move common code into server, update tests and makefile (#2425)

* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests

server/cli/upgrade.py

@@ -0,0 +1,85 @@
+import re
+
+import click
+import requests
+from requests.exceptions import ConnectionError
+
+from .. import __version__
+
+# Official SemVer regex: https://semver.org/
+SEMVER_FORMAT = re.compile(
+    r"^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*["
+    r"a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+(?P<buildmetadata>[0-9a-zA-Z-]+("
+    r"?:\.[0-9a-zA-Z-]+)*))?$"
+)
+
+
+def log_upgrade_check():
+    # Sanity-check that the CLI version is a properly-formatted SemVer string
+    assert validate_version_str(__version__, release_only=False)
+
+    # Get the current latest release
+    try:
+        release_tag_generator = (r["tag_name"] for r in _request_cellxgene_releases())
+        latest_release = next(release_tag_generator, lambda tag_name: validate_version_str(tag_name))
+        if version_gt(latest_release, __version__):
+            click.echo(f"There's a new version of cellxgene available ({latest_release})!", err=True)
+            click.echo("To upgrade, run the following: pip install --upgrade cellxgene\n", err=True)
+    except (ConnectionError, RateLimitException):
+        click.echo("Upgrade check failed.\n")
+
+
+class RateLimitException(Exception):
+    """
+    Github API Rate Limit Exception
+    """
+
+
+def _request_cellxgene_releases():
+    def raise_on_rate_limit(response):
+        if response.status_code == 403 and res.headers.get("X-RateLimit-Remaining") == "0":
+            raise RateLimitException
+
+    url = "https://api.github.com/repos/chanzuckerberg/cellxgene/releases"
+    res = requests.get(url)
+    raise_on_rate_limit(res)
+    for release in res.json():
+        yield release
+    while "next" in res.links.keys():
+        res = requests.get(res.links["next"]["url"])
+        raise_on_rate_limit(res)
+        for release in res.json():
+            yield release
+
+
+def validate_version_str(version_str, release_only=True):
+    """
+    Test if a string conforms to SemVer format (https://semver.org/)
+    :param version_str: a string to be validated
+    :param release_only: only declare releases (not prereleases) valid
+    :return: True if the version string is of a valid SemVer format else False
+    """
+    match = SEMVER_FORMAT.match(version_str)
+    has_match = match is not None
+    if has_match and release_only:
+        return not match.group("prerelease")
+    return has_match
+
+
+def split_version(version_string):
+    """
+    Split a SemVer-formatted string into its component integers
+    :param version_string: a SemVer string to be split
+    :return: an array of three integers
+    """
+    match = SEMVER_FORMAT.match(version_string)
+    return [int(match.group(group)) for group in ["major", "minor", "patch"]]
+
+
+def version_gt(left_version, right_version):
+    for left, right in zip(split_version(left_version), split_version(right_version)):
+        if left > right:
+            return True
+        elif right > left:
+            return False
+    return False