Merge pull request #3203 from antgonza/artifact-archive-gui

add artifact archive GUI

Author: charles-cowart

qiita_db/artifact.py

@@ -11,6 +11,7 @@
 from os.path import isfile, relpath
 from shutil import rmtree
 from collections import namedtuple
+from json import dumps
 from qiita_db.util import create_nested_path
 
 import networkx as nx
@@ -48,6 +49,7 @@ class Artifact(qdb.base.QiitaObject):
     create
     delete
     being_deleted_by
+    archive
 
     See Also
     --------
@@ -701,6 +703,7 @@ def archive(cls, artifact_id):
         fids = [x['fp_id'] for x in artifact.filepaths
                 if x['fp_type'] == 'log']
 
+        archive_data = dumps({"merging_scheme": artifact.merging_scheme})
         with qdb.sql_connection.TRN:
             artifact._set_visibility('archived', propagate=False)
             sql = 'DELETE FROM qiita.parent_artifact WHERE artifact_id = %s'
@@ -715,6 +718,11 @@ def archive(cls, artifact_id):
                          WHERE filepath_id IN %s'''
                 qdb.sql_connection.TRN.add(sql, [tuple(fids)])
 
+            sql = """UPDATE qiita.{0}
+                     SET archive_data = %s
+                     WHERE artifact_id = %s""".format(cls._table)
+            qdb.sql_connection.TRN.add(sql, [archive_data, artifact_id])
+
             qdb.sql_connection.TRN.execute()
 
         # cleaning the extra artifacts
@@ -1461,39 +1469,51 @@ def merging_scheme(self):
             The human readable merging scheme and the parent software
             information for this artifact
         """
-        processing_params = self.processing_parameters
-        if processing_params is None:
-            return '', ''
-
-        cmd_name = processing_params.command.name
-        ms = processing_params.command.merging_scheme
-        afps = [x['fp'] for x in self.filepaths if x['fp'].endswith('biom')]
-
-        merging_schemes = []
-        parent_softwares = []
-        # this loop is necessary as in theory an artifact can be
-        # generated from multiple prep info files
-        for p in self.parents:
-            pparent = p.processing_parameters
-            # if parent is None, then is a direct upload; for example
-            # per_sample_FASTQ in shotgun data
-            if pparent is None:
-                parent_cmd_name = None
-                parent_merging_scheme = None
-                parent_pp = None
-                parent_software = 'N/A'
-            else:
-                parent_cmd_name = pparent.command.name
-                parent_merging_scheme = pparent.command.merging_scheme
-                parent_pp = pparent.values
-                psoftware = pparent.command.software
-                parent_software = '%s v%s' % (
-                    psoftware.name, psoftware.version)
-
-            merging_schemes.append(qdb.util.human_merging_scheme(
-                cmd_name, ms, parent_cmd_name, parent_merging_scheme,
-                processing_params.values, afps, parent_pp))
-            parent_softwares.append(parent_software)
+        vid = qdb.util.convert_to_id(self.visibility, "visibility")
+        if vid in qdb.util.artifact_visibilities_to_skip():
+            with qdb.sql_connection.TRN:
+                sql = f"""SELECT archive_data
+                          FROM qiita.{self._table}
+                          WHERE artifact_id = %s"""
+                qdb.sql_connection.TRN.add(sql, [self.id])
+                archive_data = qdb.sql_connection.TRN.execute_fetchlast()
+            merging_schemes = [archive_data['merging_scheme'][0]]
+            parent_softwares = [archive_data['merging_scheme'][1]]
+        else:
+            processing_params = self.processing_parameters
+            if processing_params is None:
+                return '', ''
+
+            cmd_name = processing_params.command.name
+            ms = processing_params.command.merging_scheme
+            afps = [x['fp'] for x in self.filepaths
+                    if x['fp'].endswith('biom')]
+
+            merging_schemes = []
+            parent_softwares = []
+            # this loop is necessary as in theory an artifact can be
+            # generated from multiple prep info files
+            for p in self.parents:
+                pparent = p.processing_parameters
+                # if parent is None, then is a direct upload; for example
+                # per_sample_FASTQ in shotgun data
+                if pparent is None:
+                    parent_cmd_name = None
+                    parent_merging_scheme = None
+                    parent_pp = None
+                    parent_software = 'N/A'
+                else:
+                    parent_cmd_name = pparent.command.name
+                    parent_merging_scheme = pparent.command.merging_scheme
+                    parent_pp = pparent.values
+                    psoftware = pparent.command.software
+                    parent_software = '%s v%s' % (
+                        psoftware.name, psoftware.version)
+
+                merging_schemes.append(qdb.util.human_merging_scheme(
+                    cmd_name, ms, parent_cmd_name, parent_merging_scheme,
+                    processing_params.values, afps, parent_pp))
+                parent_softwares.append(parent_software)
 
         return ', '.join(merging_schemes), ', '.join(parent_softwares)
 

qiita_db/metadata_template/prep_template.py

@@ -923,3 +923,23 @@ def _get_predecessors(workflow, node):
                         previous_jobs[current_job] = params
 
         return workflow
+
+    @property
+    def archived_artifacts(self):
+        """List of archived Artifacts
+
+        Returns
+        -------
+        list of qiita_db.artifact.Artifact
+            The list of archivde Artifacts
+        """
+        with qdb.sql_connection.TRN:
+
+            sql = """SELECT artifact_id
+                     FROM qiita.preparation_artifact
+                        LEFT JOIN qiita.artifact USING (artifact_id)
+                     WHERE prep_template_id = %s AND visibility_id IN %s"""
+            qdb.sql_connection.TRN.add(
+                sql, [self.id, qdb.util.artifact_visibilities_to_skip()])
+            return [qdb.artifact.Artifact(ai)
+                    for ai in qdb.sql_connection.TRN.execute_fetchflatten()]

qiita_db/support_files/patches/86.sql

@@ -23,3 +23,7 @@ BEGIN
   RETURN artifacts;
 END
 $$ LANGUAGE plpgsql;
+
+-- Jun 13, 2022
+-- adding an archive_data column to the artifact
+ALTER TABLE qiita.artifact ADD archive_data JSONB DEFAULT NULL;