geoseeq 0.2.15__tar.gz → 0.2.17__tar.gz

{geoseeq-0.2.15 → geoseeq-0.2.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.2.15
+Version: 0.2.17
 Summary: # Geoseeq API Client
 Author: David C. Danko
 Author-email: dcdanko@biotia.io

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/__init__.py

@@ -30,4 +30,5 @@ from .work_orders import (
     WorkOrder,
     WorkOrderProto,
 )
-from .app import App
+from .app import App
+from .id_constructors import *

geoseeq-0.2.17/geoseeq/blob_constructors.py

@@ -0,0 +1,6 @@
+"""Alias for id_constructors.from_blobs and id_constructors.from_uuids
+
+For backwards compatibility.
+"""
+from .id_constructors.from_blobs import *
+from .id_constructors.from_uuids import *

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/cli/main.py

@@ -30,7 +30,7 @@ main.add_command(cli_view)
 @main.command()
 def version():
     """Print the version of the Geoseeq API being used."""
-    click.echo('0.2.15')  # remember to update setup
+    click.echo('0.2.17')  # remember to update setup
 
 
 @main.group('advanced')

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/cli/shared_params/id_handlers.py

@@ -9,7 +9,7 @@ from geoseeq.blob_constructors import (
 )
 from geoseeq.knex import GeoseeqNotFoundError
 from os.path import isfile
-from .id_utils import *
+from geoseeq.id_constructors.utils import is_grn, is_uuid, is_grn_or_uuid
 from .obj_getters import (
     _get_org,
     _get_org_and_proj,

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/cli/view.py

@@ -1,7 +1,7 @@
 import click
 
 from geoseeq import Organization, App
-from geoseeq.utils import paginated_iterator
+from geoseeq.id_constructors import resolve_id
 from .shared_params import (
     use_common_state,
     project_id_arg,
@@ -210,4 +210,36 @@ def cli_view_sample(state, project_id, sample_ids):
         print(sample)
         for field_name, field_value, optional in sample.get_remote_fields():
             optional = "Optional" if optional else "Required"
-            print(f'\t{field_name} :: "{field_value}" ({optional})')
+            print(f'\t{field_name} :: "{field_value}" ({optional})')
+
+
+@cli_view.command('object')
+@use_common_state
+@click.argument('ids', nargs=-1)
+def cli_view_object(state, ids):
+    """Print the specified object as well as its type.
+
+    ---
+
+    Example Usage:
+
+    \b
+    # Print the object with name "My Org/My Project/My Sample/My Result Folder"
+    $ geoseeq view object "My Org/My Project/My Sample/My Result Folder"
+
+    \b
+    # Print the object with GRN "grn:geoseeq:sample::d051ce05-f799-4aa7-8d8f-5cbf99136543"
+    $ geoseeq view object "grn:geoseeq:sample::d051ce05-f799-4aa7-8d8f-5cbf99136543"
+
+    ---
+
+    Command Arguments:
+
+    [ID] is the name or GRN of the object to print. UUIDs cannot be resolved without a type.
+
+    ---
+    """
+    knex = state.get_knex()
+    for id in ids:
+        obj_type, obj = resolve_id(knex, id)
+        print(f'{obj_type}:\t{obj}', file=state.outfile)

geoseeq-0.2.17/geoseeq/id_constructors/__init__.py

@@ -0,0 +1,5 @@
+from .from_blobs import *
+from .from_ids import *
+from .from_names import *
+from .from_uuids import *
+from .resolvers import *

geoseeq-0.2.15/geoseeq/blob_constructors.py → geoseeq-0.2.17/geoseeq/id_constructors/from_blobs.py

