j@287: (cl:in-package #:amuse-database-admin)
j@287: 
j@287: ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
j@287: ;;; Constructors
j@287: 
j@287: (defun make-amuse-dataset-identifier (dataset-id)
j@287:   (make-instance 'amuse-dataset-identifier
j@287: 		 :dataset-id dataset-id))
j@287: 
j@287: (defun %make-amuse-dataset (dataset-identifier description
j@287: 			    composition-identifiers)
j@287:   (make-instance 'amuse-dataset
j@287: 		 :%data composition-identifiers
j@287: 		 :identifier dataset-identifier
j@287: 		 :description description))
j@287: 
j@287: 
j@287: ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
j@287: ;;; Database functions
j@287: 
j@287: (defun make-new-dataset (description &optional (database
j@287: 						*amuse-database*))
j@287:   "A dataset is a set of pieces used for a particualar analytical
j@287: task. A dataset is not necessarily the same thing as a corpus or
j@287: collection (are these things different?). Corpus indicates that a set
j@287: of pieces have been curated in some way and in that sense `belong
j@287: together'. A dataset is just simply a set of pieces gathered together
j@287: to analyse, and the pieces can be from any corpus or backend."
j@287:   (let (dataset-id)
j@287:     #.(clsql:locally-enable-sql-reader-syntax)
j@287:     (clsql:insert-records :into "amuse_datasets"
j@287: 			  :attributes '([description])
j@287: 			  :values (list description)
j@287: 			  :database database)
j@287:     #.(clsql:locally-disable-sql-reader-syntax)
j@287:     (setf dataset-id (clsql-mysql::mysql-insert-id
j@287: 		      (clsql-mysql::database-mysql-ptr
j@287: 		       database)))
j@287:     (make-amuse-dataset-identifier dataset-id)))
j@287: 
j@287: (defun assign-composition-to-dataset (composition-identifier
j@287: 				      dataset-identifier
j@287: 				      &optional (database
j@287: 						 *amuse-database*))
j@287:   (clsql:execute-command (format nil "
j@287: INSERT INTO amuse_datasets_join
j@287: SET dataset_id := ~S,
j@287: implementation_id := (SELECT get_impl_id('~A')),
j@287: composition_id := ~S;"
j@287: 					(dataset-id dataset-identifier)
j@287: 					(implementation-namestring
j@287: 					 composition-identifier)
j@287: 					(composition-id
j@287: 					 composition-identifier)))
j@287: 			 :database database)
j@287: 
j@289: (defun assign-compositions-to-dataset (composition-identifiers
j@289: 				       dataset-identifier
j@289: 				       &optional (database
j@289: 						  *amuse-database*))
j@289:   "This should be done more sensibly."
j@289:   (loop for identifier in composition-identifiers
j@289:      do (assign-composition-to-dataset identifier
j@289: 				       dataset-identifier
j@289: 				       database)))
j@289: 
j@295: (defun make-composition-identifiers-from-file (package pathname)
j@295:   "This reads a file that contains one id per line, and returns a list
j@295: of composition-identifiers (specialised on package). It is useful for
j@295: reading files that have been exported from the database, for use with
j@295: the above functions."
j@295:   (with-open-file (stream pathname :direction :input)
j@295:     (loop for id = (read stream nil)
j@295:        while id
j@295:        collect (make-composition-identifier package id))))
j@295: 
j@287: (defun get-dataset (dataset-identifier &optional (database
j@287: 						  *amuse-database*))
j@287:   (let ((dataset-header (clsql:query (format nil "
j@287: SELECT description
j@287: FROM amuse_datasets
j@287: WHERE dataset_id = ~S" (dataset-id dataset-identifier))
j@287: 				     :database database
j@287: 				     :flatp t
j@287: 				     :field-names nil))
j@287: 	(dataset-rows (clsql:query (format nil "
j@287: SELECT implementation_name, composition_id
j@287: FROM amuse_datasets_join
j@287: LEFT JOIN amuse_implementations
j@287: USING (implementation_id)
j@287: WHERE dataset_id = ~S"
j@287: 					   (dataset-id
j@287: 					    dataset-identifier))
j@287: 				   :flatp t
j@287: 				   :field-names nil
j@287: 				   :database database)))
j@287:     (%make-amuse-dataset dataset-identifier (car dataset-header)
j@287: 			 (%init-dataset-rows dataset-rows))))
j@287: 
j@287: (defun %init-dataset-rows (dataset-rows)
j@287:   (loop for row in dataset-rows
j@287:      collect (make-composition-identifier (find-package
j@287: 					   (first row)) (second row))
j@287:      into composition-identifiers
j@287:      finally (return composition-identifiers)))