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- PianaInsertSQL
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- CreateIndice
- DeleteElementsFromTempTable
- DeleteExternalDatabase
- DeleteInteraction
- DeleteInteractionMethod
- DeleteInteractionProteinSource
- DeleteInteractionScores
- DeleteRecords
- DeleteTempTableIdentifier
- DropIndice
- InsertBlastResult
- InsertCog
- InsertElementsFromTempTable
- InsertExternalDatabaseInformationType
- InsertGeneralizedProteinExternalID
- InsertGo
- InsertGo_term2term_distance
- InsertInteraction
- InsertInteractionFeatures
- InsertInteractionMethod
- InsertInteractionProteinSource
- InsertInteractionScores
- InsertNewExternalDatabase
- InsertNewProteinIdType
- InsertProtein
- InsertProteinAttributeRelationship
- InsertProteinCathRelationship
- InsertProteinCode2
- InsertProteinDBAliRelationship
- InsertProteinExternalID
- InsertProteinPdbCode
- InsertProteinPianaCounter
- InsertProteinScopRelationship
- InsertProteinSimilarity
- InsertReactome
- InsertSequence
- InsertSpecies
- InsertTemporalTable
- MultipleInsert
- UpdateENUMcolumn
- UpdateSourceDBID
- UpdateSourceDBIDfromTempTable
- UpdateSourceDBSet
- UpdateSpeciesKingdom
- UpdateTableColumn
class CreateIndice(PianaInsertSQL) |
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Generates sql statement to insert information on a Buffer Element Object |
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Static methods defined here:
- get_sqlquery(table, indice_name, columns)
- "columns" must be a tuple with the name of the columns
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class DeleteInteractionMethod(PianaInsertSQL) |
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Generates sql statement to delete an interaction entry from table interactionMethod
It can be used to delete a particular interactionPiana or just those entries that belong to a specific source db or those with a method ID
- if interactionPiana_value 'not None' --> delete entries where interactionPiana = interactionPiana_value
- if sourceDBID_value 'not None' --> delete entries where sourceDBID = sourceDBID_value
- if methodID_value 'not None' --> delete entries where methodID = methodID_value
Only one argument can be 'not None' |
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Static methods defined here:
- get_sqlquery(interactionPiana_value=None, sourceDBID_value=None, methodID_value=None)
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class DeleteInteractionProteinSource(PianaInsertSQL) |
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Generates sql statement to delete an interaction protein source entry from table interactionProteinSource
It can be used to delete a particular interactionPiana or just those entries that belong to a specific source db
- if interactionPiana_value 'not None' --> delete entries where interactionPiana = interactionPiana_value
- if sourceDBID_value 'not None' --> delete entries where sourceDBID = sourceDBID_value
Only one argument can be 'not None' |
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Static methods defined here:
- get_sqlquery(interactionPiana_value=None, sourceDBID_value=None)
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class DeleteInteractionScores(PianaInsertSQL) |
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Generates sql statement to delete an interaction scores entry from table interactionScores
It can be used to delete a particular interactionPiana or just those entries that belong to a specific source db
- if interactionPiana_value 'not None' --> delete entries where interactionPiana = interactionPiana_value
- if sourceDBID_value 'not None' --> delete entries where sourceDBID = sourceDBID_value
Only one argument can be 'not None' |
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Static methods defined here:
- get_sqlquery(interactionPiana_value=None, sourceDBID_value=None)
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class InsertBlastResult(PianaInsertSQL) |
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Generates sql statement to insert blast result on table blastResults |
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Static methods defined here:
- get_sqlquery(sequenceID_A, sequenceID_B, score, bit_score, start_A, end_A, start_B, end_B, identities, similarity, gaps, program, filter, buffer=None)
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class InsertCog(PianaInsertSQL) |
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Generates sql statement to insert information on table cog |
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Static methods defined here:
- get_sqlquery(cogID_value, cogDescription_value, cogFunction_value, cogSource_value, buffer=None)
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class InsertGo(PianaInsertSQL) |
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Generates sql statement to insert information on table go |
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Static methods defined here:
- get_sqlquery(goID_value, go_name_value, go_acc_value, go_term_type_value, go_distance2root_value, goSource_value, buffer=None)
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class InsertInteraction(PianaInsertSQL) |
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Generates sql statement to insert information on table interaction |
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Static methods defined here:
- get_sqlquery(interactionPiana_value, proteinPianaA_value, isSourceA_value, proteinPianaB_value, isSourceB_value, sourceDBID_value, interactionConfidence_value, buffer=None)
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class InsertInteractionScores(PianaInsertSQL) |
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Generates sql statement to insert information on table interactionScores |
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Static methods defined here:
- get_sqlquery(interactionPiana_value, sourceDBID_value, equiv_nscore_value, equiv_nscore_transferred_value, equiv_fscore_value, equiv_pscore_value, equiv_hscore_value, array_score_value, array_score_transferred_value, experimental_score_value, experimental_score_transferred_value, database_score_value, database_score_transferred_value, textmining_score_value, textmining_score_transferred_value, combined_score_value)
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class InsertProteinAttributeRelationship(PianaInsertSQL) |
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Generates sql statement to insert information on protein attributes relationship tables
the tables must follow the structure:
(currently for tables:
proteinCog_table
proteinGo_table
proteinEC_table
proteinSpecies_table
proteinDescription_table
proteinKeyword_table
proteinFunction_table
proteinSubcellularLocation_table
) |
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Static methods defined here:
- get_sqlquery(attribute_relationship_table, attribute_value, proteinPiana_value, attributeSource_value, buffer=None)
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class InsertProteinCode2(PianaInsertSQL) |
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Generates sql statement to insert protein information on tables that follow the structure:
code ID (external code, for example interProID) (string)
proteinPiana (internal piana protein code)
description (description of codeID) (string)
codeSource (name of origin of the data being inserted)
Instead of writing one class for each table, this class is designed to handle all these similar tables
current tables managed through this class are: interPro and pfam |
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Static methods defined here:
- get_sqlquery(table_name, code_value, proteinPiana_value, description_value, codeSource_value, buffer=None)
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class InsertProteinDBAliRelationship(PianaInsertSQL) |
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Generates sql statement to insert information of DBAli clustering of pibase patches to table proteinDBAliCluster |
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Static methods defined here:
- get_sqlquery(dbali_cluster_id_value, proteinPiana_value, clustering_method_value, patch_residues_value, protein_dbali_cluster_source)
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class InsertProteinExternalID(PianaInsertSQL) |
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Generates sql statement to insert protein ids on tables that follow the structure:
codeID (external code, for example uniprotEntry) (string)
proteinPiana (internal piana protein code)
codeSource (name of origin of the data being inserted)
isPrimary [optional] (indicates whether it is a primary code or not
Instead of writing one class for each table, this class is designed to handle all these similar tables. This is somehow
dangerous, since we are hardcoding the order of the fields of the tables. If the order is changed, this class
will not work... and we would need to de-generalize it to insert information separately in each table.
