firecloud-api-cds 0.2.0__py3-none-any.whl

firecloud_api_cds/workspace.py

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+import json
+
+import api as fapi
+from .entity import Entity
+
+class Workspace(object):
+    """A FireCloud Workspace.
+
+    Attributes:
+        api_url (str): API root used to interact with FireCloud,
+            normally https://api.firecloud.org/api
+        namespace (str): Google project for this workspace
+        name (str): Workspace name
+    """
+
+    def __init__(self, namespace, name, api_url=fapi.PROD_API_ROOT):
+        """Get an existing workspace from firecloud_api_cds by name.
+
+        This method assumes that a workspace with the given name and
+        namespace is present at the api_url given, and raises an error
+        if it does not exist. To create a new workspace, use
+        Workspace.new()
+
+        Raises:
+            FireCloudServerError:  Workspace does not exist, or
+                API call fails
+        """
+        self.api_url = api_url
+        self.namespace = namespace
+        self.name = name
+
+        ## Call out to FireCloud
+        r = fapi.get_workspace(namespace, name, api_url)
+
+        fapi._check_response_code(r, 200)
+        self.data = r.json()
+
+
+    @staticmethod
+    def new(namespace, name, protected=False,
+            attributes=dict(), api_url=fapi.PROD_API_ROOT):
+        """Create a new FireCloud workspace.
+
+        Returns:
+            Workspace: A new FireCloud workspace
+
+        Raises:
+            FireCloudServerError: API call failed.
+        """
+        r = fapi.create_workspace(namespace, name, protected, attributes, api_url)
+        fapi._check_response_code(r, 201)
+        return Workspace(namespace, name, api_url)
+
+    def refresh(self):
+        """Reload workspace metadata from firecloud_api_cds.
+
+        Workspace metadata is cached in the data attribute of a Workspace,
+        and may become stale, requiring a refresh().
+        """
+        r = fapi.get_workspace(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 200)
+        self.data = r.json()
+        return self
+
+    def delete(self):
+        """Delete the workspace from firecloud_api_cds.
+
+        Note:
+            This action cannot be undone. Be careful!
+        """
+        r = fapi.delete_workspace(self.namespace, self.name)
+        fapi._check_response_code(r, 202)
+
+    # Getting useful information out of the bucket
+    def __str__(self):
+        """Return a JSON representation of the bucket."""
+        return json.dumps(self.data, indent=2)
+
+    def bucket(self):
+        """Return google bucket id for this workspace."""
+        return str(self.data["workspace"]["bucketName"])
+
+    def lock(self):
+        """Lock this Workspace.
+
+        This causes the workspace to behave in a read-only way,
+        regardless of access permissions.
+        """
+        r = fapi.lock_workspace(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 204)
+        self.data['workspace']['isLocked'] = True
+        return self
+
+    def unlock(self):
+        """Unlock this Workspace."""
+        r = fapi.unlock_workspace(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 204)
+        self.data['workspace']['isLocked'] = False
+        return self
+
+    def attributes(self):
+        """Return a dictionary of workspace attributes"""
+        return self.data["workspace"]["attributes"]
+
+    def get_attribute(self, attr):
+        """Return value of workspace attribute.
+
+        If the attribute does not exist, return None
+        """
+        return self.data["workspace"]["attributes"].get(attr, None)
+
+    def update_attribute(self, attr, value):
+        """Set the value of a workspace attribute."""
+        update = [fapi._attr_up(attr, value)]
+        r = fapi.update_workspace_attributes(self.namespace, self.name,
+                                             update, self.api_url)
+        fapi._check_response_code(r, 200)
+
+    def remove_attribute(self, attr):
+        """Remove attribute from a workspace.
+
+        Args:
+            attr (str): attribute name
+        """
+        update = [fapi._attr_rem(attr)]
+        r = fapi.update_workspace_attributes(self.namespace, self.name,
+                                                update, self.api_url)