@@ -1,16 +1,17 @@
-from .result import (
+from geoseeq.result import (
     SampleResultFolder,
     SampleResultFile,
     ProjectResultFolder,
     ProjectResultFile,
 )
-from .organization import Organization
-from .sample import Sample
-from .project import Project 
-from .knex import GeoseeqNotFoundError
+from geoseeq.organization import Organization
+from geoseeq.sample import Sample
+from geoseeq.project import Project 
+from geoseeq import GeoseeqNotFoundError
 
 
 def org_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return an Organization object from a blob."""
     org = Organization(knex, blob["name"])
     org.load_blob(blob)
     org._already_fetched = already_fetched
@@ -19,6 +20,7 @@ def org_from_blob(knex, blob, already_fetched=True, modified=False):
 
 
 def project_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return a Project object from a blob."""
     org = org_from_blob(
         knex, blob["organization_obj"], already_fetched=already_fetched, modified=modified
     )
@@ -32,6 +34,7 @@ sample_group_from_blob = project_from_blob  # Alias
 
 
 def sample_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return a Sample object from a blob."""
     lib = sample_group_from_blob(
         knex, blob["library_obj"], already_fetched=already_fetched, modified=modified
     )
@@ -43,6 +46,7 @@ def sample_from_blob(knex, blob, already_fetched=True, modified=False):
 
 
 def project_result_folder_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return a ProjectResultFolder object from a blob."""
     group = project_from_blob(
         knex, blob["sample_group_obj"], already_fetched=already_fetched, modified=modified
     )
@@ -58,6 +62,7 @@ sample_group_ar_from_blob = project_result_folder_from_blob  # Alias
 
 
 def sample_result_folder_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return a SampleResultFolder object from a blob."""
     sample = sample_from_blob(
         knex, blob["sample_obj"], already_fetched=already_fetched, modified=modified
     )
@@ -73,6 +78,7 @@ sample_ar_from_blob = sample_result_folder_from_blob  # Alias
 
 
 def sample_result_file_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return a SampleResultFile object from a blob."""
     ar = sample_result_folder_from_blob(
         knex, blob["analysis_result_obj"], already_fetched=already_fetched, modified=modified
     )
@@ -88,6 +94,7 @@ sample_ar_field_from_blob = sample_result_file_from_blob  # Alias
 
 
 def project_result_file_from_blob(knex, blob, already_fetched=True, modified=False):
+    """Return a ProjectResultFile object from a blob."""
     ar = project_result_folder_from_blob(
         knex, blob["analysis_result_obj"], already_fetched=already_fetched, modified=modified
     )
@@ -100,74 +107,3 @@ def project_result_file_from_blob(knex, blob, already_fetched=True, modified=Fal
     return arf
 
 sample_group_ar_field_from_blob = project_result_file_from_blob  # Alias
-
-def org_from_uuid(knex, uuid):
-    """Return the organization object which the uuid points to."""
-    blob = knex.get(f"organizations/{uuid}")
-    org = org_from_blob(knex, blob)
-    return org
-
-def project_from_uuid(knex, uuid):
-    """Return the project object which the uuid points to."""
-    blob = knex.get(f"sample_groups/{uuid}")
-    project = project_from_blob(knex, blob)
-    return project
-
-sample_group_from_uuid = project_from_uuid  # Alias
-
-
-def sample_from_uuid(knex, uuid):
-    blob = knex.get(f"samples/{uuid}")
-    sample = sample_from_blob(knex, blob)
-    return sample
-
-
-def sample_result_folder_from_uuid(knex, uuid):
-    blob = knex.get(f"sample_ars/{uuid}")
-    ar = sample_result_folder_from_blob(knex, blob)
-    return ar
-
-sample_ar_from_uuid = sample_result_folder_from_uuid  # Alias
-
-
-def project_result_folder_from_uuid(knex, uuid):
-    blob = knex.get(f"sample_group_ars/{uuid}")
-    ar = project_result_folder_from_blob(knex, blob)
-    return ar
-
-sample_group_ar_from_uuid = project_result_folder_from_uuid  # Alias
-
-
-def sample_result_file_from_uuid(knex, uuid):
-    blob = knex.get(f"sample_ar_fields/{uuid}")
-    ar = sample_result_file_from_blob(knex, blob)
-    return ar
-
-sample_ar_field_from_uuid = sample_result_file_from_uuid  # Alias
-
-
-def project_result_file_from_uuid(knex, uuid):
-    blob = knex.get(f"sample_group_ar_fields/{uuid}")
-    ar = project_result_file_from_blob(knex, blob)
-    return ar
-
-sample_group_ar_field_from_uuid = project_result_file_from_uuid  # Alias
-
-
-def resolve_brn(knex, brn):
-    """Return the object which the brn points to."""
-    assert brn.startswith(f'brn:{knex.instance_code()}:')
-    _, _, object_type, uuid = brn.split(':')
-    if object_type == 'project':
-        return object_type, sample_group_from_uuid(knex, uuid)
-    if object_type == 'sample':
-        return object_type, sample_from_uuid(knex, uuid)
-    if object_type == 'sample_result':
-        return object_type, sample_ar_from_uuid(knex, uuid)
-    if object_type == 'sample_result_field':
-        return object_type, sample_ar_field_from_uuid(knex, uuid)
-    if object_type == 'project_result':
-        return object_type, sample_group_ar_from_uuid(knex, uuid)
-    if object_type == 'project_result_field':
-        return object_type, sample_group_ar_field_from_uuid(knex, uuid)
-    raise GeoseeqNotFoundError(f'Type "{object_type}" not found')