All protein identifier tables are managed through this class |
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Static methods defined here:
- get_sqlquery(table_name, code_value, proteinPiana_value, codeSource_value, isPrimary_value=None, buffer=None)
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class InsertProteinPdbCode(PianaInsertSQL) |
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Generates sql statement to insert protein information on tables that follow the structure:
code ID (external code, for example PDB ID) (string)
proteinPiana (internal piana protein code)
chain ID (specific to codeID) (string)
codeSource (name of origin of the data being inserted)
Instead of writing one class for each table, this class is designed to handle all these similar tables
current tables managed through this class are: pdb |
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Static methods defined here:
- get_sqlquery(table_name, code_value, proteinPiana_value, chain_value, codeSource_value, combined_pdb_chain, range_value=None, buffer=<type 'buffer'>)
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class InsertProteinPianaCounter(PianaInsertSQL) |
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Generates sql statement to generate the SQL statement that obtains a new proteinPiana identifier from proteinPianaCounter table
After getting the new proteinPiana identifier, the method calling this class must make sure that the counter in increased by 1 |
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Static methods defined here:
- get_sqlquery(updated_value, updated_col)
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class InsertSequence(PianaInsertSQL) |
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Generates sql statement to insert information on sequence
Buffer cannot be used |
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Static methods defined here:
- get_sqlquery(sequenceID_value, sequence_value, sequenceMD5_value, sequenceLength_value, sequenceMW_value, sequenceIP_value, sourceDBID, buffer=None)
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class InsertSpecies(PianaInsertSQL) |
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Generates sql statement to insert information on table species |
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Static methods defined here:
- get_sqlquery(taxID_value, speciesName_value, speciesDescription_value, speciesSource_value, speciesKingdom_value=None, buffer=None)
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class InsertTemporalTable(PianaInsertSQL) |
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Generates sql statement to insert data in a temporal table:
"db_temp_buffer" As all data inserted in temporal table must be processed before the connection to the database is closed, it is mandatory to pass a
te buffer that contains the information about how to do the queries
"conditions" is a list of the name of the columns that will be used to update parent table |
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Static methods defined here:
- get_sqlquery(table_name, column_values, sourceDBID, db_temp_buffer, conditions, buffer=None)
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class MultipleInsert(PianaInsertSQL) |
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Generates sql statement to insert information on a Buffer Element Object |
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Static methods defined here:
- get_sqlquery(table, columns, values)
- "columns" must be a tuple with the name of the columns
"values" must be a dictionary which keys are the tuples of values to be inserted
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class PianaInsertSQL |
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General class for generating Piana SQL INSERT queries. All SQL queries inserting data into piana should be extensions of this class |
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Static methods defined here:
- get_sqlquery()
- Override this with the sql query that inserts the desired values
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class UpdateENUMcolumn(PianaInsertSQL) |
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Generates sql statement to update an ENUM datatype in a table in the database |
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Static methods defined here:
- get_sqlquery(table, column, list_enum)
- "table" is the table that contains the ENUM column
"column" is the name of the column to update
"list" is the list with all the values of the ENUM Set
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class UpdateSourceDBID(PianaInsertSQL) |
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Generates sql statement to update SET datatype in a table in the database
Used to insert or remove and element in a sourceDBID SET datatype |
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Static methods defined here:
- get_sqlquery(table, field, value, conditions=[], type='insert')
- Used to insert or remove an element in sourceDBID SET datatype
"type" can be "insert" to add a new element
"remove" to remove an element
"field" is the SourceDBID field name
"value" is the value to add/remove (it must be in its decimal value!)
"conditions" is a list of tuples of length 2, with the following format: (field_name,value)
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class UpdateSourceDBSet(PianaInsertSQL) |
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Generates sql statement to update SET datatype in a table in the database
Used to insert or remove and element in a sourceDBID SET datatype |
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Static methods defined here:
- get_sqlquery(table, field, values)
- Used to insert or remove an element in sourceDBID SET datatype
"field" is the SET field name
"values" must be a list of all current values to be in the SET datatype
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