+        self.data["workspace"]["attributes"].pop(attr, None)
+        fapi._check_response_code(r, 200)
+
+    def import_tsv(self, tsv_file):
+        """Upload entity data to workspace from tsv loadfile.
+
+        Args:
+            tsv_file (file): Tab-delimited file of entity data
+        """
+        r = fapi.upload_entities_tsv(self.namespace, self.name,
+                                     self.tsv_file, self.api_url)
+        fapi._check_response_code(r, 201)
+
+    def get_entity(self, etype, entity_id):
+        """Return entity in this workspace.
+
+        Args:
+            etype (str): Entity type
+            entity_id (str): Entity name/unique id
+        """
+        r = fapi.get_entity(self.namespace, self.name, etype,
+                               entity_id, self.api_url)
+        fapi._check_response_code(r, 200)
+        dresp = r.json()
+        return Entity(etype, entity_id, dresp['attributes'])
+
+    def delete_entity(self, etype, entity_id):
+        """Delete an entity in this workspace.
+
+        Args:
+            etype (str): Entity type
+            entity_id (str): Entity name/unique id
+        """
+        r = fapi.delete_entity(self.namespace, self.name, etype,
+                                  entity_id, self.api_url)
+        fapi._check_response_code(r, 202)
+
+    def import_entities(self, entities):
+        """Upload entity objects.
+
+        Args:
+            entities: iterable of firecloud.Entity objects.
+        """
+        edata = Entity.create_payload(entities)
+        r = fapi.upload_entities(self.namespace, self.name,
+                                 edata, self.api_url)
+        fapi._check_response_code(r, 201)
+
+    def create_set(self, set_id, etype, entities):
+        """Create a set of entities and upload to FireCloud.
+
+        Args
+            etype (str): one of {"sample, "pair", "participant"}
+            entities: iterable of firecloud.Entity objects.
+        """
+        if etype not in {"sample", "pair", "participant"}:
+            raise ValueError("Unsupported entity type:" + str(etype))
+
+        payload = "membership:" + etype + "_set_id\t" + etype + "_id\n"
+
+        for e in entities:
+            if e.etype != etype:
+                msg =  "Entity type '" + e.etype + "' does not match "
+                msg += "set type '" + etype + "'"
+                raise ValueError(msg)
+            payload += set_id + '\t' + e.entity_id + '\n'
+
+
+        r = fapi.upload_entities(self.namespace, self.name,
+                                    payload, self.api_url)
+        fapi._check_response_code(r, 201)
+
+    def create_sample_set(self, sset_id, samples):
+        """Create FireCloud sample_set"""
+        return self.create_set(sset_id, "sample", samples)
+
+    def create_pair_set(self, pset_id, pairs):
+        """Create FireCloud pair_set"""
+        return self.create_set(pset_id, "pair", pairs)
+
+    def create_participant_set(self, pset_id, participants):
+        """Create FireCloud participant_set"""
+        return self.create_set(pset_id, "participant", participants)
+
+    def submissions(self):
+        """List job submissions in workspace."""
+        r = fapi.get_submissions(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 200)
+        return r.json()
+
+    def entity_types(self):
+        """List entity types in workspace."""
+        r = fapi.get_entity_types(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 200)
+        return r.json().keys()
+
+    def entities(self):
+        """List all entities in workspace."""
+        r = fapi.get_entities_with_type(self.namespace,
+                                        self.name, self.api_url)
+        fapi._check_response_code(r, 200)
+        edicts = r.json()
+        return [Entity(e['entityType'], e['name'], e['attributes'])
+                for e in edicts]
+
+    def __get_entities(self, etype):
+        """Helper to get entities for a given type."""
+        r = fapi.get_entities(self.namespace, self.name,
+                              etype, self.api_url)
+        fapi._check_response_code(r, 200)
+        return [Entity(e['entityType'], e['name'], e['attributes'])
+                for e in r.json()]
+
+    def samples(self):
+        """List samples in a workspace."""
+        return self.__get_entities("sample")
+
+    def participants(self):
