remove pdb data tables: pdb_uniprot_alignment, pdb_uniprot_residue_mapping

[jagnathan]

Part of epic cBioPortal/cbioportal#2054 remove pdb data tables: pdb_uniprot_alignment, pdb_uniprot_residue_mapping

SQL files

• [x] db-scripts/src/main/resources/migration.sql
• [x] db-scripts/src/main/resources/cgds.sql
• [x] seed_mini.sql - no change

Scripts

• [x] core/src/main/scripts/init.sh - modify
• [x] core/src/main/scripts/importPdbUniprotResidueMappingFromSifts.pl - delete
• [x] core/src/main/scripts/importPdbUniprotResidueMappingFromMA.pl - delete
• [x] core/src/main/scripts/prepareEbiSiftsPdbUniprotMappingData.sh - delete
• [x] core/src/main/scripts/convertPdbUniprotMappingFromMaDb.py - delete Java files
• [x] core/src/main/java/org/mskcc/cbio/portal/model/PdbUniprotAlignment.java
• [x] core/src/main/java/org/mskcc/cbio/portal/model/PdbUniprotResidueMapping.java
• [x] core/src/main/java/org/mskcc/cbio/portal/dao/DaoPdbUniprotResidueMapping.java
• [x] core/src/main/java/org/mskcc/cbio/portal/scripts/ImportPdbUniprotResidueMappingFromSifts.java
• [x] core/src/main/java/org/mskcc/cbio/portal/scripts/ImportPdbUniprotResidueMappingFromMA.java

[jagnathan]

https://github.com/cBioPortal/cbioportal/pull/8778

PR created. This can be tested against rc branch.

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