Launch validation (#414)

* WIP

* Cleanup

* Validation

* typo

* Max category limit 100 -> 500

server/app/driver/driver.py

@@ -14,9 +14,9 @@ class CXGDriver(metaclass=ABCMeta):
 
     def __init__(self, data, args):
         self.data = self._load_data(data)
-        self.layout_method = args['layout']
+        self.layout_method = args["layout"]
-        self.diffexp_method = args['diffexp']
+        self.diffexp_method = args["diffexp"]
-        self.max_category_items = args['max_category_items']
+        self.max_category_items = args["max_category_items"]
         self.cluster = None
 
     @property

server/app/rest_api/rest.py

@@ -10,7 +10,8 @@ from werkzeug.datastructures import ImmutableMultiDict
 from server.app.util.constants import Axis, DiffExpMode
 from server.app.util.filter import parse_filter, QueryStringError
 from server.app.util.models import FilterModel
-from server.app.util.utils import FilterError, InteractiveError, MimeTypeError, PrepareError, get_mime_type
+from server.app.util.utils import get_mime_type
+from server.app.util.errors import MimeTypeError, FilterError, InteractiveError, PrepareError
 
 """
 Sort order for routes

server/app/scanpy_engine/scanpy_engine.py

@@ -2,12 +2,13 @@ import warnings
 
 import numpy as np
 from pandas import DataFrame
+from pandas.core.dtypes.dtypes import CategoricalDtype
 import scanpy.api as sc
 from scipy import stats, sparse
 
 from server.app.driver.driver import CXGDriver
 from server.app.util.constants import Axis, DEFAULT_TOP_N, DiffExpMode
-from server.app.util.utils import FilterError, InteractiveError, PrepareError
+from server.app.util.errors import FilterError, InteractiveError, PrepareError, ScanpyFileError
 
 """
 Sort order for methods
@@ -23,9 +24,10 @@ class ScanpyEngine(CXGDriver):
 
     def __init__(self, data, args):
         super().__init__(data, args)
-        self._alias_annotation_names(Axis.OBS, args['obs_names'])
+        self._alias_annotation_names(Axis.OBS, args["obs_names"])
-        self._alias_annotation_names(Axis.VAR, args['var_names'])
+        self._alias_annotation_names(Axis.VAR, args["var_names"])
         self._validate_data_types()
+        self._validate_data_calculations()
         self.cell_count = self.data.shape[0]
         self.gene_count = self.data.shape[1]
         self.layout_options = ["umap", "tsne"]
@@ -39,27 +41,28 @@ class ScanpyEngine(CXGDriver):
         As a *critical* side-effect, ensure the indices are simple number ranges
         (accomplished by calling pandas.DataFrame.reset_index())
         """
-        if name == 'name':
+        if name == "name":
             # a noop, so skip it
             return
 
         ax_name = str(axis)
         df_axis = getattr(self.data, ax_name)
         if name is None:
-            # reset index to simple range; alias 'name' to point at the
+            # reset index to simple range; alias "name" to point at the
             # previously specified index.
-            df_axis = df_axis.reset_index().rename(columns={'index': 'name'})
+            df_axis.reset_index(inplace=True)
+            df_axis.rename(inplace=True, columns={"index": "name"})
         elif name in df_axis.columns:
             if name not in df_axis.columns:
                 raise KeyError(f"Annotation name {name}, specified in --{ax_name}-name does not exist.")
             if not df_axis[name].is_unique:
                 raise KeyError(f"Values in -{ax_name}-name must be unique. "
                                "Please prepare data to contain unique values.")
-            # reset index to simple range; alias user-specified annotation to 'name'
+            # reset index to simple range; alias user-specified annotation to "name"
-            df_axis = df_axis.reset_index(drop=True).rename(columns={name: 'name'})
+            df_axis.reset_index(drop=True, inplace=True)
+            df_axis.rename(inplace=True, columns={name: "name"})
         else:
             raise KeyError(f"Annotation name {name}, specified in --{ax_name}_name does not exist.")
-        setattr(self.data, ax_name, df_axis)
 
     def _create_schema(self):
         self.schema = {
@@ -78,9 +81,9 @@ class ScanpyEngine(CXGDriver):
             for ann in curr_axis:
                 ann_schema = {"name": ann}
                 data_kind = curr_axis[ann].dtype.kind
-                if data_kind == 'f':
+                if data_kind == "f":
                     ann_schema["type"] = "float32"
-                elif data_kind in ['i', 'u']:
+                elif data_kind in ["i", "u"]:
                     ann_schema["type"] = "int32"
                 elif data_kind == "?":
                     ann_schema["type"] = "boolean"
@@ -98,7 +101,18 @@ class ScanpyEngine(CXGDriver):
         # Based on benchmarking, cache=True has no impact on perf.
         # Note: as of current scanpy/anndata release, setting backed='r' will
         # result in an error.  https://github.com/theislab/anndata/issues/79
-        return sc.read(data, cache=False)
+        try:
+            result = sc.read(data, cache=True)
+        except ValueError:
+            raise ScanpyFileError("File must be in the .h5ad format. Please read "
+                                  "https://github.com/theislab/scanpy_usage/blob/master/170505_seurat/info_h5ad.md to "
+                                  "learn more about this format. You may be able to convert your file into this format "
+                                  "using `cellxgene prepare`, please run `cellxgene prepare --help` for more "
+                                  "information.")
+        except Exception as e:
+            raise ScanpyFileError(f"Error while loading file: {e}, File must be in the .h5ad format, please check "
+                                  f"that your input and try again.")
+        return result
 
     @staticmethod
     def _top_sort(values, sort_order, top_n=None):
@@ -137,14 +151,34 @@ class ScanpyEngine(CXGDriver):
             curr_axis = getattr(self.data, str(ax))
             for ann in curr_axis:
                 datatype = curr_axis[ann].dtype
-                downcast_map = {'int64': 'int32',
+                downcast_map = {"int64": "int32",
-                                'uint32': 'int32',
+                                "uint32": "int32",
-                                'uint64': 'int32',
+                                "uint64": "int32",
-                                'float64': 'float32',
+                                "float64": "float32",
                                 }
                 if datatype in downcast_map:
                     warnings.warn(f"Scanpy annotation {ax}:{ann} is in unsupported format: {datatype}. "
                                   f"Data will be downcast to {downcast_map[datatype]}.")
+                if isinstance(datatype, CategoricalDtype):
+                    category_num = len(curr_axis[ann].dtype.categories)
+                    if category_num > 500 and category_num > self.max_category_items:
+                        warnings.warn(
+                            f"{str(ax).title()} annotation '{ann}' has {category_num} categories, this may be "
+                            f"cumbersome or slow to display. We recommend setting the "
+                            f"--max-category-items option to 500, this will hide categorical "
+                            f"annotations with more than 500 categories in the UI")
+
+    def _validate_data_calculations(self):
+        layout_key = f"X_{self.layout_method}"
+        try:
+            assert layout_key in self.data.obsm_keys()
+        except AssertionError:
+            raise PrepareError(
+                f"Cannot find a field with coordinates for the {self.layout_method} layout requested. A different"
+                f" layout may have been computed. The requested layout must be pre-calculated and saved "
+                f"back in the h5ad file. You can run "
+                f"`cellxgene prepare --layout {self.layout_method} <datafile>` "
+                f"to solve this problem. ")
 
     def filter_dataframe(self, filter, include_uns=False):
         """
@@ -232,8 +266,8 @@ class ScanpyEngine(CXGDriver):
 
         https://docs.scipy.org/doc/scipy/reference/sparse.html
         """
-        prefer_row_access = sparse.isspmatrix_csr(data._X) or \
+        prefer_row_access = sparse.isspmatrix_csr(data._X) or sparse.isspmatrix_lil(data._X) \
-            sparse.isspmatrix_lil(data._X) or sparse.isspmatrix_bsr(data._X)
+            or sparse.isspmatrix_bsr(data._X)
         if prefer_row_access:
             # Row-major slicing
             if obs_selector is not None:

server/app/util/errors.py

@@ -0,0 +1,43 @@
+class FilterError(Exception):
+    """
+    Raised when filter is malformed
+    """
+
+    def __init__(self, message):
+        self.message = message
+
+
+class InteractiveError(Exception):
+    """
+    Raised when computation would exceed interactive time
+    """
+
+    def __init__(self, message):
+        self.message = message
+
+
+class MimeTypeError(Exception):
+    """
+    Raised when incompatible MIME type selected
+    """
+
+    def __init__(self, message):
+        self.message = message
+
+
+class PrepareError(Exception):
+    """
+    Raised when data is misprepared
+    """
+
+    def __init__(self, message):
+        self.message = message
+
+
+class ScanpyFileError(Exception):
+    """
+    Raised when file loaded into scanpy is misformatted
+    """
+
+    def __init__(self, message):
+        self.message = message

