Plugins oauth2

qiita_core/configuration_manager.py

@@ -171,6 +171,15 @@ def _get_main(self, config):
             self.valid_upload_extension = []
             print 'No files will be allowed to be uploaded.'
 
+        self.certificate_file = config.get('main', 'CERTIFICATE_FILE')
+        if not self.certificate_file:
+            self.certificate_file = join(install_dir, 'qiita_core',
+                                         'support_files', 'server.crt')
+        self.key_file = config.get('main', 'KEY_FILE')
+        if not self.key_file:
+            self.key_file = join(install_dir, 'qiita_core', 'support_files',
+                                 'server.key')
+
     def _get_postgres(self, config):
         """Get the configuration of the postgres section"""
         self.user = config.get('postgres', 'USER')

qiita_core/support_files/config_test.cfg

@@ -22,7 +22,7 @@ LOG_PATH =
 REQUIRE_APPROVAL = True
 
 # Base URL: DO NOT ADD TRAILING SLASH
-BASE_URL = http://localhost
+BASE_URL = https://localhost
 
 # Download path files
 UPLOAD_DATA_DIR = /tmp/
@@ -39,12 +39,16 @@ BASE_DATA_DIR =
 # Valid upload extension, comma separated. Empty for no uploads
 VALID_UPLOAD_EXTENSION = fastq,fastq.gz,txt,tsv,sff,fna,qual
 
-#Portal the site is working under
+# Portal the site is working under
 PORTAL = QIITA
 
-#Script used for launching plugins
+# Script used for launching plugins
 PLUGIN_LAUNCHER = qiita-plugin-launcher
 
+# Webserver certificate files
+CERTIFICATE_FILE =
+KEY_FILE =
+
 # ----------------------------- SMTP settings -----------------------------
 [smtp]
 # The hostname to connect to

qiita_core/support_files/server.crt

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

qiita_core/support_files/server.csr

@@ -0,0 +1,17 @@
+-----BEGIN CERTIFICATE REQUEST-----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+-----END CERTIFICATE REQUEST-----

qiita_core/support_files/server.key

@@ -0,0 +1,27 @@
+-----BEGIN RSA PRIVATE KEY-----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+-----END RSA PRIVATE KEY-----

qiita_db/artifact.py

@@ -8,8 +8,11 @@
 
 from __future__ import division
 from future.utils import viewitems
+from itertools import chain
 from datetime import datetime
 
+import networkx as nx
+
 import qiita_db as qdb
 
 
@@ -79,6 +82,63 @@ def iter_public(cls):
         """
         return cls.iter_by_visibility('public')
 
+    @classmethod
+    def copy(cls, artifact, prep_template):
+        """Creates a copy of `artifact` and attaches it to `prep_template`
+
+        Parameters
+        ----------
+        artifact : qiita_db.artifact.Artifact
+            Artifact to copy from
+        prep_template : qiita_db.metadata_template.prep_template.PrepTemplate
+            The prep template to attach the new artifact to
+
+        Returns
+        -------
+        qiita_db.artifact.Artifact
+            A new instance of Artifact
+        """
+        with qdb.sql_connection.TRN:
+            visibility_id = qdb.util.convert_to_id("sandbox", "visibility")
+            atype = artifact.artifact_type
+            atype_id = qdb.util.convert_to_id(atype, "artifact_type")
+            dtype_id = qdb.util.convert_to_id(
+                prep_template.data_type(), "data_type")
+            sql = """INSERT INTO qiita.artifact (
+                        generated_timestamp, visibility_id, artifact_type_id,
+                        data_type_id, can_be_submitted_to_ebi,
+                        can_be_submitted_to_vamps, submitted_to_vamps)
+                     VALUES (%s, %s, %s, %s, %s, %s, %s)
+                     RETURNING artifact_id"""
+            sql_args = [datetime.now(), visibility_id, atype_id, dtype_id,
+                        artifact.can_be_submitted_to_ebi,
+                        artifact.can_be_submitted_to_vamps, False]
+            qdb.sql_connection.TRN.add(sql, sql_args)
+            a_id = qdb.sql_connection.TRN.execute_fetchlast()
+
+            # Associate the artifact with the prep template
+            instance = cls(a_id)
+            prep_template.artifact = instance
+
+            # Associate the artifact with the study
+            sql = """INSERT INTO qiita.study_artifact (study_id, artifact_id)
+                     VALUES (%s, %s)"""
+            sql_args = [prep_template.study_id, a_id]
+            qdb.sql_connection.TRN.add(sql, sql_args)
+
+            # Associate the artifact with its filepaths
+            filepaths = [(fp, f_type) for _, fp, f_type in artifact.filepaths]
+            fp_ids = qdb.util.insert_filepaths(
+                filepaths, a_id, atype, "filepath", copy=True)
+            sql = """INSERT INTO qiita.artifact_filepath
+                        (artifact_id, filepath_id)
+                     VALUES (%s, %s)"""
+            sql_args = [[a_id, fp_id] for fp_id in fp_ids]
+            qdb.sql_connection.TRN.add(sql, sql_args, many=True)
+            qdb.sql_connection.TRN.execute()
+
+        return instance
+
     @classmethod
     def create(cls, filepaths, artifact_type, prep_template=None,
                parents=None, processing_parameters=None,
@@ -646,6 +706,65 @@ def parents(self):
             return [Artifact(p_id)
                     for p_id in qdb.sql_connection.TRN.execute_fetchflatten()]
 
