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Merge pull request #74 from josenavas/checksum
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Adding checksum into the DB
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@wasade
wasade committed Jun 10, 2014
2 parents a120cce + a68eb5e commit d1d64e1
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Showing 5 changed files with 3,050 additions and 2,881 deletions.
3 changes: 3 additions & 0 deletions qiita_db/support_files/initialize.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -33,3 +33,6 @@ INSERT INTO qiita.required_sample_info_status (status) VALUES ('received'), ('in

-- Populate filepath_type table
INSERT INTO qiita.filepath_type (filepath_type) VALUES ('raw_sequences'), ('raw_barcodes'), ('raw_spectra'), ('preprocessed_sequences'), ('preprocessed_sequences_qual'), ('biom');

-- Populate checksum_algorithm table
INSERT INTO qiita.checksum_algorithm (name) VALUES ('crc32')
6 changes: 3 additions & 3 deletions qiita_db/support_files/populate_test_db.sql
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Expand Up @@ -47,7 +47,7 @@ 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) VALUES ('s_G1_L001_sequences.fastq.gz', 1), ('s_G1_L001_sequences_barcodes.fastq.gz', 2), ('sequences.fastq.gz', 1), ('sequences_barcodes.fastq.gz', 2);
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 the raw data information for study 1
INSERT INTO qiita.raw_data (filetype_id, submitted_to_insdc) VALUES (2, FALSE), (2, TRUE);
Expand Down Expand Up @@ -287,7 +287,7 @@ 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) VALUES ('seqs.fna', 4), ('seqs.qual', 5);
INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('seqs.fna', 4, '852952723', 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);
Expand All @@ -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) VALUES ('study_1001_closed_reference_otu_table.biom', 6);
INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('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);
140 changes: 77 additions & 63 deletions qiita_db/support_files/qiita-db.dbs
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Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,13 @@ If a given analysis is not in child_id, it is the root of the chain. </comment>
<fk_column name="term_id" pk="term_id" />
</fk>
</table>
<table name="checksum_algorithm" >
<column name="checksum_algorithm_id" type="bigserial" jt="-5" mandatory="y" />
<column name="name" type="varchar" jt="12" mandatory="y" />
<index name="pk_checksum_algorithm" unique="PRIMARY_KEY" >
<column name="checksum_algorithm_id" />
</index>
</table>
<table name="column_controlled_vocabularies" >
<comment>Table relates a column with a controlled vocabulary.</comment>
<column name="controlled_vocab_id" type="bigserial" jt="-5" mandatory="y" />
Expand Down Expand Up @@ -319,6 +326,8 @@ If a given analysis is not in child_id, it is the root of the chain. </comment>
<column name="filepath_id" type="bigserial" jt="-5" mandatory="y" />
<column name="filepath" type="varchar" jt="12" mandatory="y" />
<column name="filepath_type_id" type="bigint" jt="-5" mandatory="y" />
<column name="checksum" type="varchar" jt="12" mandatory="y" />
<column name="checksum_algorithm_id" type="bigint" jt="-5" mandatory="y" />
<index name="pk_filepath" unique="PRIMARY_KEY" >
<column name="filepath_id" />
</index>
Expand All @@ -328,6 +337,9 @@ If a given analysis is not in child_id, it is the root of the chain. </comment>
<fk name="fk_filepath" to_schema="qiita" to_table="filepath_type" >
<fk_column name="filepath_type_id" pk="filepath_type_id" />
</fk>
<fk name="fk_filepath_0" to_schema="qiita" to_table="checksum_algorithm" >
<fk_column name="checksum_algorithm_id" pk="checksum_algorithm_id" />
</fk>
</table>
<table name="filepath_type" >
<column name="filepath_type_id" type="bigserial" jt="-5" mandatory="y" />
Expand Down Expand Up @@ -1159,69 +1171,70 @@ Controlled Vocabulary]]></comment>
</schema>
<connector name="PostgreSQL" database="PostgreSQL" driver_class="org.postgresql.Driver" driver_jar="postgresql-9.2-1003.jdbc3.jar" host="localhost" port="5432" instance="qiita_test" user="defaultuser" passwd="ZGVmYXVsdHBhc3N3b3Jk" schema_mapping="" />
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<entity schema="qiita" name="filepath_type" color="c0d4f3" x="600" y="870" />
<entity schema="qiita" name="checksum_algorithm" color="b2cdf7" x="750" y="870" />
<entity schema="qiita" name="data_type" color="d0def5" x="690" y="990" />
<entity schema="qiita" name="filepath" color="c0d4f3" x="660" y="660" />
<group name="Group_analyses" color="c4e0f9" >
<comment>analysis tables</comment>
<entity schema="qiita" name="analysis" />
Expand Down Expand Up @@ -1297,6 +1310,7 @@ Controlled Vocabulary]]></comment>
<group name="Group_filepaths" color="c4e0f9" >
<entity schema="qiita" name="filepath" />
<entity schema="qiita" name="filepath_type" />
<entity schema="qiita" name="checksum_algorithm" />
</group>
</layout>
</project>
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