server/app/util/utils.py

@@ -3,6 +3,8 @@ from argparse import ArgumentTypeError
 
 from numpy import float32, integer
 
+from server.app.util.errors import MimeTypeError
+
 
 class Float32JSONEncoder(json.JSONEncoder):
     def default(self, obj):
@@ -13,30 +15,6 @@ class Float32JSONEncoder(json.JSONEncoder):
         return json.JSONEncoder.default(self, obj)
 
 
-class MimeTypeError(Exception):
-
-    def __init__(self, message):
-        self.message = message
-
-
-class FilterError(Exception):
-
-    def __init__(self, message):
-        self.message = message
-
-
-class InteractiveError(Exception):
-
-    def __init__(self, message):
-        self.message = message
-
-
-class PrepareError(Exception):
-
-    def __init__(self, message):
-        self.message = message
-
-
 def get_mime_type(default="application/json", acceptable_types=["application/json", "text/csv"], query_param=None,
                   header=None):
     mime_type = default

server/cli/cli.py

@@ -4,8 +4,8 @@ from .launch import launch
 from .prepare import prepare
 
 
-@click.group(name='cellxgene', context_settings=dict(max_content_width=85))
+@click.group(name="cellxgene", context_settings=dict(max_content_width=85))
-@click.version_option(version='0.0.1', prog_name='cellxgene', message='[%(prog)s] Version %(version)s')
+@click.version_option(version="0.0.1", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
 def cli():
     pass
 

server/cli/launch.py

@@ -1,31 +1,32 @@
 import sys
 import click
 import logging
+from os.path import splitext, basename
 import webbrowser
 
-from os.path import splitext, basename
+from server.app.util.errors import ScanpyFileError
 
 
 @click.command()
-@click.argument('data', metavar='<data file>', type=click.Path(exists=True, file_okay=True, dir_okay=False))
+@click.argument("data", metavar="<data file>", type=click.Path(exists=True, file_okay=True, dir_okay=False))
-@click.option('--layout', '-l', type=click.Choice(['umap', 'tsne']), default='umap', show_default=True,
+@click.option("--layout", "-l", type=click.Choice(["umap", "tsne"]), default="umap", show_default=True,
-              help='Method for layout.')
+              help="Method for layout.")
-@click.option('--diffexp', '-d', type=click.Choice(['ttest']), default='ttest', show_default=True,
+@click.option("--diffexp", "-d", type=click.Choice(["ttest"]), default="ttest", show_default=True,
-              help='Method for differential expression.')
+              help="Method for differential expression.")
-@click.option('--title', '-t', help='Title to display (if omitted will use file name).', metavar='')
+@click.option("--title", "-t", help="Title to display (if omitted will use file name).", metavar="")
-@click.option('--verbose', '-v', is_flag=True, default=False, show_default=True,
+@click.option("--verbose", "-v", is_flag=True, default=False, show_default=True,
-              help='Provide verbose output, including warnings and all server requests.')
+              help="Provide verbose output, including warnings and all server requests.")
-@click.option('--debug', '-d', is_flag=True, default=False, show_default=True,
+@click.option("--debug", "-d", is_flag=True, default=False, show_default=True,
-              help='Run in debug mode.')
+              help="Run in debug mode.")
-@click.option('--open', '-o', 'open_browser', is_flag=True, default=False, show_default=True,
+@click.option("--open", "-o", "open_browser", is_flag=True, default=False, show_default=True,
-              help='Open the web browser after launch.')
+              help="Open the web browser after launch.")
-@click.option('--port', '-p', help="Port to run server on.", metavar='', default=5005, show_default=True)
+@click.option("--port", "-p", help="Port to run server on.", metavar="", default=5005, show_default=True)
-@click.option('--obs-names', default=None, metavar='', help='Name of annotation field to use for observations.')
+@click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
-@click.option('--var-names', default=None, metavar='', help='Name of annotation to use for variables.')
+@click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
-@click.option('--listen-all', is_flag=True, default=False, show_default=True,
+@click.option("--listen-all", is_flag=True, default=False, show_default=True,
-              help='Bind to all interfaces (this makes the server accessible beyond this computer).')
+              help="Bind to all interfaces (this makes the server accessible beyond this computer).")
-@click.option('--max-category-items', default=100, metavar='', show_default=True,
+@click.option("--max-category-items", default=100, metavar="", show_default=True,
-              help='Limits the number of categorical annotation items displayed.')
+              help="Limits the number of categorical annotation items displayed.")
 def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
            open_browser, port, listen_all, max_category_items):
     """Launch the cellxgene data viewer.
@@ -40,15 +41,15 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
     > cellxgene launch <your data file> --title <your title>"""
 
