fix issue with trackhub metadata

weng-lab · Dec 11, 2021 · 78fc063 · 78fc063
1 parent 3e268b0
commit 78fc063
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/api/models/datasets.py b/api/models/datasets.py
@@ -37,7 +37,7 @@ def __init__(self, assembly, pgSearch):
                     dnase: experimentAccession(assay: "DNase")                                                                                                                                       
                     h3k4me3: experimentAccession(assay: "H3K4me3")                                                                                                                                   
                     h3k27ac: experimentAccession(assay: "H3K27ac")                                                                                                                                   
-                    ctcf: experimentAccession(assay: "CTCF")                                                                                                                                                            }                                                                                                                                                                                 
+                    ctcf: experimentAccession(assay: "CTCF")                                                                                                                                                            }
                 }
             }""", "variables": { "assembly": assembly.lower() }
         }).json()["data"]["ccREBiosampleQuery"]["biosamples"]
@@ -55,7 +55,7 @@ def __init__(self, assembly, pgSearch):
                 "synonyms": None,
                 "tissue": x["ontology"],
                 "value": x["name"]
-            } for a in [ "CTCF", "H3K4me3", "H3K27ac", "DNase" ] if x[a.lower()] is not None ]
+            } for a in [ "CTCF", "H3K4me3", "H3K27ac", "DNase" ] if x[a.lower()] is not None and x[a.lower() + "File"] is not None ]
 
         # used by trees
         self.biosampleTypeToCellTypes = {}

diff --git a/api/models/trackhubdb.py b/api/models/trackhubdb.py
@@ -145,7 +145,7 @@ def __init__(self, assembly, expID, fileID, assay, parent, active, ct):
 
     def _init(self):
         p = OrderedDict()
-        p["track"] = Helpers.sanitize(self.expID + '_' + self.fileID)
+        p["track"] = Helpers.sanitize(str(self.expID) + '_' + str(self.fileID))
         p["parent"] = self.parent
         p["bigDataUrl"] = self._url()
         p["visibility"] = Helpers.viz("full", self.active)
@@ -326,6 +326,7 @@ def _add_ct_bigWigs(self, ct, show7group, superTrackName):
 
         cache = self.cacheW[self.assembly if self.assembly != "hg38" else "GRCh38"]
         for expInfo in cache.datasets.byCellType[ct]:
+            if expInfo["expID"] is None or expInfo["fileID"] is None: continue
             tt = BigWigTrack(self.assembly, expInfo["expID"], expInfo["fileID"],
                             expInfo["assay"], superTrackName, True, ct)
             t = tt.lines(self.priority)