Add specimen_id attribute to the study object

qiita_db/metadata_template/base_metadata_template.py

@@ -647,13 +647,24 @@ def delete_column(self, column_name):
             If the `column_name` doesn't exist
         QiitaDBOperationNotPermittedError
             If a the info file can't be updated
+            If the column_name is selected as a specimen_id_column in the
+            study.
         """
         if column_name not in self.categories():
             raise qdb.exceptions.QiitaDBColumnError(
                 "'%s' not in info file %d" % (column_name, self._id))
         if not self.can_be_updated(columns={column_name}):
             raise qdb.exceptions.QiitaDBOperationNotPermittedError(
                 '%s cannot be deleted' % column_name)
+
+        # if a tube identifier column is selected disallow its deletion
+        specimen_id_column = qdb.study.Study(self.study_id).specimen_id_column
+        if specimen_id_column == column_name:
+            raise qdb.exceptions.QiitaDBOperationNotPermittedError(
+                    '"%s" cannot be deleted, this column is currently selected'
+                    ' as the tube identifier (specimen_id_column)' %
+                    column_name)
+
         with qdb.sql_connection.TRN:
             sql = 'ALTER TABLE qiita.%s%d DROP COLUMN %s' % (
                 self._table_prefix, self._id, column_name)
@@ -1516,3 +1527,17 @@ def validate(self, restriction_dict):
                 "columns:\n\t%s.\nSee the Templates tutorial for a description"
                 " of these fields." % ";\n\t".join(warning_msg),
                 qdb.exceptions.QiitaDBWarning)
+
+    def unique_columns(self):
+        """Get the unique columns in a template object
+
+        Returns
+        -------
+        set of str
+            Returns a set of the columns that are unique in a template object.
+        """
+
+        df = self.to_dataframe()
+
+        n = len(df)
+        return {k for k, v in df.nunique().items() if v == n}

qiita_db/metadata_template/test/test_prep_template.py

@@ -1508,6 +1508,13 @@ def test_name_setter(self):
         pt.name = 'Prep information 1'
         self.assertEqual(pt.name, 'Prep information 1')
 
+    def test_unique(self):
+        pt = qdb.metadata_template.prep_template.PrepTemplate(1)
+        observed = pt.unique_columns()
+        expected = {'barcode'}
+
+        self.assertEqual(observed, expected)
+
 
 EXP_PREP_TEMPLATE = (
     'sample_name\tbarcode\tcenter_name\tcenter_project_name\t'

qiita_db/metadata_template/test/test_sample_template.py

@@ -2159,6 +2159,19 @@ def test_delete_column(self):
         st.delete_column('dna_extracted')
         self.assertNotIn('dna_extracted', st.categories())
 
+    def test_delete_column_specimen_id(self):
+        st = qdb.metadata_template.sample_template.SampleTemplate.create(
+            self.metadata, self.new_study)
+        self.new_study.specimen_id_column = 'latitude'
+
+        with self.assertRaisesRegexp(
+                qdb.exceptions.QiitaDBOperationNotPermittedError,
+                '"latitude" cannot be deleted, this column is currently '
+                'selected as the tube identifier \(specimen_id_column\)'):
+            st.delete_column('latitude')
+
+        self.new_study.specimen_id_column = None
+
     def test_delete_sample(self):
         QE = qdb.exceptions
         st = qdb.metadata_template.sample_template.SampleTemplate(1)
@@ -2187,6 +2200,13 @@ def test_delete_sample(self):
         with self.assertRaises(QE.QiitaDBOperationNotPermittedError):
             st.delete_sample('1.SKM5.640177')
 
+    def test_unique(self):
+        st = qdb.metadata_template.sample_template.SampleTemplate(1)
+        observed = st.unique_columns()
+        expected = {'anonymized_name', 'host_subject_id', 'longitude'}
+
+        self.assertEqual(observed, expected)
+
 
 EXP_SAMPLE_TEMPLATE = (
     "sample_name\tcollection_timestamp\tdescription\tdna_extracted\t"

qiita_db/study.py

@@ -59,6 +59,7 @@ class Study(qdb.base.QiitaObject):
     status
     title
     owner
+    specimen_id_column
 
     Methods
     -------
@@ -627,6 +628,65 @@ def publications(self, values):
             qdb.sql_connection.TRN.add(sql, sql_args, many=True)
             qdb.sql_connection.TRN.execute()
 
