geoseeq 0.6.2__tar.gz → 0.6.4__tar.gz

{geoseeq-0.6.2 → geoseeq-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.6.2
+Version: 0.6.4
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>
@@ -12,6 +12,11 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: click
+Requires-Dist: pandas
+Requires-Dist: biopython
+Requires-Dist: tqdm
 
 # Geoseeq API Client
 

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/cli/download.py

@@ -160,8 +160,8 @@ def cli_download_files(
 
     \b
     # Download assembly contigs from two samples in the MetaSUB Consortium CSD16 project
-    $ geoseeq download files "MetaSUB Consortium/CSD16" `# specify the project` \ 
-        haib17CEM4890_H2NYMCCXY_SL254769 haib17CEM4890_H2NYMCCXY_SL254773 `# specify the samples by name` \ 
+    $ geoseeq download files "MetaSUB Consortium/CSD16" `# specify the project` \\ 
+        haib17CEM4890_H2NYMCCXY_SL254769 haib17CEM4890_H2NYMCCXY_SL254773 `# specify the samples by name` \\ 
         --folder-type sample --extension '.contigs.fasta' # filter for contig files
 
     ---

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/cli/main.py

@@ -26,7 +26,7 @@ handler.setFormatter(logging.Formatter('[%(levelname)s] %(name)s :: %(message)s'
 logger.addHandler(handler)
 
 
-@click.group()
+@click.group(context_settings={'show_default': True})
 def main():
     """Command line interface for the GeoSeeq API.
     
@@ -54,7 +54,7 @@ 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('0.6.2')  # remember to update setup
+    click.echo('0.6.4')  # remember to update setup
 
 
 @main.group('advanced')

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/constants.py

@@ -2,7 +2,7 @@ from os import environ
 from os.path import join
 
 FIVE_MB = 5 * (1024 ** 2)
-FASTQ_MODULE_NAMES = ['short_read::paired_end', 'short_read::single_end', 'long_read::nanopore']
+FASTQ_MODULE_NAMES = ['short_read::paired_end', 'short_read::single_end', 'long_read::nanopore', 'raw::raw_reads']
 DEFAULT_ENDPOINT = "https://backend.geoseeq.com"
 
 CONFIG_FOLDER = environ.get("XDG_CONFIG_HOME", join(environ["HOME"], ".config"))

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/organization.py

@@ -1,6 +1,8 @@
 
-from .remote_object import RemoteObject
+import urllib
+
 from .project import Project
+from .remote_object import RemoteObject
 
 
 class Organization(RemoteObject):
@@ -19,7 +21,8 @@ class Organization(RemoteObject):
         self.name = name
 
     def nested_url(self):
-        return f'nested/{self.name}'
+        escaped_name = urllib.parse.quote(self.name, safe="")
+        return f'nested/{escaped_name}'
 
     def _save(self):
         data = {

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/project.py

@@ -1,11 +1,13 @@
-from .result import ProjectResultFolder
+import logging
+import urllib
+
+import pandas as pd
+
+from .pipeline import Pipeline
 from .remote_object import RemoteObject
+from .result import ProjectResultFolder
 from .sample import Sample
 from .utils import paginated_iterator
-from .pipeline import Pipeline
-import json
-import pandas as pd
-import logging
 
 logger = logging.getLogger("geoseeq_api")
 
@@ -72,7 +74,8 @@ class Project(RemoteObject):
         return data
 
     def nested_url(self):
-        return self.org.nested_url() + f"/sample_groups/{self.name}"
+        escaped_name = urllib.parse.quote(self.name, safe="")
+        return self.org.nested_url() + f"/sample_groups/{escaped_name}"
 
     def _save_group_obj(self):
         data = self.get_post_data()

