geoseeq 0.2.15__py3-none-any.whl → 0.2.17__py3-none-any.whl

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/blob_constructors.py

@@ -1,173 +1,6 @@
-from .result import (
-    SampleResultFolder,
-    SampleResultFile,
-    ProjectResultFolder,
-    ProjectResultFile,
-)
-from .organization import Organization
-from .sample import Sample
-from .project import Project 
-from .knex import GeoseeqNotFoundError
+"""Alias for id_constructors.from_blobs and id_constructors.from_uuids
 
-
-def org_from_blob(knex, blob, already_fetched=True, modified=False):
-    org = Organization(knex, blob["name"])
-    org.load_blob(blob)
-    org._already_fetched = already_fetched
-    org._modified = modified
-    return org
-
-
-def project_from_blob(knex, blob, already_fetched=True, modified=False):
-    org = org_from_blob(
-        knex, blob["organization_obj"], already_fetched=already_fetched, modified=modified
-    )
-    grp = Project(knex, org, blob["name"], is_library=blob["is_library"])
-    grp.load_blob(blob)
-    grp._already_fetched = already_fetched
-    grp._modified = modified
-    return grp
-
-sample_group_from_blob = project_from_blob  # Alias
-
-
-def sample_from_blob(knex, blob, already_fetched=True, modified=False):
-    lib = sample_group_from_blob(
-        knex, blob["library_obj"], already_fetched=already_fetched, modified=modified
-    )
-    sample = Sample(knex, lib, blob["name"], metadata=blob["metadata"])
-    sample.load_blob(blob)
-    sample._already_fetched = already_fetched
-    sample._modified = modified
-    return sample
-
-
-def project_result_folder_from_blob(knex, blob, already_fetched=True, modified=False):
-    group = project_from_blob(
-        knex, blob["sample_group_obj"], already_fetched=already_fetched, modified=modified
-    )
-    ar = ProjectResultFolder(
-        knex, group, blob["module_name"], replicate=blob["replicate"], metadata=blob["metadata"]
-    )
-    ar.load_blob(blob)
-    ar._already_fetched = already_fetched
-    ar._modified = modified
-    return ar
-
-sample_group_ar_from_blob = project_result_folder_from_blob  # Alias
-
-
-def sample_result_folder_from_blob(knex, blob, already_fetched=True, modified=False):
-    sample = sample_from_blob(
-        knex, blob["sample_obj"], already_fetched=already_fetched, modified=modified
-    )
-    ar = SampleResultFolder(
-        knex, sample, blob["module_name"], replicate=blob["replicate"], metadata=blob["metadata"]
-    )
-    ar.load_blob(blob)
-    ar._already_fetched = already_fetched
-    ar._modified = modified
-    return ar
-
-sample_ar_from_blob = sample_result_folder_from_blob  # Alias
-
-
-def sample_result_file_from_blob(knex, blob, already_fetched=True, modified=False):
-    ar = sample_result_folder_from_blob(
-        knex, blob["analysis_result_obj"], already_fetched=already_fetched, modified=modified
-    )
-    arf = SampleResultFile(
-        knex, ar, blob["name"], data=blob["stored_data"]
-    )
-    arf.load_blob(blob)
-    ar._already_fetched = already_fetched
-    ar._modified = modified
-    return arf
-
-sample_ar_field_from_blob = sample_result_file_from_blob  # Alias
-
-
-def project_result_file_from_blob(knex, blob, already_fetched=True, modified=False):
-    ar = project_result_folder_from_blob(
-        knex, blob["analysis_result_obj"], already_fetched=already_fetched, modified=modified
-    )
-    arf = ProjectResultFile(
-        knex, ar, blob["name"], data=blob["stored_data"]
-    )
-    arf.load_blob(blob)
-    ar._already_fetched = already_fetched
-    ar._modified = modified
-    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')
+For backwards compatibility.
+"""
+from .id_constructors.from_blobs import *
+from .id_constructors.from_uuids import *

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/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/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/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/id_constructors/from_blobs.py

