cell_description with both quotation mark. As an example:

B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209)

acanakoglu commented 7 years ago

it is not correct yet.

marcomass commented 7 years ago

@acanakoglu Still not working completely. In the following case: DATA_SET_VAR = SELECT(cell_description == "B lymphocyte, \"The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209)") HG19_ENCODE_NARROW; escape \ should be added also in the second " contained in the value of the attribute cell_description

pp86 commented 7 years ago

@marcomass

Could you report the query as you had written?

marcomass commented 7 years ago

@pp86 Sorry, I do not understand. The query is just the select I wrote plus its materialize DATA_SET_VAR = SELECT(cell_description == "B lymphocyte, \"The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209)") HG19_ENCODE_NARROW; materialize DATA_SET_VAR INTO DATA_SET_VAR; Possibly the issue depend on adding the escape\ also to the second " contained as value of the attribute; should this be done by Arif? @acanakoglu

acanakoglu commented 7 years ago

This is a problem of GMQL-WEB. I am opening issue again under GMQL-WEB project. The selection query should be like the below: DATA_SET_VAR = SELECT(cell_description == "B lymphocyte, \"The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male.\" - ATCC. (PMID: 14086209)") HG19_ENCODE_NARROW;

@pp86 : I check on the server, and compilation and execution is working properly