Added export of browse tags.

scripts/browsetags_to_tagtypes.py

@@ -0,0 +1,128 @@
+#! /usr/bin/env python
+# :noTabs=true:
+# (c) Copyright (c) 2016  The Hyve
+# (c) This file is distributed under the Apache Software License, Version 2.0
+# (c) (https://www.apache.org/licenses/LICENSE-2.0.txt).
+"""
+browsetags_to_tagtypes.py
+
+Brief: Converts concept codes from TranSMART, used in fixed vocabulary meta tags
+in the 'browse' tab to tag types, to be used in the 'analyze' tab.
+The file formats are the one exported by transmart-batch used for
+browse tags export (in.tsv) and the one used by transmart-batch for tag type
+import (out.tsv).
+
+Usage: browsetags_to_tagtypes.py <in.tsv> [out.tsv]
+
+Author: Gijs Kant <gijs@thehyve.nl>
+
+"""
+import csv
+import os
+import sys
+import StringIO
+
+class ConverterException(Exception):
+    pass
+
+class Converter:
+
+    input_line_length = 5
+
+    @staticmethod
+    def read(tsv_in):
+        types = {}
+        reader = csv.reader(tsv_in, dialect="excel-tab")
+        for line in reader:
+            if not len(line) == Converter.input_line_length:
+                raise ConverterException(
+                    'Invalid line length on line %d: %d (expected: %d).' % (
+                        reader.line_num,
+                        len(line),
+                        Converter.input_line_length))
+            folder_type = line[0]
+            code = line[1]
+            name = line[2]
+            value = line[3]
+            printvalue = line[4]
+            if folder_type == 'STUDY':
+                t = types.get(name)
+                if t is None:
+                    t = dict()
+                    t['name'] = name
+                    t['code'] = code
+                    t['values'] = []
+                    types[name] = t
+                t['values'].append(printvalue)
+        return types
+
+    @staticmethod
+    def write(tsv_out, types):
+        writer = csv.writer(tsv_out, dialect="excel-tab")
+        writer.writerow([
+            'node_type',
+            'title',
+            'solr_field_name',
+            'value_type',
+            'shown_if_empty',
+            'values',
+            'index'
+        ])
+        i = 1
+        for t in types.values():
+            csv_out = StringIO.StringIO()
+            csv_writer = csv.writer(csv_out, lineterminator = '')
+            csv_writer.writerow(t['values'])
+            writer.writerow([
+                'STUDY',
+                t['name'],
+                t['code'],
+                'ANALYZED_STRING',
+                'Y',
+                csv_out.getvalue(),
+                i
+            ])
+            csv_out.close()
+            i = i + 1
+
+
+def main():
+    if len(sys.argv) < 2:
+        print >> sys.stderr, ("Usage: %s <in.tsv> [out.tsv]"
+            % os.path.basename(sys.argv[0]))
+        sys.exit()
+
+    in_file = sys.argv[1]
+    out_file = 'stdout'
+    write_to_stdout = True
+    if len(sys.argv) > 2:
+        out_file = sys.argv[2]
+        write_to_stdout = False
+
+    types = None
+    print >> sys.stderr, "Reading browse tags from %s ..." % in_file
+    try:
+        with open(in_file) as tsv_in:
+            types = Converter.read(tsv_in)
+    except ConverterException as e:
+        print e
+
+    if types is None:
+        print >> sys.stderr, "Reading browse tags failed."
+        sys.exit(1)
+
+    if write_to_stdout:
+        tsv_out = sys.stdout
+    else:
+        tsv_out = open(out_file, 'w')
+    print >> sys.stderr, "Writing tag types to %s ..." % out_file
+    Converter.write(tsv_out, types)
+
+    if not write_to_stdout:
+        tsv_out.close()
+
+    print >> sys.stderr, "Done."
+
+
+if __name__ == '__main__':
+    main()

src/main/groovy/org/transmartproject/batch/browsetag/BrowseFolder.groovy

@@ -0,0 +1,19 @@
+package org.transmartproject.batch.browsetag
+
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ *
+ */
+@ToString
+@EqualsAndHashCode(includes = ['id', 'level', 'name', 'type', 'parent'])
+class BrowseFolder {
+    BrowseFolderType type
+    Long id
+    Integer level
+    String name
+    String fullName
+    String description
+    String parent
+}

