Encd 6122 fce series ucsc viz

src/encoded/loadxl.py

@@ -664,7 +664,7 @@ def get_pipeline(testapp, docsdir, test_only, item_type, phase=None, method=None
         remove_keys('related_files'),
     ],
     'functional_characterization_series': [
-        remove_keys('related_datasets'),
+        remove_keys('related_datasets', 'analyses'),
     ],
     'single_cell_rna_series': [
         remove_keys('related_datasets'),
@@ -777,7 +777,7 @@ def get_pipeline(testapp, docsdir, test_only, item_type, phase=None, method=None
         skip_rows_missing_all_keys('related_files'),
     ],
     'functional_characterization_series': [
-        skip_rows_missing_all_keys('related_datasets'),
+        skip_rows_missing_all_keys('related_datasets', 'analyses'),
     ],
     'single_cell_rna_series': [
         skip_rows_missing_all_keys('related_datasets'),

src/encoded/static/vis_defs/FCS_vis_def.json

@@ -0,0 +1,71 @@
+{
+    "FCS": {
+        "rule": "'{@id}'.startswith('/functional-characterization-series/')",
+        "assay_composite": {
+            "longLabel":  "Collection of ENCODE functional characterization series",
+            "shortLabel": "ENCODE functional characterization series"
+        },
+        "longLabel":  "{assay_title} series of {biosample_summary} - {accession}",
+        "shortLabel": "{assay_title} series of {biosample_term_name} {accession}",
+        "sortOrder": [ "Biosample", "Replicates", "Views" ],
+        "Views":  {
+            "tag": "view",
+            "group_order": [ "Guide locations", "Perturbation signal", "Element gene interactions signal", "Element gene interactions p-value" ],
+            "groups": {
+                "Guide locations": {
+                    "tag": "aGL",
+                    "type": "bigBed",
+                    "visibility": "dense",
+                    "output_type": [ "guide locations" ]
+                },
+                "Peturbation Signal": {
+                    "tag": "bPSIG",
+                    "visibility": "full",
+                    "type": "bigWig",
+                    "viewLimits": "0:10",
+                    "autoScale": "off",
+                    "maxHeightPixels": "64:18:8",
+                    "windowingFunction": "mean+whiskers",
+                    "output_type": [ "perturbation signal" ]
+                },
+                "Element gene interactions signal": {
+                    "tag": "cEGIS",
+                    "type": "bigInteract",
+                    "visibility": "full",
+                    "interactUp": true,
+                    "output_type": [ "element gene interactions signal" ]
+                },
+                "Element gene interactions p-value": {
+                    "tag": "dEGIPV",
+                    "type": "bigInteract",
+                    "visibility": "full",
+                    "interactUp": true,
+                    "output_type": [ "element gene interactions p-value" ]
+                }
+            }
+        },
+        "other_groups":  {
+            "dimensions": { "Biosample": "dimY", "Replicates": "dimA" },
+            "dimensionAchecked": "all",
+            "groups": {
+                "Replicates": {
+                    "tag": "REP",
+                    "groups": {
+                        "replicate": {
+                            "title_mask": "Replicate_{replicate_number}",
+                            "combined_title": "Pooled"
+                        }
+                    }
+                },
+                "Biosample": {
+                    "tag": "BS",
+                    "groups": { "one": { "title_mask": "{biosample_term_name}"} }
+                }
+            }
+        },
+        "file_defs": {
+            "longLabel": "{assay_title} series of {biosample_term_name} {output_type} {replicate}",
+            "shortLabel": "{replicate} {output_type_short_label}"
+        }
+    }
+}

src/encoded/tests/data/inserts/analysis.json

@@ -51,5 +51,12 @@
         "files": ["ENCFF762DWI"],
         "submitted_by": "76091563-a959-4a9c-929c-9acfa1a0a078",
         "status": "released"
+    },
+    {
+        "uuid": "d97c36ed-62dc-47a9-926d-e63a31d90615",
+        "accession": "ENCAN287CSA",
+        "files": ["ENCFF761PSF"],
+        "submitted_by": "76091563-a959-4a9c-929c-9acfa1a0a078",
+        "status": "released"
     }
 ]