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/result/file_download.py

@@ -6,6 +6,7 @@ import os
 from os.path import basename, getsize, join, isfile, getmtime, dirname
 from pathlib import Path
 from tempfile import NamedTemporaryFile
+from math import ceil
 
 from geoseeq.utils import download_ftp
 from geoseeq.constants import FIVE_MB
@@ -43,7 +44,7 @@ def _download_resumable(response, filename, total_size_in_bytes, progress_tracke
     target_id = url_to_id(response.url)
     tracker = ResumableDownloadTracker(chunk_size, target_id, filename)
     if not tracker.download_started: tracker.start_download(response.url)
-    n_chunks = total_size_in_bytes // chunk_size
+    n_chunks = ceil(total_size_in_bytes / chunk_size)
     for i in range(n_chunks):
         bytes_start, bytes_end = i * chunk_size, min((i + 1) * chunk_size - 1, total_size_in_bytes - 1)
         if tracker.part_has_been_downloaded(i):

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/result/result_folder.py

@@ -1,9 +1,6 @@
-import json
-import logging
 import os
-import time
-import urllib.request
-from os.path import basename, getsize, join, isfile, isdir, dirname
+import urllib
+from os.path import basename, dirname, getsize, isdir, isfile, join
 from pathlib import Path
 from tempfile import NamedTemporaryFile
 
@@ -155,7 +152,8 @@ class SampleResultFolder(ResultFolder, SampleBioInfoFolder):
         self.is_private = is_private
 
     def nested_url(self):
-        return self.sample.nested_url() + f"/analysis_results/{self.module_name}"
+        escaped_name = urllib.parse.quote(self.module_name, safe="")
+        return self.sample.nested_url() + f"/analysis_results/{escaped_name}"
 
     def _save(self):
         data = {field: getattr(self, field) for field in self.remote_fields if hasattr(self, field)}

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq/sample.py

@@ -1,5 +1,7 @@
-from .result import SampleResultFolder, SampleResultFile
+import urllib
+
 from .remote_object import RemoteObject
+from .result import SampleResultFile, SampleResultFolder
 
 
 class Sample(RemoteObject):
@@ -33,7 +35,8 @@ class Sample(RemoteObject):
         return f'brn:{self.knex.instance_code()}:sample:{self.uuid}'
 
     def nested_url(self):
-        return self.lib.nested_url() + f"/samples/{self.name}"
+        escaped_name = urllib.parse.quote(self.name, safe="")
+        return self.lib.nested_url() + f"/samples/{escaped_name}"
 
     def change_library(self, new_lib):
         self.new_lib = new_lib
@@ -212,9 +215,19 @@ class Sample(RemoteObject):
                         )
                     else:
                         files[read_type][folder_name].append(
-                            self._grn_to_file(file_grn[0])
+                            self._grn_to_file(file_grn)
                         )
         return files
+    
+    def get_one_fasta(self):
+        """Return a 2-ple, a fasta ResultFile and a string with the read type.
+
+        Does not download the file.
+        """
+        url = f"data/samples/{self.uuid}/one-fasta"
+        blob = self.knex.get(url)
+        file = self._grn_to_file(blob["grn"])
+        return file, blob["read_type"]
 
     def __str__(self):
         return f"<Geoseeq::Sample {self.name} {self.uuid} />"

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.6.2
+Version: 0.6.4
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>
@@ -12,6 +12,11 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: click
+Requires-Dist: pandas
+Requires-Dist: biopython
+Requires-Dist: tqdm
 
 # Geoseeq API Client
 

{geoseeq-0.6.2 → geoseeq-0.6.4}/geoseeq.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ geoseeq.egg-info/PKG-INFO
 geoseeq.egg-info/SOURCES.txt
 geoseeq.egg-info/dependency_links.txt
 geoseeq.egg-info/entry_points.txt
+geoseeq.egg-info/requires.txt
 geoseeq.egg-info/top_level.txt
 geoseeq/cli/__init__.py
 geoseeq/cli/constants.py
@@ -57,9 +58,6 @@ geoseeq/contrib/ncbi/api.py
 geoseeq/contrib/ncbi/bioproject.py
 geoseeq/contrib/ncbi/cli.py
 geoseeq/contrib/ncbi/setup_logging.py
-geoseeq/file_system/__init__.py
-geoseeq/file_system/filesystem_download.py
-geoseeq/file_system/main.py
 geoseeq/id_constructors/__init__.py
 geoseeq/id_constructors/from_blobs.py
 geoseeq/id_constructors/from_ids.py

geoseeq-0.6.4/geoseeq.egg-info/requires.txt

@@ -0,0 +1,5 @@
+requests
+click
+pandas
+biopython
+tqdm

{geoseeq-0.6.2 → geoseeq-0.6.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "geoseeq"
-version = "0.6.2"
+version = "0.6.4"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]
@@ -16,10 +16,17 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
+dependencies = [
+    "requests",
+    "click",
+    "pandas",
+    "biopython",
+    "tqdm",
+]
 