+    @property
+    def specimen_id_column(self):
+        """Returns the specimen identifier column
+
+        Returns
+        -------
+        str
+            The name of the specimen id column
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT specimen_id_column
+                     FROM qiita.study
+                     WHERE study_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [self._id])
+            return qdb.sql_connection.TRN.execute_fetchlast()
+
+    @specimen_id_column.setter
+    def specimen_id_column(self, value):
+        """Sets the specimen identifier column
+
+        Parameters
+        ----------
+        value : str
+            The name of the column with the specimen identifiers.
+
+        Raises
+        ------
+        QiitaDBLookupError
+            If value is not in the sample information for this study.
+            If the study does not have sample information.
+        QiitaDBColumnError
+            Category is not unique.
+        """
+        st = self.sample_template
+        if st is None:
+            raise qdb.exceptions.QiitaDBLookupError("Study does not have a "
+                                                    "sample information.")
+
+        if value is not None:
+            if value not in st.categories():
+                raise qdb.exceptions.QiitaDBLookupError("Category '%s' is not "
+                                                        "present in the sample"
+                                                        " information."
+                                                        % value)
+
+            observed_values = st.get_category(value)
+            if len(observed_values) != len(set(observed_values.values())):
+                raise qdb.exceptions.QiitaDBColumnError("The category does not"
+                                                        " contain unique "
+                                                        "values.")
+
+        with qdb.sql_connection.TRN:
+            # Set the new ones
+            sql = """UPDATE qiita.study SET
+                     specimen_id_column = %s
+                     WHERE study_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [value, self._id])
+            qdb.sql_connection.TRN.execute()
+
     @property
     def investigation(self):
         """ Returns Investigation this study is part of

qiita_db/support_files/patches/66.sql

@@ -0,0 +1,7 @@
+-- August 22, 2018
+-- add specimen_id_column to study table (needed to plate samples in labman)
+
+ALTER TABLE qiita.study ADD specimen_id_column varchar(256);
+
+COMMENT ON COLUMN qiita.study.specimen_id_column IS 'The name of the column that describes the specimen identifiers (such as what is written on the tubes).';
+

qiita_db/support_files/qiita-db.dbs

@@ -1373,6 +1373,9 @@ Controlled Vocabulary]]></comment>
 			<column name="study_abstract" type="text" jt="12" mandatory="y" />
 			<column name="vamps_id" type="varchar" jt="12" />
 			<column name="ebi_study_accession" type="varchar" jt="12" />
+			<column name="specimen_id_column" type="varchar" length="256" jt="12" >
+				<comment><![CDATA[The name of the column that describes the specimen identifiers (such as what is written on the tubes).]]></comment>
+			</column>
 			<index name="pk_study" unique="PRIMARY_KEY" >
 				<column name="study_id" />
 			</index>
@@ -1691,7 +1694,6 @@ Controlled Vocabulary]]></comment>
 		<entity schema="qiita" name="study_environmental_package" color="b2cdf7" x="2085" y="45" />
 		<entity schema="qiita" name="environmental_package" color="b2cdf7" x="2160" y="180" />
 		<entity schema="qiita" name="study_person" color="c0d4f3" x="2010" y="135" />
-		<entity schema="qiita" name="study" color="d0def5" x="1785" y="240" />
 		<entity schema="qiita" name="per_study_tags" color="b2cdf7" x="2145" y="450" />
 		<entity schema="qiita" name="study_tags" color="b2cdf7" x="2295" y="480" />
 		<entity schema="qiita" name="timeseries_type" color="c0d4f3" x="2010" y="540" />
@@ -1725,6 +1727,7 @@ Controlled Vocabulary]]></comment>
 		<entity schema="qiita" name="software_command" color="b2cdf7" x="2160" y="1245" />
 		<entity schema="qiita" name="processing_job_validator" color="b2cdf7" x="2160" y="1410" />
 		<entity schema="qiita" name="processing_job" color="b2cdf7" x="1935" y="1140" />
+		<entity schema="qiita" name="study" color="d0def5" x="1785" y="240" />
 		<group name="Group_analyses" color="c4e0f9" >
 			<comment>analysis tables</comment>
 			<entity schema="qiita" name="analysis" />