src/main/groovy/org/transmartproject/batch/browsetag/BrowseFolderType.groovy

@@ -0,0 +1,19 @@
+package org.transmartproject.batch.browsetag
+
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ * Represents a node type with which tags can be associated.
+ * This is called a 'tag template' in the database.
+ */
+@ToString
+@EqualsAndHashCode(includes = ['type', 'displayName'])
+class BrowseFolderType implements Serializable {
+
+    private static final long serialVersionUID = 1L
+
+    String type
+    String displayName
+
+}

src/main/groovy/org/transmartproject/batch/browsetag/BrowseTagAssociation.groovy

@@ -0,0 +1,14 @@
+package org.transmartproject.batch.browsetag
+
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ *
+ */
+@ToString
+@EqualsAndHashCode(includes = ['folder', 'value'])
+class BrowseTagAssociation {
+    BrowseFolder folder
+    BrowseTagValue value
+}

src/main/groovy/org/transmartproject/batch/browsetag/BrowseTagAssociationDatabaseReader.groovy

@@ -0,0 +1,195 @@
+package org.transmartproject.batch.browsetag
+
+import groovy.util.logging.Slf4j
+import org.springframework.batch.item.ItemStreamReader
+import org.springframework.batch.item.database.JdbcCursorItemReader
+import org.springframework.beans.factory.annotation.Autowired
+import org.springframework.jdbc.core.RowMapper
+import org.transmartproject.batch.clinical.db.objects.Tables
+
+import javax.annotation.PostConstruct
+import javax.sql.DataSource
+import java.sql.ResultSet
+import java.sql.SQLException
+
+/**
+ * Gets the current patients (for the study) from database.
+ */
+@Slf4j
+class BrowseTagAssociationDatabaseReader implements ItemStreamReader<BrowseTagAssociation> {
+
+    @Delegate
+    JdbcCursorItemReader<BrowseTagAssociation> delegate
+
+    @Autowired
+    DataSource dataSource
+
+    @PostConstruct
+    void init() {
+        delegate = new JdbcCursorItemReader<>(
+                driverSupportsAbsolute: true,
+                dataSource: dataSource,
+                sql: sql,
+                rowMapper: this.&mapRow as RowMapper<BrowseTagAssociation>)
+
+        delegate.afterPropertiesSet()
+    }
+
+    private String getSql() {
+        /*
+            Table {@link $Tables.BIO_CONCEPT_CODE}:
+            primary key: bio_concept_code_id
+            unique: (code_type_name, bio_concept_code)
+            index: code_type_name
+
+            Table {@link $Tables.AM_TAG_ITEM}:
+            primary key: (tag_template_id, tag_item_id)
+         */
+
+        """
+                (SELECT
+                    f.folder_id,
+                    f.folder_name,
+                    f.folder_full_name,
+                    f.folder_level,
+                    f.folder_type,
+                    f.folder_tag,
+                    f.parent_id,
+                    f.description as folder_description,
+                    fp.folder_name as parent_name,
+                    fp.folder_full_name as parent_full_name,
+                    fp.folder_type as parent_type,
+                    ati.tag_template_id,
+                    ati.tag_item_id,
+                    ati.tag_item_uid,
+                    ati.display_name,
+                    ati.tag_item_type,
+                    ati.tag_item_subtype,
+                    ati.code_type_name,
+                    ati.required,
+                    tv.value as value,
+                    tv.value as description
+                FROM $Tables.FM_FOLDER f
+                INNER JOIN $Tables.FM_DATA_UID fuid
+                ON f.folder_id = fuid.fm_data_id
+                INNER JOIN $Tables.AM_TAG_ASSOCIATION ata
+                ON fuid.unique_id = ata.subject_uid
+                INNER JOIN $Tables.AM_TAG_ITEM ati
+                ON ata.tag_item_id = ati.tag_item_id
+                INNER JOIN $Tables.AM_DATA_UID tuid
+                ON ata.object_uid = tuid.unique_id
+                INNER JOIN $Tables.AM_TAG_VALUE tv
+                ON tuid.am_data_id = tv.tag_value_id
+                LEFT OUTER JOIN $Tables.FM_FOLDER fp
+                ON f.parent_id = fp.folder_id
+                WHERE ata.object_type = 'AM_TAG_VALUE')
+                UNION
+                (SELECT