src/encoded/tests/data/inserts/file.json

@@ -4770,5 +4770,19 @@
         "file_size": 370148294,
         "output_type": "regulatory elements prediction model",
         "lab": "/labs/richard-myers/"
+    },
+    {
+        "accession": "ENCFF761PSF",
+        "assembly": "GRCh38",
+        "award": "/awards/U54HG006997/",
+        "dataset": "ENCSR913CSS",
+        "file_format": "bigWig",
+        "file_size": 4859023,
+        "lab": "bing-ren",
+        "md5sum": "e224bff2b137f7a4427f948810189134",
+        "output_type": "perturbation signal",
+        "status": "released",
+        "submitted_by": "[email protected]",
+        "uuid": "c6dee687-4030-4edb-85a4-12cf7f9d4183"
     }
 ]

src/encoded/tests/data/inserts/functional_characterization_series.json

@@ -13,5 +13,21 @@
         ],
         "uuid": "cc54569d-6a9c-4c47-bd85-9f406a0ddbbc",
         "date_released": "2020-01-10"
-    }
+    },
+    {
+      "_test": "CRISPR screen series",
+      "accession": "ENCSR913CSS",
+      "award": "U54HG006997",
+      "description": "CRISPR screen series",
+      "lab": "bing-ren",
+      "status": "released",
+      "submitted_by": "[email protected]",
+      "related_datasets": [
+          "/experiments/ENCSR112TRG",
+          "/experiments/ENCSR113TRG"
+      ],
+      "uuid": "2c2a6143-adcc-4c6d-a36a-20f9387a9a41",
+      "date_released": "2021-03-23",
+      "analyses": ["ENCAN287CSA"]
+  }
 ]

src/encoded/tests/features/test_trackhubs.py

@@ -301,7 +301,7 @@ def test_PCS_bigWig_trackDb(testapp, index_workbook, expected):
     "        parent ENCSR222MPR_aEQS_view on",
     "        bigDataUrl /files/ENCFF527MEQ/@@download/ENCFF527MEQ.bigBed?proxy=true",
     "        longLabel MPRA of K562 element quantifications rep1 ENCSR222MPR - ENCFF527MEQ",
-    "        shortLabel rep1 element quantifications",
+    "        shortLabel rep1 elem qt",
     "        type bigBed",
     "        subGroups BS=K562 EXP=ENCSR222MPR REP=rep01 view=aEQS",
 ])

src/encoded/vis_defines.py

@@ -155,8 +155,8 @@
 HIC_FILE_TYPES = ['hic']
 BIGINTERACT_FILE_TYPES = ['bigInteract']
 VISIBLE_FILE_FORMATS = BIGBED_FILE_TYPES + BIGWIG_FILE_TYPES + HIC_FILE_TYPES + BIGINTERACT_FILE_TYPES
-VISIBLE_DATASET_TYPES = ["Experiment", "Annotation", "FunctionalCharacterizationExperiment"]
-VISIBLE_DATASET_TYPES_LC = ["experiment", "annotation", "functional_characterization_experiment"]
+VISIBLE_DATASET_TYPES = ["Experiment", "Annotation", "FunctionalCharacterizationExperiment", "FunctionalCharacterizationSeries"]
+VISIBLE_DATASET_TYPES_LC = ["experiment", "annotation", "functional_characterization_experiment", "functional_characterization_series"]
 
 
 # Supported tokens are the only tokens the code currently knows how to look up.
@@ -177,6 +177,7 @@
     "{target.title}",
     "{target.name}",                          # Used in metadata URLs
     "{target.investigated_as}",
+    "{biosample_summary}",
     "{biosample_term_name}", "{biosample_term_name|multiple}",  # "|multiple": none means multiple
     "{output_type_short_label}",                # hard-coded translation from output_type to very
                                                 # short version
@@ -364,7 +365,11 @@
     "optimal IDR thresholded peaks":        "oIDR pk",
     "conservative IDR thresholded peaks":   "cIDR pk",
     "enhancer validation":                  "enh val",
-    "semi-automated genome annotation":     "saga"
+    "semi-automated genome annotation":     "saga",
+    "element quantifications":              "elem qt",
+    "guide locations":                      "g locs",
+    "element gene interactions signal":     "egi sig",
+    "element gene interactions p-value":    "egi pval"
     }
 
 # Track coloring is defined by biosample
@@ -790,6 +795,12 @@ def lookup_token(self, token, dataset, a_file=None):
             if token.endswith("|multiple}"):
                 return "multiple biosamples"
             return "Unknown Biosample"
+        elif token == "{biosample_summary}":
+            biosample_summary = dataset.get('biosample_summary')
+            if biosample_summary is None:
+                return "Unknown Biosample"
+            else:
+                return biosample_summary
         elif token == "{biosample_term_name}":
             biosample_ontology = dataset.get('biosample_ontology')
             if biosample_ontology is None: