Exemplo n.º 1
0
def do_view(path, source_name=None):
    source = matching_source(source_name)
    match = cache.check_path(source, path)

    if match is None:
        lookup = source.lookup(path)
        if lookup is None:
            raise CellxgeneException(
                f"Could not find item for path {path} in source {source.name}",
                404,
            )
        key = CacheKey.for_lookup(source, lookup)
        print(
            f"view path={path}, source_name={source_name}, dataset={key.file_path}, annotation_file= {key.annotation_file_path}, key={key.descriptor}, source={key.source_name}"
        )
        with entry_lock:
            match = cache.check_entry(key)
            if match is None:
                uascripts = get_extra_scripts()
                match = cache.create_entry(key, uascripts)

    match.timestamp = current_time_stamp()

    if (match.status == CacheEntryStatus.loaded
            or match.status == CacheEntryStatus.loading):
        if source.is_authorized(match.key.descriptor):
            return match.serve_content(path)
        else:
            raise CellxgeneException("User not authorized to access this data",
                                     403)
    elif match.status == CacheEntryStatus.error:
        raise ProcessException.from_cache_entry(match)
Exemplo n.º 2
0
def create_dir(parent_path, dir_name):
    full_path = os.path.join(parent_path, dir_name)

    if "/" in dir_name:
        raise CellxgeneException(
            "Please have no slashes in the intended directory.",
            status.HTTP_400_BAD_REQUEST,
        )
    elif not os.path.exists(parent_path):
        raise CellxgeneException(
            "The selected User directory does not exist.",
            status.HTTP_400_BAD_REQUEST,
        )
    elif os.path.exists(full_path):
        raise CellxgeneException(
            "The provided subdirectory already exists within Directory.",
            status.HTTP_400_BAD_REQUEST,
        )
    elif not is_subdir(full_path, parent_path):
        raise CellxgeneException(
            "The directory must be a subdirectory of the parent path.",
            status.HTTP_400_BAD_REQUEST,
        )
    elif not os.path.isdir(parent_path):
        raise CellxgeneException(
            "The parent is not a directory.", status.HTTP_400_BAD_REQUEST
        )
    else:
        os.mkdir(full_path)
Exemplo n.º 3
0
def upload_file():
    upload_dir = request.form["path"]

    full_upload_path = os.path.join(env.cellxgene_data, upload_dir)
    if is_subdir(full_upload_path,
                 env.cellxgene_data) and os.path.isdir(full_upload_path):
        if request.method == "POST":
            if "file" in request.files:
                f = request.files["file"]
                if f and f.filename.endswith(".h5ad"):
                    f.save(
                        os.path.join(full_upload_path,
                                     secure_filename(f.filename)))
                    return redirect("/filecrawl.html", code=302)
                else:
                    raise CellxgeneException(
                        "Uploaded file must be in anndata (.h5ad) format.",
                        status.HTTP_400_BAD_REQUEST,
                    )
            else:
                raise CellxgeneException(
                    "A file must be chosen to upload.",
                    status.HTTP_400_BAD_REQUEST,
                )
    else:
        raise CellxgeneException("Invalid directory.",
                                 status.HTTP_400_BAD_REQUEST)

    return redirect(location, code=302)
Exemplo n.º 4
0
def validate_is_dir(file_path):
    validate_exists(file_path)
    if not os.path.isdir(file_path):
        raise CellxgeneException(
            "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
        )
    return
Exemplo n.º 5
0
def get_key(path):
    if path == "/" or path == "":
        raise CellxgeneException(
            "No matching dataset found.", status.HTTP_404_NOT_FOUND
        )

    trimmed = path[:-1] if path[-1] == "/" else path
    try:
        # valid paths come in three forms:
        if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
            # 1) somedir/dataset.h5ad: a dataset
            return CacheKey(trimmed, trimmed, None)
        elif trimmed.endswith('.csv'):

            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
            annotations_dir = os.path.split(trimmed)[0]
            dataset = make_h5ad(annotations_dir)
            if data_file_exists(dataset):
                data_dir_ensure(annotations_dir)
                return CacheKey(trimmed, dataset, trimmed)
        elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
            # 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
            dataset = make_h5ad(trimmed)
            if data_file_exists(dataset):
                return CacheKey(trimmed, dataset, '')
    except CellxgeneException:
        pass
    split = os.path.split(trimmed)
    return get_key(split[0])
Exemplo n.º 6
0
def do_filecrawl(path):
    filecrawl_path = os.path.join(env.cellxgene_data, path)
    if not os.path.isdir(filecrawl_path):
        raise CellxgeneException("Path is not directory: " + filecrawl_path,
                                 status.HTTP_400_BAD_REQUEST)
    entries = recurse_dir(filecrawl_path)
    rendered_html = render_entries(entries)
    return render_template(
        "filecrawl.html",
        extra_scripts=get_extra_scripts(),
        rendered_html=rendered_html,
        path=path,
    )
Exemplo n.º 7
0
    def check_entry(self, key):
        contents = self.entry_list
        matches = [
            c for c in contents
            if c.key.equals(key) and c.status != CacheEntryStatus.terminated
        ]