 [project.urls]
 Homepage = "https://github.com/biotia/geoseeq_api_client"
 Issues = "https://github.com/biotia/geoseeq_api_client/issues"
 
 [project.scripts]
-geoseeq = "geoseeq.cli:main"
+geoseeq = "geoseeq.cli:main"

geoseeq-0.6.2/geoseeq/file_system/filesystem_download.py

@@ -1,434 +0,0 @@
-
-import os
-import json
-from geoseeq import (
-    result_file_from_id,
-    result_folder_from_id,
-    sample_from_id,
-    project_from_id,
-)
-from geoseeq.utils import md5_checksum
-from time import time
-
-FILE_STATUS_MODIFIED_REMOTE = 'MODIFIED_REMOTE'
-FILE_STATUS_MODIFIED_LOCAL = 'MODIFIED_LOCAL'
-FILE_STATUS_NEW_LOCAL = 'NEW_LOCAL'
-FILE_STATUS_NEW_REMOTE = 'NEW_REMOTE'
-FILE_STATUS_IS_LOCAL_STUB = 'IS_LOCAL_STUB'
-
-
-def dedupe_modified_files(modified_files):
-    """Remove duplicates from a list of modified files.
-    
-    This function will remove duplicates from a list of modified files
-    based on the path to the file. The first instance of the file will be
-    kept and all others will be removed.
-    """
-    seen = set()
-    deduped = []
-    for x in modified_files:
-        if x[2] not in seen:
-            deduped.append(x)
-            seen.add(x[2])
-    return deduped
-
-
-class ResultFileOnFilesystem:
-    """
-
-    Note: unlike other filesystem classes the `path` is a file, not
-    a directory. This is because the file is downloaded directly to 
-    the path.
-    """
-
-    def __init__(self, result_file, path, kind):
-        self.result_file = result_file
-        self.path = path
-        self.kind = kind
-
-    @property
-    def info_filepath(self):
-        dirpath = os.path.dirname(self.path)
-        basename = os.path.basename(self.path)
-        return os.path.join(dirpath, f'.gs_result_file__{basename}')
-    
-    @property
-    def is_stub(self):
-        return os.path.exists(self.path) and os.path.getsize(self.path) == 0
-    
-    def file_is_ok(self, stubs_are_ok=False):
-        if self.is_stub:
-            return stubs_are_ok
-        return self.result_file.download_needs_update(self.path)
-
-    def download(self, use_stubs=False, exists_ok=False):
-        if os.path.exists(self.info_filepath):
-            if exists_ok and self.file_is_ok(stubs_are_ok=use_stubs):
-                return
-            elif not exists_ok:
-                raise ValueError('Result file already exists at path: {}'.format(self.info_filepath))
-        
-        # Download the file
-        if use_stubs:
-            open(self.path, 'w').close()
-        else:
-            self.result_file.download(self.path)
-
-        self.write_info_file()
-
-    def local_file_checksum(self):
-        if self.is_stub:
-            return "__STUB__"
-        return md5_checksum(self.path)
-    
-    def locally_modified(self):
-        raise NotImplementedError('This function is not implemented')
-
-    def status_is_ok(self, stubs_are_ok=False):
-        # check for an info file
-        if not os.path.exists(self.info_filepath):
-            return False
-        if stubs_are_ok:
-            return True
-        return not self.result_file.download_needs_update(self.path)
-    
-    def write_info_file(self):
-        result_file_info = {
-            "uuid": self.result_file.uuid,
-            "kind": self.kind,
-            "checksum": self.local_file_checksum(),
-        }
-        with open(self.info_filepath, 'w') as f:
-            json.dump(result_file_info, f)
-
-    @classmethod
-    def from_path(cls, path):
-        obj = cls(None, path, None)
-        try:
-            with open(obj.info_filepath, 'r') as f:
-                result_file_info = json.load(f)
-            obj.result_file = result_file_from_id(result_file_info['uuid'])
-            obj.kind = result_file_info['kind']
-            obj.stored_checksum = result_file_info['checksum']
-        except FileNotFoundError:
-            pass
-        return obj
-    
-    def write_info_file(self):
-        result_file_info = {
-            "uuid": self.result_file.uuid,
-            "kind": self.kind,
-            "checksum": self.local_file_checksum(),
-        }
-        with open(self.info_filepath, 'w') as f:
-            json.dump(result_file_info, f)
-    
-    def list_abnormal_objects(self):
-        """Return a list of files that have been modified.
-        
-        Since this class is a single file the list will either be empty
-        or have one element.
