geoseeq 0.6.14.dev7__tar.gz → 0.6.15.dev1__tar.gz

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev7
+Version: 0.6.15.dev1
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq/cli/main.py

@@ -55,7 +55,7 @@ def version():
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo('0.6.14dev7')  # remember to update pyproject.toml
+    click.echo('0.6.15dev1')  # remember to update pyproject.toml
 
 
 @main.group('advanced')

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq/cli/upload/__init__.py

@@ -4,6 +4,8 @@ from .upload import (
     cli_upload_file,
     cli_upload_folder,
     cli_metadata,
+    cli_upload_smart_table,
+    cli_upload_smart_tree,
 )
 from .upload_reads import cli_upload_reads_wizard
 from .upload_advanced import cli_find_urls_for_reads
@@ -17,6 +19,8 @@ cli_upload.add_command(cli_upload_reads_wizard)
 cli_upload.add_command(cli_upload_file)
 cli_upload.add_command(cli_upload_folder)
 cli_upload.add_command(cli_metadata)
+cli_upload.add_command(cli_upload_smart_table)
+cli_upload.add_command(cli_upload_smart_tree)
 
 @click.group('upload')
 def cli_upload_advanced():

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq/cli/upload/upload.py

@@ -263,3 +263,117 @@ def cli_metadata(state, overwrite, yes, private, create, index_col, encoding, pr
             sample.metadata = new_meta
             sample.idem()
     click.echo(f'Wrote metadata for {len(samples)} samples')
+
+
+@click.command('smart-table')
+@use_common_state
+@overwrite_option
+@yes_option
+@private_option
+@click.option('-n', '--geoseeq-file-name', default=None,
+              help='Specify a different name for the file on GeoSeeq than the local file name.',
+              show_default=True)
+@folder_id_arg
+@click.argument('file_path', type=click.Path(exists=True), nargs=1)
+def cli_upload_smart_table(state, overwrite, yes, private, folder_id, geoseeq_file_name, file_path):
+    """Upload a smart table to GeoSeeq.
+
+    This command uploads a smart table to a project or sample on GeoSeeq. It can be used to upload
+    a single file to a folder at once.
+    
+    ---
+
+    Example Usage:
+
+    \b
+    # Upload a smart table from a file
+    $ geoseeq upload smart-table "My Org/My Project/My Sample/My Folder" /path/to/my_table.csv
+
+    \b
+    # Upload a smart table from a file but name it "My Smart Table" on GeoSeeq
+    $ geoseeq upload smart-table "My Org/My Project/My Sample/My Folder" /path/to/my_table.csv -n "My Smart Table"
+
+    ---
+
+    Command Arguments:
+
+    [FOLDER_ID] Can be a folder UUID, GeoSeeq Resource Number (GRN), or an
+    names for an org, project, sample, folder separated by a slash. Can exclude
+    the sample name if the folder is for a project.
+
+    [FILE_PATH] A path to a file on your local machine.
+
+    ---
+    """
+    knex = state.get_knex()
+    result_folder = handle_folder_id(knex, folder_id, yes=yes, private=private)
+    
+    if not geoseeq_file_name:
+        geoseeq_file_name = basename(file_path)
+    
+    if not overwrite and result_folder.result_file(geoseeq_file_name).exists():
+        raise click.UsageError(f'{geoseeq_file_name} already exists in {result_folder}. Use --overwrite to overwrite it.')
+
+    result_file = result_folder.result_file(geoseeq_file_name)
+    smart_table = result_file.as_smart_table()
+    smart_table.import_csv(file_path)
+
+
+@click.command('smart-tree')
+@use_common_state
+@click.option('-m/-nm', '--make-name-map/--no-name-map', default=True, help="Create a sample name map with all samples currently in the project.")
+@overwrite_option
+@yes_option
+@private_option
+@click.option('-n', '--geoseeq-file-name', default=None,
+              help='Specify a different name for the file on GeoSeeq than the local file name.',
+              show_default=True)
+@folder_id_arg
+@click.argument('newick_file_path', type=click.Path(exists=True), nargs=1)
+def cli_upload_smart_tree(state, make_name_map, overwrite, yes, private, folder_id, geoseeq_file_name, newick_file_path):
+    """Upload a smart tree to GeoSeeq.
+
+    This command uploads a smart tree to a project or sample on GeoSeeq. It can be used to upload
+    a single file to a folder at once.
+    
+    ---
+
+    Example Usage:
+
+    \b
+    # Upload a smart tree from a file
+    $ geoseeq upload smart-tree "My Org/My Project/My Sample/My Folder" /path/to/my_tree.nwk
+
+    \b
+    # Upload a smart tree from a file but name it "My Smart Tree" on GeoSeeq
+    $ geoseeq upload smart-tree "My Org/My Project/My Sample/My Folder" /path/to/my_tree.nwk -n "My Smart Tree"
+
+    ---
+
+    Command Arguments:
+
+    [FOLDER_ID] Can be a folder UUID, GeoSeeq Resource Number (GRN), or an
+    names for an org, project, sample, folder separated by a slash. Can exclude
+    the sample name if the folder is for a project.
+
+    [NEWICK_FILE_PATH] A path to a newick file on your local machine.
+
+    ---
+    """
+    knex = state.get_knex()
+    result_folder = handle_folder_id(knex, folder_id, yes=yes, private=private)
+    
+    if not geoseeq_file_name:
+        geoseeq_file_name = basename(newick_file_path)
+    
+    if not overwrite and result_folder.result_file(geoseeq_file_name).exists():
+        raise click.UsageError(f'{geoseeq_file_name} already exists in {result_folder}. Use --overwrite to overwrite it.')
+
+    result_file = result_folder.result_file(geoseeq_file_name)
+    smart_tree = result_file.as_smart_tree()
+    with open(newick_file_path) as f:
+        newick_str = f.read()
+    smart_tree.create_from_newick(newick_str)
+    if make_name_map:
+        smart_tree.add_all_samples_to_map(result_folder.project)
+    smart_tree.idem()