geoseeq-0.2.17/geoseeq/id_constructors/from_ids.py

@@ -0,0 +1,87 @@
+from geoseeq import GeoseeqNotFoundError
+from .from_uuids import (
+    org_from_uuid,
+    project_from_uuid,
+    sample_from_uuid,
+    sample_result_folder_from_uuid,
+    project_result_folder_from_uuid,
+    result_folder_from_uuid,
+    sample_result_file_from_uuid,
+    project_result_file_from_uuid,
+    result_file_from_uuid,
+)
+from .from_names import (
+    org_from_name,
+    project_from_name,
+    sample_from_name,
+    sample_result_folder_from_name,
+    project_result_folder_from_name,
+    result_folder_from_name,
+    sample_result_file_from_name,
+    project_result_file_from_name,
+    result_file_from_name,
+)
+from .utils import is_grn_or_uuid, is_name
+
+
+def _generic_from_id(knex, id, from_uuid_func, from_name_func):
+    """Return the object which the id points to."""
+    if is_grn_or_uuid(id):
+        return from_uuid_func(knex, id)
+    if is_name(id):
+        return from_name_func(knex, id)
+    raise ValueError(f'"{id}" is not a GRN, UUID, or name')
+
+
+def org_from_id(knex, id):
+    """Return the organization object which the id points to."""
+    return _generic_from_id(knex, id, org_from_uuid, org_from_name)
+
+
+def project_from_id(knex, id):
+    """Return the project object which the id points to."""
+    return _generic_from_id(knex, id, project_from_uuid, project_from_name)
+
+
+def sample_from_id(knex, id):
+    """Return the sample object which the id points to."""
+    return _generic_from_id(knex, id, sample_from_uuid, sample_from_name)
+
+
+def sample_result_folder_from_id(knex, id):
+    """Return the sample result folder object which the id points to."""
+    return _generic_from_id(knex, id, sample_result_folder_from_uuid, sample_result_folder_from_name)
+
+
+def project_result_folder_from_id(knex, id):
+    """Return the project result folder object which the id points to."""
+    return _generic_from_id(knex, id, project_result_folder_from_uuid, project_result_folder_from_name)
+
+
+def result_folder_from_id(knex, id):
+    """Return a result folder object which the id points to.
+    
+    Guess the result folder is a sample result folder. If not, try a project result folder.
+    """
+    return _generic_from_id(knex, id, result_folder_from_uuid, result_folder_from_name)
+
+
+def sample_result_file_from_id(knex, id):
+    """Return the sample result file object which the id points to."""
+    return _generic_from_id(knex, id, sample_result_file_from_uuid, sample_result_file_from_name)
+
+
+def project_result_file_from_id(knex, id):
+    """Return the project result file object which the id points to."""
+    return _generic_from_id(knex, id, project_result_file_from_uuid, project_result_file_from_name)
+
+
+def result_file_from_id(knex, id):
+    """Return a result file object which the id points to.
+    
+    Guess the result file is a sample result file. If not, try a project result file.
+    """
+    return _generic_from_id(knex, id, result_file_from_uuid, result_file_from_name)
+
+
+