-
-        Note that if a file was modified locally then uploaded to the server
-        the file will be marked as modified remote.
-        """
-        if self.result_file is None:
-            return [('FILE', FILE_STATUS_NEW_LOCAL, self.path, None)]
-        if not os.path.exists(self.path):
-            return [('FILE', FILE_STATUS_NEW_REMOTE, self.path, self.result_file)]
-        if self.is_stub:
-            return [('FILE', FILE_STATUS_IS_LOCAL_STUB, self.path, self.result_file)]
-        if self.result_file and self.result_file.download_needs_update(self.path):
-            return [('FILE', FILE_STATUS_MODIFIED_REMOTE, self.path, self.result_file)]
-        if self.locally_modified():
-            return [('FILE', FILE_STATUS_MODIFIED_LOCAL, self.path, self.result_file)]
-
-        return []
-
-    
-class ResultFolderOnFilesystem:
-
-    def __init__(self, result_folder, path, kind):
-        self.result_folder = result_folder
-        self.path = path
-        self.kind = kind
-
-    @property
-    def info_filepath(self):
-        return os.path.join(self.path, '.gs_result_folder')
-
-    def download(self, use_stubs=False, exists_ok=False):
-        if os.path.exists(self.info_filepath) and not exists_ok:
-            raise ValueError('Result folder already exists at path: {}'.format(self.info_filepath))
-        
-        # Download the files in the result folder
-        for result_file in self.result_folder.get_fields():
-            result_file_local_path = os.path.join(self.path, result_file.name)
-            os.makedirs(os.path.dirname(result_file_local_path), exist_ok=True)
-            ResultFileOnFilesystem(result_file, result_file_local_path, self.kind)\
-                .download(use_stubs=use_stubs, exists_ok=exists_ok)
-        
-        # Write the result folder data
-        result_folder_info = {
-            "uuid": self.result_folder.uuid,
-            "kind": self.kind
-        }
-        with open(self.info_filepath, 'w') as f:
-            json.dump(result_folder_info, f)
-
-    def status_is_ok(self):
-        # check for an info file
-        if not os.path.exists(self.info_filepath):
-            return False
-        
-        # check that all files are downloaded
-        for result_file in self.result_folder.get_files():
-            result_file_path = os.path.join(self.path, result_file.name)
-            if not os.path.exists(result_file_path):
-                return False
-        
-        return True
-    
-    @classmethod
-    def from_path(cls, path):
-        obj = cls(None, path, None)
-        try:
-            with open(os.path.join(path, '.gs_result_folder'), 'r') as f:
-                result_folder_info = json.load(f)
-            obj.result_folder = result_folder_from_id(result_folder_info['uuid'])
-            obj.kind = result_folder_info['kind']
-        except FileNotFoundError:
-            pass
-        return obj
-    
-    def list_abnormal_objects(self):
-        """Return a list of files that have been modified.
-        
-        This function will return a list of tuples where the first element
-        is the status of the file and the second element is the path to the file.
-        """
-        modified_files = []
-        if not self.result_folder:
-            modified_files.append(('FOLDER', FILE_STATUS_NEW_LOCAL, self.path, None))
-        if not os.path.exists(self.path):
-            modified_files.append(('FOLDER', FILE_STATUS_NEW_REMOTE, self.path, self.result_folder))
-
-        # list local files
-        if os.path.exists(self.path):
-            for local_file in os.listdir(self.path):
-                if local_file.startswith('.gs_'):
-                    continue
-                local_file_path = os.path.join(self.path, local_file)
-                result_file_on_fs = ResultFileOnFilesystem.from_path(local_file_path)
-                modified_files.extend(result_file_on_fs.list_abnormal_objects())
-
-        # list remote files
-        if self.result_folder:
-            for result_file in self.result_folder.get_fields():
-                result_file_path = os.path.join(self.path, result_file.name)
-                result_file_on_fs = ResultFileOnFilesystem(result_file, result_file_path, self.kind)
-                modified_files.extend(result_file_on_fs.list_abnormal_objects())
-    
-        return dedupe_modified_files(modified_files)
