Data objects

qiita_db/sql_connection.py

@@ -53,9 +53,9 @@ def _check_sql_args(self, sql_args):
             otherwise it just returns the execution to the caller
         """
         # Check that sql arguments have the correct type
-        if sql_args and type(sql_args) not in [tuple, list]:
-            raise TypeError("sql_args should be tuple or list. Found %s " %
-                            type(sql_args))
+        if sql_args and type(sql_args) not in [tuple, list, dict]:
+            raise TypeError("sql_args should be tuple, list or dict. Found %s "
+                            % type(sql_args))
 
     @contextmanager
     def _sql_executor(self, sql, sql_args=None, many=False):

qiita_db/support_files/populate_test_db.sql

@@ -47,13 +47,13 @@ INSERT INTO qiita.investigation_study (investigation_id, study_id) VALUES (1, 1)
 INSERT INTO qiita.study_experimental_factor (study_id, efo_id) VALUES (1, 1);
 
 -- Insert the raw data filepaths for study 1
-INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('s_G1_L001_sequences.fastq.gz', 1, '852952723', 1), ('s_G1_L001_sequences_barcodes.fastq.gz', 2, '852952723', 1), ('sequences.fastq.gz', 1, '852952723', 1), ('sequences_barcodes.fastq.gz', 2, '852952723', 1);
+INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('1_s_G1_L001_sequences.fastq.gz', 1, '852952723', 1), ('1_s_G1_L001_sequences_barcodes.fastq.gz', 2, '852952723', 1), ('2_sequences.fastq.gz', 1, '852952723', 1), ('2_sequences_barcodes.fastq.gz', 2, '852952723', 1);
 
 -- Insert the raw data information for study 1
 INSERT INTO qiita.raw_data (filetype_id, submitted_to_insdc) VALUES (2, FALSE), (2, TRUE);
 
 -- Insert (link) the raw data with the raw filepaths
-INSERT INTO qiita.raw_filepath (raw_data_id, filepath_id) VALUES (1, 1), (1, 2), (1, 3), (1, 4);
+INSERT INTO qiita.raw_filepath (raw_data_id, filepath_id) VALUES (1, 1), (1, 2), (2, 3), (2, 4);
 
 -- Insert (link) the study with the raw data
 INSERT INTO qiita.study_raw_data (study_id, raw_data_id) VALUES (1, 1), (1, 2);
@@ -287,10 +287,10 @@ INSERT INTO qiita.preprocessed_data (raw_data_id, preprocessed_params_table, pre
 INSERT INTO qiita.study_preprocessed_data (preprocessed_data_id, study_id) VALUES (1, 1), (2, 1);
 
 -- Insert the preprocessed filepath for raw data 1
-INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('seqs.fna', 4, '852952723', 1), ('seqs.qual', 5, '852952723', 1);
+INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('1_seqs.fna', 4, '852952723', 1), ('1_seqs.qual', 5, '852952723', 1);
 
 -- Insert (link) the preprocessed data with the preprocessed filepaths
-INSERT INTO qiita.preprocessed_filepath (preprocessed_data_id, filepath_id) VALUES (1, 3), (1, 4);
+INSERT INTO qiita.preprocessed_filepath (preprocessed_data_id, filepath_id) VALUES (1, 5), (1, 6);
 
 -- Insert the preprocessed illumina params used for raw data 1
 INSERT INTO qiita.preprocessed_sequence_illumina_params (trim_length) VALUES (151), (100);
@@ -305,7 +305,7 @@ INSERT INTO qiita.reference (reference_name, reference_version, sequence_filepat
 INSERT INTO qiita.processed_params_uclust (similarity, enable_rev_strand_match, suppress_new_clusters, reference_id) VALUES (0.97, TRUE, TRUE, 1);
 
 -- Insert the biom table filepath for processed data 1
-INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('study_1001_closed_reference_otu_table.biom', 6, '852952723', 1);
+INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('1_study_1001_closed_reference_otu_table.biom', 6, '852952723', 1);
 
 -- Insert (link) the processed data with the processed filepath
-INSERT INTO qiita.processed_filepath (processed_data_id, filepath_id) VALUES (1, 5);
+INSERT INTO qiita.processed_filepath (processed_data_id, filepath_id) VALUES (1, 7);