+                    f.folder_id,
+                    f.folder_name,
+                    f.folder_full_name,
+                    f.folder_level,
+                    f.folder_type,
+                    f.folder_tag,
+                    f.parent_id,
+                    f.description as folder_description,
+                    fp.folder_name as parent_name,
+                    fp.folder_full_name as parent_full_name,
+                    fp.folder_type as parent_type,
+                    ati.tag_template_id,
+                    ati.tag_item_id,
+                    ati.tag_item_uid,
+                    ati.display_name,
+                    ati.tag_item_type,
+                    ati.tag_item_subtype,
+                    ati.code_type_name,
+                    ati.required,
+                    bcc.bio_concept_code as value,
+                    bcc.code_description as description
+                FROM $Tables.FM_FOLDER f
+                INNER JOIN $Tables.FM_DATA_UID fuid
+                ON f.folder_id = fuid.fm_data_id
+                INNER JOIN $Tables.AM_TAG_ASSOCIATION ata
+                ON fuid.unique_id = ata.subject_uid
+                INNER JOIN $Tables.AM_TAG_ITEM ati
+                ON ata.tag_item_id = ati.tag_item_id
+                INNER JOIN $Tables.BIO_CONCEPT_CODE bcc
+                ON ata.object_uid = concat(bcc.code_type_name, ':', bcc.bio_concept_code)
+                LEFT OUTER JOIN $Tables.FM_FOLDER fp
+                ON f.parent_id = fp.folder_id
+                WHERE ata.object_type = 'BIO_CONCEPT_CODE')
+        """
+    }
+
+    private final Map<String, BrowseFolderType> folderTypes = [:]
+
+    private BrowseFolderType getFolderType(ResultSet rs) {
+        String folderTypeName = rs.getString('folder_type')
+        BrowseFolderType folderType = folderTypes[folderTypeName]
+        if (folderType == null) {
+            folderType = new BrowseFolderType(
+                    type: folderTypeName,
+                    displayName: rs.getString('folder_description')
+            )
+            folderTypes[folderTypeName] = folderType
+        }
+        folderType
+    }
+
+    private final Map<Long, BrowseTagType> tagTypes = [:]
+
+    private BrowseTagType getTagType(ResultSet rs) {
+        Long tagItemId = rs.getLong('tag_item_id')
+        BrowseTagType tagType = tagTypes[tagItemId]
+        if (tagType == null) {
+            tagType = new BrowseTagType(
+                    code: rs.getString('code_type_name'),
+                    folderType: getFolderType(rs),
+                    type: rs.getString('tag_item_type'),
+                    subType: rs.getString('tag_item_subtype'),
+                    displayName: rs.getString('display_name'),
+                    required: rs.getBoolean('required')
+            )
+            tagTypes[tagItemId] = tagType
+        }
+        tagType
+    }
+
+    private final Map<String, BrowseFolder> folders = [:]
+
+    private BrowseFolder getFolder(ResultSet rs) {
+        String fullName = rs.getString('folder_full_name')
+        BrowseFolder folder = folders[fullName]
+        if (folder == null) {
+            folder = new BrowseFolder(
+                    fullName: fullName,
+                    id: rs.getLong('folder_id'),
+                    name: rs.getString('folder_name'),
+                    type: getFolderType(rs),
+                    level: rs.getInt('folder_level'),
+                    description: rs.getString('folder_description'),
+                    parent: rs.getString('parent_name')
+            )
+            folders[fullName] = folder
+        }
+        folder
+    }
+
+    private BrowseTagValue getValue(ResultSet rs) {
+        new BrowseTagValue(
+                type: getTagType(rs),
+                value: rs.getString('value'),
+                description: rs.getString('description')
+        )
+    }
+
+    @SuppressWarnings('UnusedPrivateMethodParameter')
+    private BrowseTagAssociation mapRow(ResultSet rs, int rowNum) throws SQLException {
+        new BrowseTagAssociation(
+                folder: getFolder(rs),
+                value: getValue(rs)
+        )
+    }
+
+}
+