-    
-
-class SampleOnFilesystem:
-
-    def __init__(self, sample, path):
-        self.sample = sample
-        self.path = path if path[-1] != '/' else path[:-1]  # remove trailing slash
-
-    @property
-    def info_filepath(self):
-        return os.path.join(self.path, '.gs_sample')
-
-    def download(self, use_stubs=False, exists_ok=False):
-        if os.path.exists(self.info_filepath) and not exists_ok:
-            raise ValueError('Sample already exists at path: {}'.format(self.info_filepath))
-        
-        # download result folders
-        for result_folder in self.sample.get_result_folders():
-            result_folder_local_path = os.path.join(self.path, result_folder.name)
-            os.makedirs(result_folder_local_path, exist_ok=True)
-            ResultFolderOnFilesystem(result_folder, result_folder_local_path, "sample")\
-                .download(use_stubs=use_stubs, exists_ok=exists_ok)
-
-        # Write the sample data
-        sample_info = {
-            "uuid": self.sample.uuid
-        }
-        with open(self.info_filepath, 'w') as f:
-            json.dump(sample_info, f)
-
-    def status_is_ok(self):
-        # check for an info file
-        if not os.path.exists(self.info_filepath):
-            return False
-        
-        # check that all result folders are downloaded
-        for result_folder in self.sample.get_result_folders():
-            result_folder_local_path = os.path.join(self.path, result_folder.name)
-            result_folder_on_fs = ResultFolderOnFilesystem.from_path(result_folder_local_path, "sample")
-            if not result_folder_on_fs.status_is_ok():
-                return False
-        
-        return True
-
-    @classmethod
-    def from_path(cls, path):
-        obj = cls(None, path)
-        try:
-            with open(os.path.join(path, '.gs_sample'), 'r') as f:
-                sample_info = json.load(f)
-            obj.sample = sample_from_id(sample_info['uuid'])
-        except FileNotFoundError:
-            pass
-        return obj
-    
-    def list_abnormal_objects(self):
-        """Return a list of files that have been modified.
-        
-        This function will return a list of tuples where the first element
-        is the status of the file and the second element is the path to the file.
-        """
-        modified_files = []
-        if not self.sample:
-            modified_files.append(('SAMPLE', FILE_STATUS_NEW_LOCAL, self.path, None))
-        if not os.path.exists(self.path):
-            modified_files.append(('SAMPLE', FILE_STATUS_NEW_REMOTE, self.path, self.sample))
-
-        # list local folders
-        if os.path.exists(self.path):
-            for local_folder in os.listdir(self.path):
-                local_folder_path = os.path.join(self.path, local_folder)
-                if not os.path.isdir(local_folder_path):
-                    continue
-                result_folder_on_fs = ResultFolderOnFilesystem.from_path(local_folder_path)
-                modified_files.extend(result_folder_on_fs.list_abnormal_objects())
-
-        # list remote folders
-        if self.sample:
-            for result_folder in self.sample.get_result_folders():
-                result_folder_path = os.path.join(self.path, result_folder.name)
-                result_folder_on_fs = ResultFolderOnFilesystem(result_folder, result_folder_path, "sample")
-                modified_files.extend(result_folder_on_fs.list_abnormal_objects())
-
-        return dedupe_modified_files(modified_files)
-
-
-class ProjectOnFilesystem:
-
-    def __init__(self, project, path):
-        self.project = project
-        self.path = path
-
-    @property
-    def info_filepath(self):
-        return os.path.join(self.path, '.gs_project')
-
-    def download(self, use_stubs=False, exists_ok=False):
-        if os.path.exists(self.info_filepath) and not exists_ok:
-            raise ValueError('Project already exists at path: {}'.format(self.info_filepath))
-        
-        # download samples
-        for sample in self.project.get_samples():
-            sample_local_path = os.path.join(self.path, "sample_results", sample.name)
-            os.makedirs(sample_local_path, exist_ok=True)
-            SampleOnFilesystem(sample, sample_local_path)\
-                .download(use_stubs=use_stubs, exists_ok=exists_ok)
-        
-        # download project result folders