        if len(matches) == 0:
            return None
        elif len(matches) == 1:
            return matches[0]
        else:
            raise CellxgeneException(
                status.HTTP_500_INTERNAL_SERVER_ERROR,
                "Found " + str(len(matches)) + " for " + key.dataset,
            )
Exemplo n.º 8
0
    def check_path(self, source, path):
        contents = self.entry_list
        matches = [
            c for c in contents
            if c.key.source.name == source.name and path.startswith(
                c.key.descriptor) and c.status != CacheEntryStatus.terminated
        ]

        if len(matches) == 0:
            return None
        elif len(matches) == 1:
            return matches[0]
        else:
            raise CellxgeneException(
                status.HTTP_500_INTERNAL_SERVER_ERROR,
                "Found " + str(len(matches)) + " for " + path,
            )
Exemplo n.º 9
0
def validate_exists(file_path):
    if not os.path.exists(file_path):
        raise CellxgeneException(
            "File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST
        )
Exemplo n.º 10
0
    def serve_content(self, path):
        gateway_basepath = self.key.gateway_basepath()
        subpath = path[len(self.key.descriptor):]  # noqa: E203
        if len(subpath) == 0:
            r = make_response(f"Redirect to {gateway_basepath}\n", 302)
            r.headers["location"] = gateway_basepath + querystring()
            return r
        elif self.status == CacheEntryStatus.loading:
            launch_time = datetime.datetime.fromtimestamp(self.launchtime)
            return render_template(
                "loading.html",
                launchtime=launch_time,
                all_output=self.all_output,
            )

        headers = {}
        copy_headers = [
            "accept",
            "accept-encoding",
            "accept-language",
            "cache-control",
            "connection",
            "content-length",
            "content-type",
            "cookie",
            "host",
            "origin",
            "pragma",
            "referer",
            "sec-fetch-mode",
            "sec-fetch-site",
            "user-agent",
        ]
        for h in copy_headers:
            if h in request.headers:
                headers[h] = request.headers[h]

        full_path = self.cellxgene_basepath() + subpath + querystring()

        if request.method in ["GET", "HEAD", "OPTIONS"]:
            cellxgene_response = get(full_path, headers=headers)
        elif request.method == "PUT":
            cellxgene_response = put(
                full_path,
                headers=headers,
                data=request.data,
            )
        elif request.method == "POST":
            cellxgene_response = post(
                full_path,
                headers=headers,
                data=request.data,
            )
        else:
            raise CellxgeneException(f"Unexpected method {request.method}",
                                     400)
        content_type = cellxgene_response.headers["content-type"]
        if "text" in content_type:
            gateway_content = self.rewrite_text_content(
                cellxgene_response.content.decode())
        else:
            gateway_content = cellxgene_response.content

        resp_headers = {}
        for h in copy_headers:
            if h in cellxgene_response.headers:
                resp_headers[h] = cellxgene_response.headers[h]

        gateway_response = make_response(
            gateway_content,
            cellxgene_response.status_code,
            resp_headers,
        )
        return gateway_response
Exemplo n.º 11
0
    def serve_content(self, path):
        gateway_basepath = (
            f"{env.external_protocol}://{env.external_host}/view/{self.key.pathpart}/"
        )
        subpath = path[len(self.key.pathpart) :]  # noqa: E203
            
        if len(subpath) == 0:
            r = make_response(f"Redirect to {gateway_basepath}\n", 301)
            r.headers["location"] = gateway_basepath+querystring()
            return r
        elif self.status == "loading":
            launch_time = datetime.datetime.fromtimestamp(self.launchtime)
            return render_template(
                "loading.html", launchtime=launch_time, all_output=self.all_output
            )

        port = self.port
        cellxgene_basepath = f"http://127.0.0.1:{port}"
        headers = {}
        copy_headers = [
            'accept',
            'accept-encoding',
            'accept-language',
            'cache-control',
            'connection',
            'content-length',
            'content-type',
            'cookie',
            'host',
            'origin',
            'pragma',
            'referer',
            'sec-fetch-mode',
            'sec-fetch-site',
            'user-agent'
        ]
        for h in copy_headers:
            if h in request.headers:
                headers[h] = request.headers[h]

        full_path = cellxgene_basepath + subpath + querystring()

        if request.method in ["GET", "HEAD", "OPTIONS"]:
            cellxgene_response = get(
                full_path, headers=headers
            )
        elif request.method == "PUT":
            cellxgene_response = put(
                full_path,
                headers=headers,
                data=request.data,
            )
        elif request.method == "POST":
            cellxgene_response = post(
                full_path,
                headers=headers,
                data=request.data,
            )
        else:
            raise CellxgeneException(
                f"Unexpected method {request.method}", 400
            )
        content_type = cellxgene_response.headers["content-type"]
        if "text" in content_type:
            cellxgene_content = cellxgene_response.content.decode()
            gateway_content = cellxgene_content.replace(
                "http://fonts.gstatic.com", "https://fonts.gstatic.com"
            ).replace(cellxgene_basepath, gateway_basepath)
        else:
            gateway_content = cellxgene_response.content

        resp_headers = {}
        for h in copy_headers:
            if h in cellxgene_response.headers:
                resp_headers[h] = cellxgene_response.headers[h]

        gateway_response = make_response(
            gateway_content,
            cellxgene_response.status_code,
            resp_headers,
        )

        return gateway_response