geoseeq-0.2.17/geoseeq/id_constructors/from_names.py

@@ -0,0 +1,137 @@
+"""Construct objects from names.
+
+This module is used to construct objects from names. It is used by the
+
+Names are human-readable ids that are used to identify objects in GeoSeeq.
+They similar to file paths, e.g.:
+ - "My Org"
+ - "My Org/My Project"
+ - "My Org/My Project/My Sample/My Result Folder/My Result File"
+ - "My Org/My Project/My Result Folder/My Result File"
+
+Unlike UUIDs or GRNs names can be changed by the user.
+This makes them more human-readable, but not reliable for permanent references.
+"""
+from geoseeq.organization import Organization
+from geoseeq import GeoseeqNotFoundError
+
+
+def org_from_name(knex, name):
+    """Return the organization object which the name points to.
+    
+    e.g. "My Org"
+    """
+    tkns = name.split("/")
+    org_name = tkns[0]
+    org = Organization(knex, org_name)
+    org.get()
+    return org
+
+
+def project_from_name(knex, name):
+    """Return the project object which the name points to.
+    
+    e.g. "My Org/My Project"
+    """
+    tkns = name.split("/")
+    proj_name = tkns[1]
+    org = org_from_name(knex, name)
+    proj = org.project(proj_name)
+    proj.get()
+    return proj
+
+
+def sample_from_name(knex, name):
+    """Return the sample object which the name points to.
+    
+    e.g. "My Org/My Project/My Sample"
+    """
+    tkns = name.split("/")
+    sample_name = tkns[2]
+    proj = project_from_name(knex, name)
+    sample = proj.sample(sample_name)
+    sample.get()
+    return sample
+
+
+def sample_result_folder_from_name(knex, name):
+    """Return the sample result folder object which the name points to.
+    
+    e.g. "My Org/My Project/My Sample/My Result Folder"
+    """
+    tkns = name.split("/")
+    result_folder_name = tkns[3]
+    sample = sample_from_name(knex, name)
+    ar = sample.result_folder(result_folder_name)
+    ar.get()
+    return ar
+
+
+def project_result_folder_from_name(knex, name):
+    """Return the project result folder object which the name points to.
+    
+    e.g. "My Org/My Project/My Result Folder"
+    """
+    tkns = name.split("/")
+    result_folder_name = tkns[2]
+    proj = project_from_name(knex, name)
+    rf = proj.result_folder(result_folder_name)
+    rf.get()
+    return rf
+
+
+def result_folder_from_name(knex, name):
+    """Return a result folder object which the name points to.
+    
+    Guess the result folder is a sample result folder. If not, try a project result folder.
+    """
+    tkns = name.split("/")
+    if len(tkns) >= 4:
+        try:
+            return sample_result_folder_from_name(knex, name)
+        except GeoseeqNotFoundError:
+            return project_result_folder_from_name(knex, name)
+    else:  # can't be a sample result folder
+        return project_result_folder_from_name(knex, name)
+
+
+def sample_result_file_from_name(knex, name):
+    """Return the sample result file object which the name points to.
+    
+    e.g. "My Org/My Project/My Sample/My Result Folder/My Result File"
+    """
+    tkns = name.split("/")
+    result_file_name = tkns[4]
+    r_folder = sample_result_folder_from_name(knex, name)
+    r_file = r_folder.result_file(result_file_name)
+    r_file.get()
+    return r_file
+
+
+def project_result_file_from_name(knex, name):
+    """Return the project result file object which the name points to.
+    
+    e.g. "My Org/My Project/My Result Folder/My Result File"
+    """
+    tkns = name.split("/")
+    result_file_name = tkns[3]
+    r_folder = project_result_folder_from_name(knex, name)
+    r_file = r_folder.result_file(result_file_name)
+    r_file.get()
+    return r_file
+
+
+def result_file_from_name(knex, name):
+    """Return a result file object which the name points to.
+    
+    Guess the result file is a sample result file. If not, try a project result file.
+    """
+    tkns = name.split("/")
+    if len(tkns) >= 5:
+        try:
+            return sample_result_file_from_name(knex, name)
+        except GeoseeqNotFoundError:
+            return project_result_file_from_name(knex, name)
+    else:  # can't be a sample result file
+        return project_result_file_from_name(knex, name)
+

