Update tractability plugin in data pipeline

[andrewhercules]

In order to process the latest tractability .tsv file generated by ChEMBL, we will need to update the pipeline as the headings for the small molecule modality have changed. Also, there is now a section for other clinical modalities (e.g. protein, enzyme) with the same clinical precedence buckets 1, 2, and 3. And there is also a single string of ChEMBL IDs that support the clinical precedence buckets 1, 2, and 3 for small molecule, antibody, and other clinical modalities.

As such, @cmalangone, can you please update the pipeline with the following changes:

1. Update the pipeline to use the data about other clinical modalities and add an entry in the gene index tractability object - see below for a scaffold of what it could look like:

"tractability": {
  "smallmolecule": {},
  "antibody": {},
  "other_modalities": {
    "buckets": [
      1
    ],
    "categories": {
      "clinical_precedence": 1
    }
  }
}

For other clinical modalities, the buckets are 1, 2, and 3 and the categories are "clinical_precedence".

2. Update the pipeline to use the new small molecule column headings

Old column name / heading	New column name / heading
Bucket_1	Bucket_1_sm
Bucket_2	Bucket_2_sm
Bucket_3	Bucket_3_sm
Bucket_4	Bucket_4_sm
Bucket_5	Bucket_5_sm
Bucket_6	Bucket_6_sm
Bucket_7	Bucket_7_sm
Bucket_8	Bucket_8_sm
Bucket_sum	Bucket_sum_sm
Top_bucket	Top_bucket_sm
Category	Category_sm
Clinical_Precedence	Clinical_Precedence_sm
Discovery_Precedence	Discovery_Precedence_sm
Predicted_Tractable	Predicted_Tractable_sm
PDB_Known_Ligand	PDB_Known_Ligand
ensemble	DrugEBIlity_score
High_Quality_ChEMBL_compounds	High_Quality_ChEMBL_compounds
Small_Molecule_Druggable_Genome_Member	Small_Molecule_Druggable_Genome_Member

[andrewhercules]

ChEMBL have made the data available and it has been uploaded into otar001-core/Tractability/20.04

[andrewhercules]

Based on a conversation with @cmalangone, we will not update the pipeline to process the ChEMBL IDs and labels for this release. Rather, we will work with ChEMBL to update the JSON generated by the tractability pipeline for 20.06.

[cmalangone]

Point 1 and 2 done.
Had a conversation with @LucaFumis about the format for the index.

PR done and merge.
Run a first test and no issue came up.

[andrewhercules]

Thank you @cmalangone - the data is now available in the API! 👍