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq/result/result_file.py

@@ -18,9 +18,10 @@ from geoseeq.knex import GeoseeqOtherError
 from .utils import *
 from .file_upload import ResultFileUpload
 from .file_download import ResultFileDownload
+from .smart_objects import ResultFileSmartObjects
 
 
-class ResultFile(RemoteObject, ResultFileUpload, ResultFileDownload):
+class ResultFile(RemoteObject, ResultFileUpload, ResultFileDownload, ResultFileSmartObjects):
     remote_fields = [
         "uuid",
         "created_at",

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq/result/result_folder.py

@@ -225,6 +225,10 @@ class SampleResultFolder(ResultFolder, SampleBioInfoFolder):
 
     def get_fields(self, *args, **kwargs):
         return self.get_result_files(*args, **kwargs)
+    
+    @property
+    def project(self):
+        return self.sample.project
 
     def __str__(self):
         return f"<Geoseeq::SampleResultFolder {self.module_name} {self.replicate} {self.uuid} />"
@@ -288,6 +292,10 @@ class ProjectResultFolder(ResultFolder):
 
     def get_fields(self, *args, **kwargs):
         return self.get_result_files(*args, **kwargs)
+    
+    @property
+    def project(self):
+        return self.grp
 
     def __str__(self):
         return f"<Geoseeq::ProjectResultFolder {self.module_name} {self.replicate} {self.uuid} />"