+    def _create_lineage_graph_from_edge_list(self, edge_list):
+        """Generates an artifact graph from the given `edge_list`
+
+        Parameters
+        ----------
+        edge_list : list of (int, int)
+            List of (parent_artifact_id, artifact_id)
+
+        Returns
+        -------
+        networkx.DiGraph
+            The graph representing the artifact lineage stored in `edge_list`
+        """
+        lineage = nx.DiGraph()
+        # In case the edge list is empty, only 'self' is present in the graph
+        if edge_list:
+            # By creating all the artifacts here we are saving DB calls
+            nodes = {a_id: Artifact(a_id)
+                     for a_id in set(chain.from_iterable(edge_list))}
+
+            for parent, child in edge_list:
+                lineage.add_edge(nodes[parent], nodes[child])
+        else:
+            lineage.add_node(self)
+
+        return lineage
+
+    @property
+    def ancestors(self):
+        """Returns the ancestors of the artifact
+
+        Returns
+        -------
+        networkx.DiGraph
+            The ancestors of the artifact
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT parent_id, artifact_id
+                     FROM qiita.artifact_ancestry(%s)"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            edges = qdb.sql_connection.TRN.execute_fetchindex()
+        return self._create_lineage_graph_from_edge_list(edges)
+
+    @property
+    def descendants(self):
+        """Returns the descendants of the artifact
+
+        Returns
+        -------
+        networkx.DiGraph
+            The descendants of the artifact
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT parent_id, artifact_id
+                     FROM qiita.artifact_descendants(%s)"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            edges = qdb.sql_connection.TRN.execute_fetchindex()
+        return self._create_lineage_graph_from_edge_list(edges)
+
     @property
     def children(self):
         """Returns the list of children of the artifact

qiita_db/support_files/patches/33.sql

@@ -811,3 +811,42 @@ BEGIN
     END IF;
 END
 $$ LANGUAGE plpgsql;
+
+
+-- Create a function to return the ancestors of an Artifact
+CREATE FUNCTION qiita.artifact_ancestry(a_id bigint) RETURNS SETOF qiita.parent_artifact AS $$
+BEGIN
+    IF EXISTS(SELECT * FROM qiita.parent_artifact WHERE artifact_id = a_id) THEN
+        RETURN QUERY WITH RECURSIVE root AS (
+            SELECT artifact_id, parent_id
+            FROM qiita.parent_artifact
+            WHERE artifact_id = a_id
+          UNION
+            SELECT p.artifact_id, p.parent_id
+            FROM qiita.parent_artifact p
+            JOIN root r ON (r.parent_id = p.artifact_id)
+        )
+        SELECT DISTINCT artifact_id, parent_id
+            FROM root;
+    END IF;
+END
+$$ LANGUAGE plpgsql;
+
+-- Create a function to return the descendants of an artifact
+CREATE FUNCTION qiita.artifact_descendants(a_id bigint) RETURNS SETOF qiita.parent_artifact AS $$
+BEGIN
+    IF EXISTS(SELECT * FROM qiita.parent_artifact WHERE parent_id = a_id) THEN
+        RETURN QUERY WITH RECURSIVE root AS (
+            SELECT artifact_id, parent_id
+            FROM qiita.parent_artifact
+            WHERE parent_id = a_id
+          UNION
+            SELECT p.artifact_id, p.parent_id
+            FROM qiita.parent_artifact p
+            JOIN root r ON (r.artifact_id = p.parent_id)
+        )
+        SELECT DISTINCT artifact_id, parent_id
+            FROM root;
+    END IF;
+END
+$$ LANGUAGE plpgsql;

qiita_db/support_files/patches/python_patches/34.py

@@ -0,0 +1,18 @@
+from random import SystemRandom
+from string import ascii_letters, digits
+
+from qiita_db.sql_connection import TRN
+
+pool = ascii_letters + digits
+client_id = ''.join([SystemRandom().choice(pool) for _ in range(50)])
+client_secret = ''.join([SystemRandom().choice(pool) for _ in range(255)])
+
+with TRN:
+    sql = """INSERT INTO qiita.oauth_identifiers (client_id, client_secret)
+             VALUES (%s, %s)"""
+    TRN.add(sql, [client_id, client_secret])
+    TRN.execute()
+
+print "Please, add these values to your target gene plugin configuration file:"
+print "CLIENT_ID = %s" % client_id
+print "CLIENT_SECRET = %s" % client_secret