-        for result_folder in self.project.get_result_folders():
-            result_folder_local_path = os.path.join(self.path, "project_results", result_folder.name)
-            os.makedirs(result_folder_local_path, exist_ok=True)
-            ResultFolderOnFilesystem(result_folder, result_folder_local_path, "project")\
-                .download(use_stubs=use_stubs, exists_ok=exists_ok)
-
-        # Write the project data
-        project_info = {
-            "uuid": self.project.uuid
-        }
-        with open(self.info_filepath, 'w') as f:
-            json.dump(project_info, f)
-
-    def status_is_ok(self):
-        # check for an info file
-        if not os.path.exists(self.info_filepath):
-            return False
-        
-        # check that all samples are downloaded
-        for sample in self.project.get_samples():
-            sample_local_path = os.path.join(self.path, "sample_results", sample.name)
-            sample_on_fs = SampleOnFilesystem.from_path(sample_local_path)
-            if not sample_on_fs.status_is_ok():
-                return False
-        
-        # check that all project result folders are downloaded
-        for result_folder in self.project.get_result_folders():
-            result_folder_local_path = os.path.join(self.path, "project_results", result_folder.name)
-            result_folder_on_fs = ResultFolderOnFilesystem.from_path(result_folder_local_path, "project")
-            if not result_folder_on_fs.status_is_ok():
-                return False
-        
-        return True
-
-    @classmethod
-    def from_path(cls, path, recursive=False):
-        try:
-            with open(os.path.join(path, '.gs_project'), 'r') as f:
-                project_info = json.load(f)
-            project = project_from_id(project_info['uuid'])
-            return cls(project, path)
-        except FileNotFoundError:
-            if not recursive:
-                raise ValueError('No project found in path or parent directories')
-            updir = os.path.dirname(os.path.abspath(path))
-            if updir == path:
-                raise ValueError('No project found in path or parent directories')
-            return cls.from_path(updir, recursive=recursive)
-        
-    def path_from_project_root(self, path):
-        if path[0] == "/":
-            return path.replace(self.path, "")[1:]
-        return path
-
-    def list_abnormal_objects(self):
-        """Return a list of files that have been modified.
-        
-        This function will return a list of tuples where the first element
-        is the status of the file and the second element is the path to the file.
-        """
-        modified_files = []
-
-        # list remote samples
-        for sample in self.project.get_samples():
-            sample_path = os.path.join(self.path, "sample_results", sample.name)
-            sample_on_fs = SampleOnFilesystem(sample, sample_path)
-            modified_files.extend(sample_on_fs.list_abnormal_objects())
-
-        # list remote project result folders
-        for result_folder in self.project.get_result_folders():
-            result_folder_path = os.path.join(self.path, "project_results", result_folder.name)
-
-            result_folder_on_fs = ResultFolderOnFilesystem(result_folder, result_folder_path, "project")
-            modified_files.extend(result_folder_on_fs.list_abnormal_objects())
-
-        # list local samples
-        for local_sample in os.listdir(os.path.join(self.path, "sample_results")):
-            local_sample_path = os.path.join(self.path, "sample_results", local_sample)
-            if not os.path.isdir(local_sample_path):
-                continue
-            sample_on_fs = SampleOnFilesystem.from_path(local_sample_path)
-            modified_files.extend(sample_on_fs.list_abnormal_objects())
-
-        # list local project result folders
-        for local_result_folder in os.listdir(os.path.join(self.path, "project_results")):
-            local_result_folder_path = os.path.join(self.path, "project_results", local_result_folder)
-            if not os.path.isdir(local_result_folder_path):
-                continue
-            result_folder_on_fs = ResultFolderOnFilesystem.from_path(local_result_folder_path)
-            modified_files.extend(result_folder_on_fs.list_abnormal_objects())
-        return dedupe_modified_files(modified_files)
-                
-
-