geoseeq-0.6.15.dev1/geoseeq/result/smart_objects.py

@@ -0,0 +1,40 @@
+
+
+class ResultFileSmartObjects:
+    """Interface for ResultFiles to easily create and use smart objects like tables"""
+
+    def is_smart_table(self):
+        """Return True iff this ResultFile is a smart table."""
+        return self.stored_data.get("__type__") == "smartTable"
+
+    def as_smart_table(self, description=""):
+        """Return a SmartTable object for this ResultFile. Will create a new SmartTable if it doesn't exist yet."""
+        if self.exists() and not self.is_smart_table():
+            raise ValueError("ResultFile exists but is not a smart table")
+        from geoseeq.smart_table import SmartTable  # import here to avoid circular import
+        if self.exists():  # already a smart table
+            smart_table = SmartTable(self.knex, self.name, connected_file_id=self.uuid).get()
+        else:  # create a new smart table
+            smart_table = SmartTable(self.knex, self.name, connected_file_id=self.uuid, description=description)
+            smart_table.create(self.parent)
+        return smart_table
+
+    def is_smart_tree(self):
+        """Return True iff this ResultFile is a smart tree."""
+        return self.stored_data.get("__type__") == "phylodynamics"
+    
+    def as_smart_tree(self, newick_str=None, sample_name_id_map=None):
+        """Return a SmartTree object for this ResultFile. Will create a new SmartTree if it doesn't exist yet."""
+        if self.exists() and not self.is_smart_tree():
+            raise ValueError("ResultFile exists but is not a smart tree")
+        from geoseeq.smart_tree import SmartTree  # import here to avoid circular import
+        if self.exists(): # already a smart tree
+            smart_tree = SmartTree.from_blob(self, self.stored_data)
+        else:  # create a new smart tree
+            smart_tree = SmartTree(self)
+            if newick_str is not None:
+                smart_tree.create_from_newick(newick_str, sample_name_id_map)
+                smart_tree.create()
+        return smart_tree
+
+        

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq/smart_table.py

@@ -53,11 +53,12 @@ class SmartTable(RemoteObject):
 
         without_default_columns: if False the server creates 3 example columns.
         """
-
+        if description:
+            self.description = description
         data = {
             "name": self.name,
             "folder_id": result_folder.uuid,
-            "description": description,
+            "description": self.description,
         }
         url = f"table?without_default_columns={without_default_columns}"
         blob = self.knex.post(url, json=data)

geoseeq-0.6.15.dev1/geoseeq/smart_tree.py

@@ -0,0 +1,57 @@
+class SmartTree:
+
+    def __init__(self, result_file):
+        self.result_file = result_file  # the result file that contains the smart tree
+        self.content = None
+
+    def create_from_newick(self, newick_str, sample_name_id_map=None):
+        self.content = {
+            "__type__": "phylodynamics",
+            "version": "1.0",
+            "tree": {
+                "value": newick_str,
+                "kind": "newick",
+                "sampleNameIdMap": {} if sample_name_id_map is None else sample_name_id_map,
+            }
+        }
+        return self
+    
+    def add_sample_to_map(self, sample):
+        if self.content is None:
+            raise ValueError("Must create tree before adding samples")
+        self.content["tree"]["sampleNameIdMap"][sample.name] = sample.uuid
+        return self
+    
+    def add_all_samples_to_map(self, project):
+        for sample in project.get_samples():
+            self.add_sample_to_map(sample)
+
+    @classmethod
+    def from_blob(cls, result_file, blob):
+        smart_tree = cls(result_file)
+        smart_tree.content = blob
+        return smart_tree
+    
+    def save(self):
+        if self.content is None:
+            raise ValueError("Must create tree before saving")
+        self.result_file.upload_json(self.content)
+        return self
+    
+    def idem(self):
+        if self.content is None:
+            raise ValueError("Must create tree before saving")
+        self.result_file.upload_json(self.content)
+        return self
+    
+    def get(self):
+        self.result_file.get()
+        self.content = self.result_file.stored_data
+        return self
+    
+    def create(self):
+        if self.content is None:
+            raise ValueError("Must create tree before saving")
+        self.result_file.upload_json(self.content)
+        return self
+        

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev7
+Version: 0.6.15.dev1
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/geoseeq.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ geoseeq/remote_object.py
 geoseeq/sample.py
 geoseeq/search.py
 geoseeq/smart_table.py
+geoseeq/smart_tree.py
 geoseeq/upload_download_manager.py
 geoseeq/user.py
 geoseeq/utils.py
@@ -84,6 +85,7 @@ geoseeq/result/result_file.py
 geoseeq/result/result_folder.py
 geoseeq/result/resumable_download_tracker.py
 geoseeq/result/resumable_upload_tracker.py
+geoseeq/result/smart_objects.py
 geoseeq/result/utils.py
 geoseeq/vc/__init__.py
 geoseeq/vc/checksum.py

{geoseeq-0.6.14.dev7 → geoseeq-0.6.15.dev1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "geoseeq"
-version = "0.6.14dev7"
+version = "0.6.15dev1"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]