     # Startup message
-    click.echo('[cellxgene] Starting the CLI...')
+    click.echo("[cellxgene] Starting the CLI...")
 
     # Import Flask app
     from server.app.app import app
 
     # Argument checking
     name, extension = splitext(data)
-    if extension != '.h5ad':
+    if extension != ".h5ad":
-        raise click.FileError(basename(data), hint='file type must be .h5ad')
+        raise click.FileError(basename(data), hint="file type must be .h5ad")
 
     if debug:
         verbose = True
@@ -62,9 +63,9 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
         title = file_parts[0]
 
     if listen_all:
-        host = '0.0.0.0'
+        host = "0.0.0.0"
     else:
-        host = '127.0.0.1'
+        host = "127.0.0.1"
 
     # Setup app
     cellxgene_url = f"http://{host}:{port}"
@@ -76,24 +77,32 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
         )
 
     if not verbose:
-        log = logging.getLogger('werkzeug')
+        log = logging.getLogger("werkzeug")
         log.setLevel(logging.ERROR)
 
-    click.echo(f'[cellxgene] Loading data from {basename(data)}, this may take awhile...')
+    click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take awhile...")
 
     from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
 
-    args = {'layout': layout, 'diffexp': diffexp, 'max_category_items': max_category_items,
+    args = {
-            'obs_names': obs_names, 'var_names': var_names}
+        "layout": layout,
+        "diffexp": diffexp,
+        "max_category_items": max_category_items,
+        "obs_names": obs_names,
+        "var_names": var_names
+    }
 
-    app.data = ScanpyEngine(data, args)
+    try:
+        app.data = ScanpyEngine(data, args)
+    except ScanpyFileError as e:
+        raise click.ClickException(f"{e}")
 
     if open_browser:
-        click.echo(f'[cellxgene] Launching! Opening your browser to {cellxgene_url} now.')
+        click.echo(f"[cellxgene] Launching! Opening your browser to {cellxgene_url} now.")
         webbrowser.open(cellxgene_url)
     else:
-        click.echo(f'[cellxgene] Launching! Please go to {cellxgene_url} in your browser.')
+        click.echo(f"[cellxgene] Launching! Please go to {cellxgene_url} in your browser.")
 
-    click.echo('[cellxgene] Type CTRL-C at any time to exit.')
+    click.echo("[cellxgene] Type CTRL-C at any time to exit.")
 
     app.run(host=host, debug=debug, port=port, threaded=True)

server/cli/prepare.py

@@ -1,26 +1,26 @@
-import click
+from os.path import expanduser, isdir, isfile, sep, splitext
 
-from numpy import unique, ndarray
+import click
+from numpy import ndarray, unique
 from scipy.sparse.csc import csc_matrix
-from os.path import isfile, isdir, splitext, expanduser, sep
 
 
 @click.command()
-@click.argument('data', nargs=1, metavar='<dataset: file or path to data>', required=True)
+@click.argument("data", nargs=1, metavar="<dataset: file or path to data>", required=True)
-@click.option('--layout', '-l', default=['umap', 'tsne'], multiple=True, type=click.Choice(['umap', 'tsne']),
+@click.option("--layout", "-l", default=["umap", "tsne"], multiple=True, type=click.Choice(["umap", "tsne"]),
-              help='Layout algorithm', show_default=True)
+              help="Layout algorithm", show_default=True)
-@click.option('--recipe', '-r', default='none', type=click.Choice(['none', 'seurat', 'zheng17']),
+@click.option("--recipe", "-r", default="none", type=click.Choice(["none", "seurat", "zheng17"]),
-              help='Preprocessing to run.', show_default=True)
+              help="Preprocessing to run.", show_default=True)
-@click.option('--output', '-o', default='', help='Save a new file to filename.', metavar='<filename>')
+@click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
-@click.option('--plotting', '-p', default=False, is_flag=True, help='Whether to generate plots.', show_default=True)
+@click.option("--plotting", "-p", default=False, is_flag=True, help="Whether to generate plots.", show_default=True)
-@click.option('--sparse', default=False, is_flag=True, help='Whether to force sparsity.', show_default=True)
+@click.option("--sparse", default=False, is_flag=True, help="Whether to force sparsity.", show_default=True)
-@click.option('--overwrite', default=False, is_flag=True, help='Allow file overwriting.', show_default=True)
+@click.option("--overwrite", default=False, is_flag=True, help="Allow file overwriting.", show_default=True)
-@click.option('--set-obs-names', default='', help='Named field to set as index for obs.', metavar='<name>')
+@click.option("--set-obs-names", default="", help="Named field to set as index for obs.", metavar="<name>")
-@click.option('--set-var-names', default='', help='Named field to set as index for var.', metavar='<name>')
+@click.option("--set-var-names", default="", help="Named field to set as index for var.", metavar="<name>")
-@click.option('--make-obs-names-unique', default=True, is_flag=True,
+@click.option("--make-obs-names-unique", default=True, is_flag=True,
-              help='Ensure obs index is unique.', show_default=True)
+              help="Ensure obs index is unique.", show_default=True)
-@click.option('--make-var-names-unique', default=True, is_flag=True,
+@click.option("--make-var-names-unique", default=True, is_flag=True,
-              help='Ensure var index is unique.', show_default=True)
+              help="Ensure var index is unique.", show_default=True)
 def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
             set_obs_names, set_var_names, make_obs_names_unique, make_var_names_unique):
     """Preprocesses data for use with cellxgene.
@@ -33,9 +33,9 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
     annotations, ensuring sparsity, and plotting results."""
 
     # collect slow imports here to make CLI startup more responsive
-    click.echo('[cellxgene] Starting CLI...')
+    click.echo("[cellxgene] Starting CLI...")
     import matplotlib
-    matplotlib.use('Agg')
+    matplotlib.use("Agg")
     import scanpy.api as sc
 
     # scanpy settings
@@ -43,45 +43,45 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
     sc.settings.autosave = True
 
     # check args
-    if sparse and not recipe == 'none':
+    if sparse and not recipe == "none":
-        raise click.UsageError('Cannot use a recipe when forcing sparsity')
+        raise click.UsageError("Cannot use a recipe when forcing sparsity")
 
     output = expanduser(output)
     if isfile(output) and not overwrite:
-        raise click.UsageError(f'Cannot overwrite existing file {output}, try using the flag --overwrite')
+        raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
 
     def load_data(data):
         if isfile(data):
             name, extension = splitext(data)
-            if extension == '.h5ad':
+            if extension == ".h5ad":
                 adata = sc.read_h5ad(data)
-            elif extension == '.loom':
+            elif extension == ".loom":
                 adata = sc.read_loom(data)
             else:
-                raise click.FileError(data, hint='does not have a valid extension [.h5ad | .loom]')
+                raise click.FileError(data, hint="does not have a valid extension [.h5ad | .loom]")
         elif isdir(data):
             if not data.endswith(sep):
                 data += sep
             adata = sc.read_10x_mtx(data)
         else:
-            raise click.FileError(data, hint='not a valid file or path')
+            raise click.FileError(data, hint="not a valid file or path")
 
-        if not set_obs_names == '':
+        if not set_obs_names == "":
             if set_obs_names not in adata.obs_keys():
-                raise click.UsageError(f'obs {set_obs_names} not found, options are: {adata.obs_keys()}')
+                raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
             adata.obs_names = adata.obs[set_obs_names]
-        if not set_var_names == '':
+        if not set_var_names == "":
             if set_var_names not in adata.var_keys():
-                raise click.UsageError(f'var {set_var_names} not found, options are: {adata.var_keys()}')
+                raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
             adata.var_names = adata.var[set_var_names]
         if make_obs_names_unique:
             adata.obs_names_make_unique()
         if make_var_names_unique:
             adata.var_names_make_unique()
         if not adata._obs.index.is_unique:
-            click.echo('Warning: obs index is not unique')
+            click.echo("Warning: obs index is not unique")
         if not adata._var.index.is_unique:
-            click.echo('Warning: var index is not unique')
+            click.echo("Warning: var index is not unique")
 