geoseeq-0.6.2/geoseeq/file_system/main.py

@@ -1,122 +0,0 @@
-from fuse import FUSE, Operations
-import os
-
-
-class GeoSeeqProjectFileSystem(Operations):
-    """Mount a GeoSeeq project as a filesystem.
-    
-    The project will automatically have this directory structure:
-    - <root>/project_results/<project_result_folder_name>/...
-    - <root>/sample_results/<sample_name>/...
-    - <root>/metadata/sample_metadata.csv
-    - <root>/.config/config.json
-    """
-
-    def __init__(self, root, project):
-        self.root = root
-        self.project = project
-
-    def access(self, path, mode):
-        pass
-
-    def chmod(self, path, mode):
-        pass
-
-    def chown(self, path, uid, gid):
-        pass
-
-    def getattr(self, path, fh=None):
-        pass
-
-    def readdir(self, path, fh):
-        pass
-
-    def readlink(self, path):
-        pass
-
-    def mknod(self, path, mode, dev):
-        pass
-
-    def rmdir(self, path):
-        pass
-
-    def mkdir(self, path, mode):
-        pass
-
-    def statfs(self, path):
-        pass
-
-    def unlink(self, path):
-        pass
-
-    def symlink(self, name, target):
-        pass
-
-    def rename(self, old, new):
-        pass
-
-    def link(self, target, name):
-        pass
-
-    def utimens(self, path, times=None):
-        pass
-
-    def open(self, path, flags):
-        tkns = path.split('/')
-        if tkns[0] == 'project_results':
-            result_folder_name, result_file_name = tkns[2], '/'.join(tkns[3:])
-            result_folder = self.project.get_result_folder(result_folder_name).get()
-            result_file = result_folder.get_file(result_file_name).get()
-            result_file.download(path)
-        elif tkns[0] == 'sample_results':
-            sample_name, result_folder_name, result_file_name = tkns[2], tkns[3], '/'.join(tkns[4:])
-            sample = self.project.get_sample(sample_name).get()
-            result_folder = sample.get_result_folder(result_folder_name).get()
-            result_file = result_folder.get_file(result_file_name).get()
-            result_file.download(path)
-        elif tkns[0] == 'metadata':
-            raise NotImplementedError('TODO')
-        
-        return os.open(self._full_local_path(path), flags)
-
-    def create(self, path, mode, fi=None):
-        tkns = path.split('/')
-        if tkns[0] == 'project_results':
-            result_name, file_name = tkns[2], '/'.join(tkns[3:])
-            result_folder = self.project.get_result_folder(result_name).idem()
-            result_file = result_folder.get_file(file_name).create()
-            result_file.download(path)  # nothing to download at this point
-        elif tkns[0] == 'sample_results':
-            sample_name, result_folder_name, result_file_name = tkns[2], tkns[3], '/'.join(tkns[4:])
-            sample = self.project.get_sample(sample_name).idem()
-            result_folder = sample.get_result_folder(result_folder_name).idem()
-            result_file = result_folder.get_file(result_file_name).create()
-            result_file.download(path)  # nothing to download at this point
-        elif tkns[0] == 'metadata':
-            raise NotImplementedError('TODO')
-
-    def read(self, path, length, offset, fh):
-        os.lseek(fh, offset, os.SEEK_SET)
-        return os.read(fh, length)
-
-    def write(self, path, buf, offset, fh):
-        pass
-
-    def truncate(self, path, length, fh=None):
-        pass
-
-    def flush(self, path, fh):
-        pass
-
-    def release(self, path, fh):
-        pass
-
-    def fsync(self, path, fdatasync, fh):
-        pass
-    
-    def _full_local_path(self, partial):
-        if partial.startswith("/"):
-            partial = partial[1:]
-        return os.path.join(self.root, partial)
-
-