From af0d1f6fb2999af07ab973e0a7ee3a67b7f02d0e Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Thu, 29 Nov 2018 16:33:21 -0800
Subject: [PATCH] issue #480 workaround (#484)

* only load annotation var names

* remove incorrect usage of var annotation data

* temporary workaround for issue #480

* lint

* issue warnings only once per item
---
 client/src/actions/index.js                   |  2 +-
 client/src/components/geneExpression/index.js |  4 +-
 server/app/scanpy_engine/scanpy_engine.py     | 51 +++++++++++++++++++
 3 files changed, 55 insertions(+), 2 deletions(-)

diff --git a/client/src/actions/index.js b/client/src/actions/index.js
index f8b2d554..35b0281a 100644
--- a/client/src/actions/index.js
+++ b/client/src/actions/index.js
@@ -24,7 +24,7 @@ const doInitialDataLoad = () =>
         "config",
         "schema",
         "annotations/obs",
-        "annotations/var",
+        "annotations/var?annotation-name=name",
         "layout/obs"
       ])
         .map(r => `${globals.API.prefix}${globals.API.version}${r}`)
diff --git a/client/src/components/geneExpression/index.js b/client/src/components/geneExpression/index.js
index 3a3a378d..5d2e550f 100644
--- a/client/src/components/geneExpression/index.js
+++ b/client/src/components/geneExpression/index.js
@@ -27,7 +27,9 @@ const renderGene = (fuzzySortResult, { handleClick, modifiers, query }) => {
     <MenuItem
       active={modifiers.active}
       disabled={modifiers.disabled}
-      label={gene.n_counts}
+      // Use of annotations in this way is incorrect and dataset specific.
+      // See https://github.com/chanzuckerberg/cellxgene/issues/483
+      // label={gene.n_counts}
       key={gene.name}
       onClick={g => {
         /* this fires when user clicks a menu item */
diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py
index 6a33b007..6090dfa3 100644
--- a/server/app/scanpy_engine/scanpy_engine.py
+++ b/server/app/scanpy_engine/scanpy_engine.py
@@ -35,6 +35,10 @@ class ScanpyEngine(CXGDriver):
         self.diffexp_options = ["ttest"]
         self._create_schema()
 
+        # TODO: temporary work-arounds
+        self._IEEE754_X_warning_issued = False
+        self._IEEE754_special_values_workaround_annotations()
+
     def _alias_annotation_names(self, axis, name):
         """
         Do all user-specified annotation aliasing.
@@ -172,6 +176,52 @@ class ScanpyEngine(CXGDriver):
                 f"`cellxgene prepare --layout {self.layout_method} <datafile>` "
                 f"to solve this problem. ")
 
+    def _IEEE754_special_values_workaround_annotations(self):
+        """
+        TODO: temporary workaround
+
+        Because all floating point data is serialized to JSON, and JSON has no means of representing
+        non-finite, floating point special values (NaN, +/-Infinity, etc), we include this temporary
+        work-around.
+
+        This will likely be removed in the future, contingent upon improved marshalling.
+
+        Where non-finite floating point is present in obs, var or X:
+        * issue a warning to the user that these values will be treated as zeros.
+        * set the value to zero within the in-memory data (self.data)
+        """
+        for ax in Axis:
+            curr_axis = getattr(self.data, str(ax))
+            for ann in curr_axis:
+                dtype = curr_axis[ann].dtype
+                if dtype.kind == 'f':
+                    not_finite = np.isfinite(curr_axis[ann]) == False   # noqa: E712
+                    if np.count_nonzero(not_finite) > 0:
+                        warnings.warn(
+                            f"{str(ax).title()} annotation '{ann}' contains floating point NaN or Infinities. "
+                            f"These values will be treated as zero."
+                        )
+                        curr_axis[ann][not_finite] = 0
+
+    def _IEEE754_special_values_workaround_X(self, _X):
+        """
+        TODO: temporary workaround
+
+        See comments in _IEEE754_special_values_workaround_annotations
+        """
+        not_finite = np.isfinite(_X) == False   # noqa: E712
+        if np.count_nonzero(not_finite) > 0:
+            _X[not_finite] = 0
+            if not self._IEEE754_X_warning_issued:
+                # only want to issue this warning once.
+                warnings.warn(
+                    "Dataframe X contains floating point NaN or Infinities. "
+                    "These values will be treated as zero."
+                )
+                self._IEEE754_X_warning_issued = True
+
+        return _X
+
     def filter_dataframe(self, filter):
         """
          Filter cells from data and return a subset of the data. They can operate on both obs and var dimension with
@@ -323,6 +373,7 @@ class ScanpyEngine(CXGDriver):
             _X = _X.toarray()
         var_index_sliced = self.data.var.index[var_selector]
         obs_index_sliced = self.data.obs.index[obs_selector]
+        _X = self._IEEE754_special_values_workaround_X(_X)
         if axis == Axis.OBS:
             result = {
                 "var": var_index_sliced.tolist(),