         return adata
 
@@ -90,9 +90,9 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
             adata.X = csc_matrix(adata.X)
 
     def run_recipe(adata):
-        if recipe == 'seurat':
+        if recipe == "seurat":
             sc.pp.recipe_seurat(adata)
-        elif recipe == 'zheng17':
+        elif recipe == "zheng17":
             sc.pp.recipe_zheng17(adata)
         else:
             sc.pp.filter_cells(adata, min_genes=5)
@@ -104,9 +104,9 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
 
     def run_pca(adata):
         if sparse:
-            sc.pp.pca(adata, svd_solver='arpack', zero_center=False)
+            sc.pp.pca(adata, svd_solver="arpack", zero_center=False)
         else:
-            sc.pp.pca(adata, svd_solver='arpack')
+            sc.pp.pca(adata, svd_solver="arpack")
 
     def run_neighbors(adata):
         sc.pp.neighbors(adata)
@@ -115,46 +115,46 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
         sc.tl.louvain(adata)
 
     def run_layout(adata):
-        if len(unique(adata.obs['louvain'].values)) < 10:
+        if len(unique(adata.obs["louvain"].values)) < 10:
-            palette = 'tab10'
+            palette = "tab10"
         else:
-            palette = 'tab20'
+            palette = "tab20"
 
-        if 'umap' in layout:
+        if "umap" in layout:
             sc.tl.umap(adata)
             if plotting:
-                sc.pl.umap(adata, color='louvain', palette=palette, save='_louvain')
+                sc.pl.umap(adata, color="louvain", palette=palette, save="_louvain")
 
-        if 'tsne' in layout:
+        if "tsne" in layout:
             sc.tl.tsne(adata)
             if plotting:
-                sc.pl.tsne(adata, color='louvain', palette=palette, save='_louvain')
+                sc.pl.tsne(adata, color="louvain", palette=palette, save="_louvain")
 
     def show_step(item):
         names = {
-            'make_sparse': 'Ensuring sparsity',
+            "make_sparse": "Ensuring sparsity",
-            'run_recipe': 'Running preprocessing recipe "%s"' % recipe,
+            "run_recipe": f"Running preprocessing recipe \"{recipe}\"",
-            'run_pca': 'Running PCA',
+            "run_pca": "Running PCA",
-            'run_neighbors': 'Calculating neighbors',
+            "run_neighbors": "Calculating neighbors",
-            'run_louvain': 'Calculating clusters',
+            "run_louvain": "Calculating clusters",
-            'run_layout': 'Computing layout'
+            "run_layout": "Computing layout"
         }
         if item is not None:
             return names[item.__name__]
 
     steps = [make_sparse, run_recipe, run_pca, run_neighbors, run_louvain, run_layout]
 
-    click.echo(f'[cellxgene] Loading data from {data}, please wait...')
+    click.echo(f"[cellxgene] Loading data from {data}, please wait...")
     adata = load_data(data)
 
-    click.echo('[cellxgene] Beginning preprocessing...')
+    click.echo("[cellxgene] Beginning preprocessing...")
-    with click.progressbar(steps, label='[cellxgene] Progress', show_eta=False, item_show_func=show_step) as bar:
+    with click.progressbar(steps, label="[cellxgene] Progress", show_eta=False, item_show_func=show_step) as bar:
         for step in bar:
             step(adata)
 
     # saving
-    if not output == '':
+    if not output == "":
-        click.echo(f'[cellxgene] Saving results to {output}...')
+        click.echo(f"[cellxgene] Saving results to {output}...")
         adata.write(output)
 
-    click.echo('[cellxgene] Success!')
+    click.echo("[cellxgene] Success!")

server/run.py

@@ -1,3 +0,0 @@
-from app.app import app
-
-app.run(host="0.0.0.0", debug=True, port=5005)

server/test/test_scanpy_engine.py

@@ -34,7 +34,8 @@ class UtilTest(unittest.TestCase):
     @pytest.mark.filterwarnings("ignore:Scanpy data matrix")
     def test_data_type(self):
         self.data.data.X = self.data.data.X.astype("float64")
-        self.assertWarns(UserWarning, self.data._validate_data_types())
+        with self.assertWarns(UserWarning):
+            self.data._validate_data_types()
 
     def test_filter_idx(self):
         filter_ = {