+        """List participants in a workspace."""
+        return self.__get_entities("participant")
+
+    def pairs(self):
+        """List pairs in a workspace."""
+        return self.__get_entities("pair")
+
+    def sample_sets(self):
+        """List sample sets in a workspace."""
+        return self.__get_entities("sample_set")
+
+    def participant_sets(self):
+        """List participant sets in a workspace."""
+        return self.__get_entities("participant_set")
+
+    def pair_sets(self):
+        """List pair sets in a workspace."""
+        return self.__get_entities("pair_set")
+
+    def copy_entities(self, from_namespace, from_workspace, etype, enames):
+        """Copy entities from another workspace.
+
+        Args:
+            from_namespace (str): Source workspace namespace
+            from_workspace (str): Source workspace name
+            etype (str): Entity type
+            enames (list(str)): List of entity names to copy
+        """
+        r = fapi.copy_entities(from_namespace, from_workspace,
+                               self.namespace, self.name, etype, enames,
+                               self.api_url)
+        fapi._check_response_code(r, 201)
+
+    def configs(self):
+        """Get method configurations in a workspace."""
+        raise NotImplementedError
+        r = fapi.get_configs(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 200)
+        cdata = r.json()
+        configs = []
+        for c in cdata:
+            cnamespace = c['namespace']
+            cname = c['name']
+            root_etype = c['rootEntityType']
+            method_namespace = c['methodRepoMethod']['methodNamespace']
+            method_name = c['methodRepoMethod']['methodName']
+            method_version = c['methodRepoMethod']['methodVersion']
+
+    def acl(self):
+        """Get the access control list for this workspace."""
+        r = fapi.get_workspace_acl(self.namespace, self.name, self.api_url)
+        fapi._check_response_code(r, 200)
+        return r.json()
+
+    def set_acl(self, role, users):
+        """Set access permissions for this workspace
+
+        Args:
+            role (str): Access level
+                one of {one of "OWNER", "READER", "WRITER", "NO ACCESS"}
+            users (list(str)): List of users to give role to
+        """
+        acl_updates = [{"email": user, "accessLevel": role} for user in users]
+        r = fapi.update_workspace_acl(self.namespace, self.name,
+                                      acl_updates, self.api_url)
+        fapi._check_response_code(r, 200)
+
+    def clone(self, to_namespace, to_name):
+        """Clone this workspace.
+
+        Args:
+            to_namespace (str): Target workspace namespace
+            to_name (str): Target workspace name
+        """
+        r = fapi.clone_workspace(self.namespace, self.name,
+                                 to_namespace, to_name, self.api_url)
+        fapi._check_response_code(r, 201)
+        return Workspace(to_namespace, to_name, self.api_url)

firecloud_api_cds-0.2.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: firecloud-api-cds
+Version: 0.2.0
+Summary: Fork of broadinstitute/fiss
+Project-URL: Homepage, https://github.com/broadinstitute/firecloud-api-cds
+License: BSD 3-Clause License
+License-File: LICENSE
+Requires-Python: >=3.9
+Requires-Dist: google-auth!=2.1.*,!=2.2.*,!=2.3.0,!=2.3.1,>=1.6.3
+Requires-Dist: google-cloud-storage>=1.36.1
+Requires-Dist: pydot>=4.0.0
+Requires-Dist: six>=1.17.0
+Description-Content-Type: text/markdown
+
+firecloud-api-cds
+===
+
+Fork of [https://github.com/broadinstitute/fiss](https://github.com/broadinstitute/fiss).

firecloud_api_cds-0.2.0.dist-info/RECORD

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firecloud_api_cds-0.2.0.dist-info/WHEEL

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+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

firecloud_api_cds-0.2.0.dist-info/licenses/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2018, Broad Institute, Inc.
+All rights reserved.
+ 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ 
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+ 
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+ 
+* Neither the name Broad Institute, Inc. nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+ 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+