@@ -0,0 +1,109 @@
+from geoseeq.result import (
+    SampleResultFolder,
+    SampleResultFile,
+    ProjectResultFolder,
+    ProjectResultFile,
+)
+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
+    org._modified = modified
+    return org
+
+
+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
+    )
+    grp = Project(knex, org, blob["name"], is_library=blob["is_library"])
+    grp.load_blob(blob)
+    grp._already_fetched = already_fetched
+    grp._modified = modified
+    return grp
+
+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
+    )
+    sample = Sample(knex, lib, blob["name"], metadata=blob["metadata"])
+    sample.load_blob(blob)
+    sample._already_fetched = already_fetched
+    sample._modified = modified
+    return sample
+
+
+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
+    )
+    ar = ProjectResultFolder(
+        knex, group, blob["module_name"], replicate=blob["replicate"], metadata=blob["metadata"]
+    )
+    ar.load_blob(blob)
+    ar._already_fetched = already_fetched
+    ar._modified = modified
+    return ar
+
+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
+    )
+    ar = SampleResultFolder(
+        knex, sample, blob["module_name"], replicate=blob["replicate"], metadata=blob["metadata"]
+    )
+    ar.load_blob(blob)
+    ar._already_fetched = already_fetched
+    ar._modified = modified
+    return ar
+
+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
+    )
+    arf = SampleResultFile(
+        knex, ar, blob["name"], data=blob["stored_data"]
+    )
+    arf.load_blob(blob)
+    ar._already_fetched = already_fetched
+    ar._modified = modified
+    return arf
+
+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
+    )
+    arf = ProjectResultFile(
+        knex, ar, blob["name"], data=blob["stored_data"]
+    )
+    arf.load_blob(blob)
+    ar._already_fetched = already_fetched
+    ar._modified = modified
+    return arf
+
+sample_group_ar_field_from_blob = project_result_file_from_blob  # Alias

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/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/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/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/{cli/shared_params/id_utils.py → 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/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/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/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/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/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.dist-info → geoseeq-0.2.17.dist-info}/METADATA

@@ -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.dist-info → geoseeq-0.2.17.dist-info}/RECORD

