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fix iRODS authentication issues
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Benedikt Obermayer committed Jan 28, 2020
1 parent 7645b5c commit bc1627a
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7 changes: 7 additions & 0 deletions HISTORY.rst
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Expand Up @@ -2,6 +2,13 @@
History
=======

------
v0.8.2
------

- fix iRODS authentication issues
- update docs for .h5ad input

------
v0.8.1
------
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2 changes: 1 addition & 1 deletion docs_manual/tutorial_input_formats.rst
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Expand Up @@ -9,7 +9,7 @@ HDF5 Input

For HDF5 input (no conversion necessary), you can do your analysis with `scanpy <http://scanpy.rtfd.io>`__ to create an anndata object ``ad``. SCelVis will use embedding coordinates from ``ad.obsm``, cell annotation from ``ad.obs`` and expression data directly from ``ad.X`` (this should contain normalized and log-transformed expression values for all genes).
If present, information about the dataset will be extracted from strings stored in ``ad.uns['about_title']``, ``ad.uns['about_short_title']`` and ``ad.uns['about_readme']`` (assumed to be Markdown).
Information about marker genes will be taken either from the ``rank_genes_groups`` slot in ``ad.uns`` or from entries starting with ``marker_`` in ``ad.uns``: entries called ``marker_gene`` (required!), ``marker_cluster``, ``marker_padj``, ``marker_LFC`` will create a table with the columns ``gene``, ``cluster``, ``padj``, and ``LFC``.
Information about marker genes will be taken from entries starting with ``marker_`` in ``ad.uns``: entries called ``marker_gene`` (required!), ``marker_cluster``, ``marker_padj``, ``marker_LFC`` will create a table with the columns ``gene``, ``cluster``, ``padj``, and ``LFC``. ``SCelVis`` will also extract marker information from ``ad.uns['rank_genes_groups']``. However, certain datatypes in ``ad.uns`` together with version mismatches of ``scanpy``, ``h5py`` and ``anndata`` can lead to ``.h5ad`` files that are not readable by ``SCelVis`` (see `issue #832 <https://github.com/theislab/scanpy/issues/832>`__). To be on the safe side, it's recommended to delete unneccessary slots in ``ad.uns`` (e.g., ``del ad.uns['rank_genes_groups']``). Also, ``ad.obsm['X_pca']`` and ``ad.varm['PCs']`` are likely dispensable.

If you prepared your data with ``Seurat`` (v2), you can use ``Convert(from = sobj, to = "anndata", filename = "data.h5ad")`` to get an HDF5 file.

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4 changes: 2 additions & 2 deletions scelvis/app.py
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Expand Up @@ -13,7 +13,7 @@
import dash
import flask
import uuid
import scanpy as sc
import anndata
from flask import request, helpers
from logzero import logger
from werkzeug.utils import secure_filename
Expand Down Expand Up @@ -143,7 +143,7 @@ def upload_route():
logger.info("Writing to %s", filepath)
file.save(filepath)
try:
sc.read(filepath)
anndata.read_h5ad(filepath)
return """
<!doctype html>
<p>upload successful!</p>
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11 changes: 9 additions & 2 deletions scelvis/data.py
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Expand Up @@ -92,7 +92,7 @@ def create_irods_session(url):
if "ssl" in url.scheme:
ssl_settings = {
"ssl_context": ssl.create_default_context(
purpose=ssl.Purpose.SERVER_AUTH, cafile=None, capath=None, cadata=None
purpose=ssl.Purpose.CLIENT_AUTH, cafile=None, capath=None, cadata=None
)
}
else:
Expand All @@ -109,8 +109,15 @@ def create_irods_session(url):
port=(url.port or 1247),
user=url.username,
password=url.password or "",
irods_authentication_scheme=irods_authentication_scheme,
zone=(url.path or "/").split("/")[1],
irods_authentication_scheme=irods_authentication_scheme,
irods_client_server_negotiation=settings.IRODS_CLIENT_SERVER_NEGOTIATION,
irods_client_server_policy=settings.IRODS_CLIENT_SERVER_POLICY,
irods_ssl_verify_server=settings.IRODS_SSL_VERIFY_SERVER,
irods_encryption_algorithm=settings.IRODS_ENCRYPTION_ALGORITHM,
irods_encryption_key_size=settings.IRODS_ENCRYPTION_KEY_SIZE,
irods_encryption_num_hash_rounds=settings.IRODS_ENCRYPTION_NUM_HASH_ROUNDS,
irods_encryption_salt_size=settings.IRODS_ENCRYPTION_SALT_SIZE,
**ssl_settings
)
query = parse_qs(url.query)
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9 changes: 9 additions & 0 deletions scelvis/settings.py
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Expand Up @@ -50,3 +50,12 @@