geoseeq-0.2.17/geoseeq/id_constructors/from_uuids.py

@@ -0,0 +1,82 @@
+from .from_blobs import *
+from geoseeq import GeoseeqNotFoundError
+
+
+def org_from_uuid(knex, uuid):
+    """Return the organization object which the uuid points to."""
+    blob = knex.get(f"organizations/{uuid}")
+    org = org_from_blob(knex, blob)
+    return org
+
+def project_from_uuid(knex, uuid):
+    """Return the project object which the uuid points to."""
+    blob = knex.get(f"sample_groups/{uuid}")
+    project = project_from_blob(knex, blob)
+    return project
+
+sample_group_from_uuid = project_from_uuid  # Alias
+
+
+def sample_from_uuid(knex, uuid):
+    """Return the sample object which the uuid points to."""
+    blob = knex.get(f"samples/{uuid}")
+    sample = sample_from_blob(knex, blob)
+    return sample
+
+
+def sample_result_folder_from_uuid(knex, uuid):
+    """Return the sample result folder object which the uuid points to."""
+    blob = knex.get(f"sample_ars/{uuid}")
+    ar = sample_result_folder_from_blob(knex, blob)
+    return ar
+
+sample_ar_from_uuid = sample_result_folder_from_uuid  # Alias
+
+
+def project_result_folder_from_uuid(knex, uuid):
+    """Return the project result folder object which the uuid points to."""
+    blob = knex.get(f"sample_group_ars/{uuid}")
+    ar = project_result_folder_from_blob(knex, blob)
+    return ar
+
+sample_group_ar_from_uuid = project_result_folder_from_uuid  # Alias
+
+
+def result_folder_from_uuid(knex, uuid):
+    """Return a result folder object which the uuid points to.
+    
+    Guess the result folder is a sample result folder. If not, try a project result folder.
+    """
+    try:
+        return sample_result_folder_from_uuid(knex, uuid)
+    except GeoseeqNotFoundError:
+        return project_result_folder_from_uuid(knex, uuid)
+
+
+def sample_result_file_from_uuid(knex, uuid):
+    """Return the sample result file object which the uuid points to."""
+    blob = knex.get(f"sample_ar_fields/{uuid}")
+    ar = sample_result_file_from_blob(knex, blob)
+    return ar
+
+sample_ar_field_from_uuid = sample_result_file_from_uuid  # Alias
+
+
+def project_result_file_from_uuid(knex, uuid):
+    """Return the project result file object which the uuid points to."""
+    blob = knex.get(f"sample_group_ar_fields/{uuid}")
+    ar = project_result_file_from_blob(knex, blob)
+    return ar
+
+sample_group_ar_field_from_uuid = project_result_file_from_uuid  # Alias
+
+
+def result_file_from_uuid(knex, uuid):
+    """Return a result file object which the uuid points to.
+    
+    Guess the result file is a sample result file. If not, try a project result file.
+    """
+    try:
+        return sample_result_file_from_uuid(knex, uuid)
+    except GeoseeqNotFoundError:
+        return project_result_file_from_uuid(knex, uuid)