@@ -1,6 +1,6 @@
-geoseeq/__init__.py,sha256=pOUrWGCAMEA-cJN9is2qkmUy_dceZcYdzlDsf1X4O9A,833
+geoseeq/__init__.py,sha256=FxA5ioZVxUR3XAjllE5F2mtcUk8NDSBD-VYmMp6U254,864
 geoseeq/app.py,sha256=Y6d1UzxFLfE3RNccATbFCVi6kH3eFmzwoUbeR2Ry09A,2387
-geoseeq/blob_constructors.py,sha256=20seQXgsr5COJb6HhV1eBpBzYQlGgS7eqRq3eElPbEI,5732
+geoseeq/blob_constructors.py,sha256=AkWpDQY0EdGMxF1p6eRspyHKubcUdiW4it-_Q7S2QWk,188
 geoseeq/bulk_creators.py,sha256=pdn-Dv7yv5SFv-PfDuQbuOnw2W4-BfIfRJVRAhM8U6s,2115
 geoseeq/constants.py,sha256=2sO50sItJsBCHFvfUCvB2NziQnJKG6lFOFDMu3IHzaw,122
 geoseeq/file_system_cache.py,sha256=7pdM-1VncOvjkYv2pOocPHOXnEWz0jKhH6sm1LaXtoU,3405
@@ -18,16 +18,15 @@ geoseeq/cli/constants.py,sha256=Do5AUf9lMO9_P8KpFJ3XwwFBAWsxSjZ6sx9_QEGyC_c,176
 geoseeq/cli/copy.py,sha256=ocJ-T6vZBTPELUSBA65KndzAugrBWMq-3ux0dbffacE,1997
 geoseeq/cli/download.py,sha256=N4eEUiQIiqpFMXOnhkMBCRCKlYyKi0QtRJk5HBEAHkA,10807
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
-geoseeq/cli/main.py,sha256=s9QZ9bNpU9RPnK5ypDFT-3lL3VAmSKE5NThrV1BL5gA,1027
+geoseeq/cli/main.py,sha256=pY8P-GsO5Rc5wAWsAg5qKzYN76rXjPOIoXSt6tfuPG0,1027
 geoseeq/cli/manage.py,sha256=xy_iMfqSSMaSTQNYiTw2xEWpH4mpTAq4Cf_6QemEMnI,5409
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/user.py,sha256=fARv_5vx-QYT765Hsjgwr6J5ddA_viCPQdv9iUoVX6w,925
 geoseeq/cli/utils.py,sha256=f0wX5-19uDrYZ8d-aBLplqfbGOkr5BH8x3AMSAyPCes,2873
-geoseeq/cli/view.py,sha256=I29klmNPn0x1QjoMueXO76-BawV6CbbeEEXboXp066E,4913
+geoseeq/cli/view.py,sha256=R5lW7Bg3oQwmzTyd_g9dssY6LDw5kemP3XpkhzZfOGo,5751
 geoseeq/cli/shared_params/__init__.py,sha256=j8RjuTB7AoEvEDczNJjyAfizrT0Rv0-eAowAPAbaVLo,231
 geoseeq/cli/shared_params/common_state.py,sha256=TQK0UXvaH5k4W6XKbaug1bdoWbD3sTcJTRoJTtUmgSQ,2569
-geoseeq/cli/shared_params/id_handlers.py,sha256=7VGM_tdKUYNCjrb7HBAhW2z3_2WuZrfsJhD3GKLdt5I,6443
-geoseeq/cli/shared_params/id_utils.py,sha256=XEQxv13fRCZxA2OHG0O3nVQYCI29YzSsz8eZs79UqFI,392
+geoseeq/cli/shared_params/id_handlers.py,sha256=7s2g-UfKoTfwmDX_FI96-M_g_U1yYBUEj-8yy8NC_c8,6493
 geoseeq/cli/shared_params/obj_getters.py,sha256=ZSkt6LnDkVFlNVYKgLrjzg60-6BthZMr3eeD3HNqzac,2741
 geoseeq/cli/shared_params/opts_and_args.py,sha256=Jy2rVQydlvkgjoA_BYjSNuI-wUSPmE2S1C1rN6bycBI,1399
 geoseeq/cli/upload/__init__.py,sha256=QqBh0WXD9BaEDcKsKpb-WgWwQ0WzZdQUgYXYwyowW_c,340
@@ -39,9 +38,17 @@ geoseeq/contrib/ncbi/api.py,sha256=WQeLoGA_-Zha-QeSO8_i7HpvXyD8UkV0qc5okm11KiA,1
 geoseeq/contrib/ncbi/bioproject.py,sha256=_oThTd_iLDOC8cLOlJKAatSr362OBYZCEV3YrqodhFg,4341
 geoseeq/contrib/ncbi/cli.py,sha256=j9zEcaZPTryK3a4xluRxigcJKDhRpRxbp3KZSx-Bfhk,2400
 geoseeq/contrib/ncbi/setup_logging.py,sha256=Tp1bY1U0f-o739aHpvVYriG2qdd1lFvCYBXZeXQgt-w,175
-geoseeq/plotting/__init__.py,sha256=XTl5y488a9Ib6Et_kSluScMr9OPYiPByoNXHfjuZFeM,115
+geoseeq/id_constructors/__init__.py,sha256=w5E0PNQ9UuAxBeZbDI7KBnUoERd85gGz3nScz45bd2o,126
+geoseeq/id_constructors/from_blobs.py,sha256=WljFMY-VHLLp0tABE0Mu5b2UXMSvD8bcHmMFfwlgpHg,3752
