REST API request for use with the Spectra package

[jorainer]

Dear @tsufz and @meier-rene ,

in order to enable integration of MassBank with the Spectra package I would need the following functionality being part of the REST API:

1) Get all spectrum IDs available (i.e. RECORD.ACCESSION) 2) Get spectra data: one element per spectrum with the following fields/rows. Here it would be important to allow specifying which fields to return in the query (to speed-up things) for the provided IDs (RECORD.ACCESSION).

• RECORD.ACCESSION
• RECORD.RECORD_TITLE
• RECORD.DATE
• RECORD.AUTHORS
• RECORD.LICENSE
• RECORD.COPYRIGHT
• RECORD.PUBLICATION
• RECORD.AC_MASS_SPECTROMETRY_MS_TYPE
• RECORD.AC_MASS_SPECTROMETRY_ION_MODE
• RECORD.PK_SPLASH
• COMPOUND.ID
• IONIZATION (from AC_MASS_SPECTROMETRY)
• IONIZATION_VOLTAGE (from AC_MASS_SPECTROMETRY)
• BASE_PEAK (from MS_FOCUSED_ION)
• PRECURSOR_M/Z (from MS_FOCUSED_ION)
• PRECURSOR_TYPE (from MS_FOCUSED_ION) 3) Get compound data:
• COMPOUND.ID
• COMPOUND.CH_FORMULA
• COMPOUND.CH_EXACT_MASS
• COMPOUND.CH_SMILES
• COMPOUND.CH_IUPAC
• compound name(s) 4) Get peaks: return the follwing fields for the provided IDs (RECORD.ACCESSION).
• PEAK.RECORD
• PEAK.PK_PEAK_MZ
• PEAK.PK_PEAK_INTENSITY

Let me know if you need anything else or if I could be of any help. Also, let me know if that is possible at all, or if I should rather work on a way to directly access the MySQL database.

cheers, jo

[meier-rene]

Thank you for your ideas. If you want to have your sql views integrated please put them in an issue and i will insert them at the appropriate places.

[jorainer]

I posted the views as issue #265