geoseeq-0.2.17/geoseeq/id_constructors/resolvers.py

@@ -0,0 +1,73 @@
+from geoseeq import GeoseeqNotFoundError
+from .from_uuids import (
+    org_from_uuid,
+    project_from_uuid,
+    sample_from_uuid,
+    sample_result_folder_from_uuid,
+    project_result_folder_from_uuid,
+    result_folder_from_uuid,
+    sample_result_file_from_uuid,
+    project_result_file_from_uuid,
+    result_file_from_uuid,
+)
+from .from_names import (
+    org_from_name,
+    project_from_name,
+    sample_from_name,
+    sample_result_folder_from_name,
+    project_result_folder_from_name,
+    result_folder_from_name,
+    sample_result_file_from_name,
+    project_result_file_from_name,
+    result_file_from_name,
+)
+from .utils import is_name, is_grn
+
+
+def resolve_id(knex, id):
+    """Return the object which the id points to."""
+    if is_grn(id):
+        return resolve_grn(knex, id)
+    if is_name(id):
+        return resolve_name(knex, id)
+    raise ValueError(f'"{id}" is not a GRN, or name. UUIDs cannot be resolved without a type')
+
+
+def resolve_name(knex, name):
+    """Return the object which the name points to."""
+    assert is_name(name), f'"{name}" is not a name'
+    tkns = name.split("/")
+    if len(tkns) == 1:  # org
+        return "org", org_from_name(knex, name)
+    if len(tkns) == 2:  # project
+        return "project", project_from_name(knex, name)
+    if len(tkns) == 3:  # sample or project result folder
+        try:
+            return "sample", sample_from_name(knex, name)
+        except GeoseeqNotFoundError:
+            return "folder", result_folder_from_name(knex, name)
+    if len(tkns) == 4:  # sample result folder or project result file
+        try:
+            return "folder", result_folder_from_name(knex, name)
+        except GeoseeqNotFoundError:
+            return "file", result_file_from_name(knex, name)
+    if len(tkns) == 5:  # sample result file
+        return "file", result_file_from_name(knex, name)
+    raise GeoseeqNotFoundError(f'Name "{name}" not found')
+
+
+def resolve_grn(knex, grn):
+    """Return the object which the grn points to."""
+    assert is_grn(grn), f'"{grn}" is not a GRN'
+    _, _, object_type, uuid = grn.split(':')
+    if object_type == 'org':
+        return object_type, org_from_uuid(knex, uuid)
+    if object_type == 'project':
+        return object_type, project_from_uuid(knex, uuid)
+    if object_type == 'sample':
+        return object_type, sample_from_uuid(knex, uuid)
+    if object_type == 'folder':
+        return object_type, result_folder_from_uuid(knex, uuid)
+    if object_type == 'file':
+        return object_type, result_file_from_uuid(knex, uuid)
+    raise GeoseeqNotFoundError(f'Type "{object_type}" not found')

geoseeq-0.2.15/geoseeq/cli/shared_params/id_utils.py → geoseeq-0.2.17/geoseeq/id_constructors/utils.py

@@ -5,6 +5,7 @@ def is_grn(el):
     """Return True if `el` is a GeoSeeq Resource Number (GRN)"""
     return el.startswith('grn:')
 
+
 def is_uuid(el):
     """Return True if `el` is a UUID"""
     try:
@@ -13,6 +14,21 @@ def is_uuid(el):
     except ValueError:
         return False
 
+
+def is_name(el):
+    """Return True if `el` is a name.
+    
+    e.g. "My Org/My Project"
+    """
+    if "/" in el:
+        # every name except org names have a slash
+        return True
+    if not is_grn_or_uuid(el):
+        # if the name has no slash and is not a grn or uuid, it's a name
+        return True
+    return False
+
+
 def is_grn_or_uuid(el):
     """Return True if `el` is a GRN or a UUID"""
     return is_grn(el) or is_uuid(el)

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/plotting/__init__.py

@@ -1,2 +1,3 @@
 from .constants import COLORS
-from .highcharts import series_is_categorical, series_is_numeric, scatter_plot_config
+from .highcharts import series_is_categorical, series_is_numeric, scatter_plot_config
+from .selectable import SelectablePlot