#: Whether or not to enable file upload for conversion, default is ``True``.
CONVERSION_ENABLED = False

#: various default iRODS settings
IRODS_CLIENT_SERVER_NEGOTIATION = "request_server_negotiation"
IRODS_CLIENT_SERVER_POLICY = "CS_NEG_REQUIRE"
IRODS_SSL_VERIFY_SERVER = "none"
IRODS_ENCRYPTION_ALGORITHM = "AES-256-CBC"
IRODS_ENCRYPTION_KEY_SIZE = 32
IRODS_ENCRYPTION_NUM_HASH_ROUNDS = 16
IRODS_ENCRYPTION_SALT_SIZE = 8
8 changes: 5 additions & 3 deletions scelvis/ui/main.py
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Expand Up @@ -53,12 +53,14 @@ def render_convert():
def render_upload():
return html.Div(
children=[
"upload .h5ad file here (you can convert your pipeline output to such a file using ",
"upload .h5ad file here (should be smaller than %.0f MB)"
% (int(settings.MAX_UPLOAD_DATA_SIZE) / 1.0e6),
html.P(),
"you can convert your pipeline output to such a file using ",
html.A(
children=[html.I(className="fas fa-redo mr-1"), "Convert Data"],
href="%s/dash/convert/" % settings.PUBLIC_URL_PREFIX,
href="/dash/convert",
),
")",
html.P(),
html.Iframe(src="/upload/", width="400", height="200"),
]
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58 changes: 49 additions & 9 deletions scelvis/webserver.py
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Expand Up @@ -121,6 +121,13 @@ def setup_argparse(parser):
action="append",
help="Path to data source(s)",
)

parser.add_argument(
"--public-url-prefix",
default=os.environ.get("SCELVIS_URL_PREFIX", ""),
help="The prefix that this app will be served under (e.g., if behind a reverse proxy.)",
)

parser.add_argument(
"--cache-dir",
default=os.environ.get("SCELVIS_CACHE_DIR"),
Expand All @@ -143,11 +150,18 @@ def setup_argparse(parser):
action="store_true",
help="whether to preload data at startup",
)

parser.add_argument(
"--upload-dir",
default=os.environ.get("SCELVIS_UPLOAD_DIR"),
help="Directory for visualization uploads, default is to create temporary directory",
)
parser.add_argument(
"--max-upload-data-size",
default=os.environ.get("SCELVIS_MAX_UPLOAD_DATA_SIZE", "1000000000"),
type=int,
help="Maximal size for data upload in bytes",
)
parser.add_argument(
"--disable-upload",
default=os.environ.get("SCELVIS_UPLOAD_DISABLED", "0") not in ("", "0", "N", "n"),
Expand All @@ -156,12 +170,6 @@ def setup_argparse(parser):
help="Whether or not to disable visualization uploads",
)

parser.add_argument(
"--public-url-prefix",
default=os.environ.get("SCELVIS_URL_PREFIX", ""),
help="The prefix that this app will be served under (e.g., if behind a reverse proxy.)",
)

parser.add_argument(
"--disable-conversion",
default=os.environ.get("SCELVIS_CONVERSION_DISABLED", "0") not in ("", "0", "N", "n"),
Expand All @@ -171,8 +179,40 @@ def setup_argparse(parser):
)

parser.add_argument(
"--max-upload-data-size",
default=os.environ.get("SCELVIS_MAX_UPLOAD_DATA_SIZE", "1000000000"),
"--irods-client-server-negotiation",
default=os.environ.get("IRODS_CLIENT_SERVER_NEGOTIATION", None),
help="IRODS setting",
)
parser.add_argument(
"--irods-client-server-policy",
default=os.environ.get("IRODS_CLIENT_SERVER_POLICY", None),
help="IRODS setting",
)
parser.add_argument(
"--irods-ssl-verify-server",
default=os.environ.get("IRODS_SSL_VERIFY_SERVER", None),
help="IRODS setting",
)
parser.add_argument(
"--irods-encryption-algorithm",
default=os.environ.get("IRODS_ENCRYPTION_ALGORITHM", None),
help="IRODS setting",
)
parser.add_argument(
"--irods-encryption-key-size",
default=os.environ.get("IRODS_ENCRYPTION_KEY_SIZE", None),
type=int,
help="Maximal size for data upload in bytes",
help="IRODS setting",
)
parser.add_argument(
"--irods-encryption-num-hash-rounds",
default=os.environ.get("IRODS_ENCRYPTION_NUM_HASH_ROUNDS", None),
type=int,
help="IRODS setting",
)
parser.add_argument(
"--irods-encryption-salt-size",
default=os.environ.get("IRODS_ENCRYPTION_SALT_SIZE", None),
type=int,
help="IRODS setting",
)

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