+geoseeq/id_constructors/from_ids.py,sha256=xFv_TeXpN03ajQTSUVeaiXQFoB5M_QIf0SlX09rW3sM,2916
+geoseeq/id_constructors/from_names.py,sha256=RMKEzpmEZKfPWQ2sMUUqao3j5NPq9-T9DnprLScUI-8,4041
+geoseeq/id_constructors/from_uuids.py,sha256=d61azvpP22a57Z-kYXLwxmIUTWB25pwqWlwnRgPXHxw,2667
+geoseeq/id_constructors/resolvers.py,sha256=zTp4uWFkThj4GhlPVnFTt7JQ7dmmUD9vRyIbTJpPcRU,2608
+geoseeq/id_constructors/utils.py,sha256=CKlZHGMiqi1b6r1KtgD3czSAomH99Gdfx5ziqaahz-0,723
+geoseeq/plotting/__init__.py,sha256=RkGoXxgu7jEfK0B7NmdalPS2AbU7I7dZwDbi4rn9CKM,154
 geoseeq/plotting/constants.py,sha256=CGUlm8WAFG3YRKdicc9Rcy5hFxUdUm2RgK0iXZWLuX8,285
 geoseeq/plotting/highcharts.py,sha256=AGzdW4VSUsL_rfEI-RiVbbtaTLFMARvzLzVUDrKTlnU,4096
+geoseeq/plotting/selectable.py,sha256=hFbVlSgklR8tkLt9H1Fi-EwjXhV72YDdkkZMoReeBbI,2554
 geoseeq/result/__init__.py,sha256=IFHIyRV8ZzuKIfwfze1SXgcKwNMcSgMAknLHMkwjXIU,356
 geoseeq/result/bioinfo.py,sha256=QQtbyogrdro9avJSN0713sxLVnVeA24mFw3hWtKDKyw,1782
 geoseeq/result/file_download.py,sha256=R087ypOAu2pMZ9vXvkO9babPBNtRXTF3ZhpPldcT_jM,4593
@@ -51,19 +58,19 @@ geoseeq/result/result_folder.py,sha256=r3r1lQx_EkN9w5e0l0DmHS2IwNZxt0Zzs2lJvEdOC
 geoseeq/result/utils.py,sha256=C-CxGzB3WddlnRiqFSkrY78I_m0yFgNqsTBRzGU-y8Q,2772
 geoseeq/vc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geoseeq/vc/checksum.py,sha256=y8rh1asUZNbE_NLiFO0-9hImLNiTOc2YXQBRKORWK7k,710
-geoseeq/vc/cli.py,sha256=VlAvBoXckENKAvREZ5nKXl2F6Z6Glh_mKBDiSfaT_lQ,2853
+geoseeq/vc/cli.py,sha256=rUspr6FUJiUWIVMvf-pmyC5psKfufN45alk8392fAfA,2803
 geoseeq/vc/clone.py,sha256=G5IUMg5QASJ5c2ii9i54DX2eVpv55rBvgYjqlayZmuU,2486
 geoseeq/vc/constants.py,sha256=b91uugHPKC3OJhCKXkL55YghzUYhY5jS15EHHqaKPKE,19
 geoseeq/vc/vc_cache.py,sha256=P4LXTbq2zOIv1OhP7Iw5MmypR2vXuy29Pq5K6gRvi-M,730
 geoseeq/vc/vc_dir.py,sha256=A9CLTh2wWCRzZjiLyqXD1vhtsWZGD3OjaMT5KqlfAXI,457
-geoseeq/vc/vc_sample.py,sha256=a15sKcPRYPO772l-kThO13J03zAmDvj9pnYGCrudoFg,3900
-geoseeq/vc/vc_stub.py,sha256=BNFr7CZtpvLPe0MOqgB0zYL037vRCSwd2A_Fcy9UTKA,3160
+geoseeq/vc/vc_sample.py,sha256=qZeioWydXvfu4rGMs20nICfNcp46y_XkND-bHdV6P5M,3850
+geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_api_client.py,sha256=DDhnNJBJgz-LAmpRzVvvfjdcm_t4meQhZLUuS7XP7fE,14452
 tests/test_work_orders.py,sha256=CB6QbGGMNeEePZiOVioiSQP2dQsyMnsy4L31AQMRs3A,498
-geoseeq-0.2.15.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.2.15.dist-info/METADATA,sha256=-cUN6cXta3rtlVdiVaYyna1HkacL97paA4hHjfMx6pw,455
-geoseeq-0.2.15.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-geoseeq-0.2.15.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.2.15.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.2.15.dist-info/RECORD,,
+geoseeq-0.2.17.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.2.17.dist-info/METADATA,sha256=MhD15WS-G8qtqJtYghJ3SiU-bJN_tIMn99z8dl5pQzA,455
+geoseeq-0.2.17.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+geoseeq-0.2.17.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.2.17.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.2.17.dist-info/RECORD,,