geoseeq-0.2.17/geoseeq/plotting/selectable.py

@@ -0,0 +1,81 @@
+
+class PlotSelector:
+
+    def __init__(self, title, kind='dropdown', options=None):
+        self.title = title
+        assert kind in ['dropdown', 'radio']
+        self.kind = kind
+        self.options = options or []
+
+    def __iter__(self):
+        return iter(self.options)
+
+    def add_option(self, option):
+        if option not in self.options:
+            self.options.append(option)
+
+    def to_dict(self):
+        assert self.options
+        return {
+            'title': self.title,
+            'kind': self.kind,
+            'options': self.options,
+        }
+
+
+class SelectablePlot:
+    VERSION = 'v0'
+
+    def __init__(self):
+        self.selectors = []
+        self.data = {}
+    
+    def add_selector(self, title, kind='dropdown', options=None):
+        """Add a selector to the selectable plot. Return the selectable plot for chaining."""
+        self.selectors.append(PlotSelector(title, kind=kind, options=options))
+        return self
+
+    def _add_keys(self, *keys):
+        """Add keys to the data structure."""
+        assert self.selectors
+        assert len(keys) == len(self.selectors)
+        subdata = self.data
+        for i, key in enumerate(keys):
+            if key not in subdata:
+                subdata[key] = {}
+                self.selectors[i].add_option(key)
+            subdata = subdata[key]
+    
+    def add_plot(self, plot, *keys):
+        """Add a plot to the selectable plot. Return the selectable plot for chaining."""
+        self._add_keys(*keys)
+        subdata = self.data
+        for key in keys:
+            if key == keys[-1]:
+                subdata[key] = plot
+            subdata = subdata[key]
+        return self
+    
+    def _check_invariants(self):
+        """Ensure we have plots for each key combo."""
+        assert self.selectors
+        
+        def check_subdata(i, subdata, key_chain):
+            if i == len(self.selectors):
+                assert subdata, f"subdata does not exist or is empty. Key Chain: {key_chain}"
+                return
+            for key in self.selectors[i]:
+                if key not in subdata:
+                    assert False, f'key: "{key}" is missing in `data`'
+                check_subdata(i + 1, subdata[key], key_chain + [key])
+        
+        check_subdata(0, self.data, [])
+
+    def to_dict(self):
+        """Return the selectable plot as a dictionary."""
+        self._check_invariants()
+        return {
+            'version': self.VERSION,
+            'selectors': [s.to_dict() for s in self.selectors],
+            'data': self.data,
+        }

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/vc/cli.py

@@ -2,7 +2,6 @@ import logging
 import click
 from os.path import isfile
 from geoseeq.cli.utils import use_common_state
-from geoseeq.blob_constructors import resolve_brn
 from .vc_dir import VCDir
 from .clone import (
     clone_project,

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/vc/vc_sample.py

@@ -4,7 +4,6 @@ from glob import glob
 from string import Template
 from os.path import join
 
-from geoseeq.blob_constructors import resolve_brn
 from .vc_stub import VCStub
 
 

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq/vc/vc_stub.py

@@ -1,6 +1,5 @@
 
 import json
-from geoseeq.blob_constructors import resolve_brn
 from os.path import join, dirname
 from .checksum import Checksum
 from os import environ, symlink, makedirs

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.2.15
+Version: 0.2.17
 Summary: # Geoseeq API Client
 Author: David C. Danko
 Author-email: dcdanko@biotia.io

{geoseeq-0.2.15 → geoseeq-0.2.17}/geoseeq.egg-info/SOURCES.txt

@@ -37,7 +37,6 @@ geoseeq/cli/view.py
 geoseeq/cli/shared_params/__init__.py
 geoseeq/cli/shared_params/common_state.py
 geoseeq/cli/shared_params/id_handlers.py
-geoseeq/cli/shared_params/id_utils.py
 geoseeq/cli/shared_params/obj_getters.py
 geoseeq/cli/shared_params/opts_and_args.py
 geoseeq/cli/upload/__init__.py
@@ -49,9 +48,17 @@ geoseeq/contrib/ncbi/api.py
 geoseeq/contrib/ncbi/bioproject.py
 geoseeq/contrib/ncbi/cli.py
 geoseeq/contrib/ncbi/setup_logging.py
+geoseeq/id_constructors/__init__.py
+geoseeq/id_constructors/from_blobs.py
+geoseeq/id_constructors/from_ids.py
+geoseeq/id_constructors/from_names.py
+geoseeq/id_constructors/from_uuids.py
+geoseeq/id_constructors/resolvers.py
+geoseeq/id_constructors/utils.py
 geoseeq/plotting/__init__.py
 geoseeq/plotting/constants.py
 geoseeq/plotting/highcharts.py
+geoseeq/plotting/selectable.py
 geoseeq/result/__init__.py
 geoseeq/result/bioinfo.py
 geoseeq/result/file_download.py

{geoseeq-0.2.15 → geoseeq-0.2.17}/setup.py

@@ -5,7 +5,7 @@ import setuptools
 
 setuptools.setup(
     name='geoseeq',
-    version='0.2.15',  # remember to update version string in CLI as well
+    version='0.2.17',  # remember to update version string in CLI as well
     author="David C. Danko",
     author_email='dcdanko@biotia.io',
     description=open('README.md').read(),