Merge pull request #208 from pepkit/dev

v0.11.0 release

docs/changelog.md

@@ -2,6 +2,12 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.11.0] - 2024-10-02
+### Fixed
+- for output schema, make samples an array type and nest under items [#204](https://github.com/pepkit/pipestat/issues/204)
+- pipeline_name not setting correctly [#207](https://github.com/pepkit/pipestat/issues/207)
+- bug with objects populating html report
+
 ## [0.10.2] - 2024-08-26
 ### Fixed
 - add obtaining pephub_path from config file, [#202](https://github.com/pepkit/pipestat/issues/202)
@@ -10,7 +16,6 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Fixed
 - add pipestat summarize and link for pephub backend
 
-
 ## [0.10.0] - 2024-07-18
 ### Fixed
 - allow for bool or boolean in schema [#189](https://github.com/pepkit/pipestat/issues/189)
@@ -20,7 +25,6 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## Added
 - pephub backend [#125](https://github.com/pepkit/pipestat/issues/125)
 
-
 ## [0.9.3] - 2024-06-06
 ### Fixed
 - fixed regression with summarizing or creating a table via aggregate_results.yaml and "{record_identifier}" in the results file path

pipestat/_version.py

@@ -1 +1 @@
-__version__ = "0.10.2"
+__version__ = "0.11.0"

pipestat/parsed_schema.py

@@ -95,10 +95,16 @@ def __init__(self, data: Union[Dict[str, Any], Path, str]) -> None:
 
             self._pipeline_name = data["properties"].pop(SCHEMA_PIPELINE_NAME_KEY, None)
 
+            # Two passes for sample-data as it is now nested under items per #204
             sample_data = _safe_pop_one_mapping(
                 subkeys=["samples"],
                 data=data["properties"],
                 info_name="sample-level",
+                mappingkey="items",
+            )
+            sample_data = _safe_pop_one_mapping(
+                data=sample_data,
+                info_name="sample-level",
                 mappingkey="properties",
             )
 

pipestat/pipestat.py

@@ -195,14 +195,15 @@ def __init__(
         )
 
         # TODO this is a work around for Looper ~ https://github.com/pepkit/looper/issues/492, sharing pipeline names
-        # In the future, we should get piepline name only from output schema.
-        self.cfg[PIPELINE_NAME] = (
-            pipeline_name
-            or self.cfg[CONFIG_KEY].get(PIPELINE_NAME)
-            or self.cfg[SCHEMA_KEY].pipeline_name
-            if self.cfg[SCHEMA_KEY] is not None
-            else DEFAULT_PIPELINE_NAME
-        )
+        # In the future, we should get pipeline name only from output schema.
+        if pipeline_name:
+            self.cfg[PIPELINE_NAME] = pipeline_name
+        elif self.cfg[CONFIG_KEY].get(PIPELINE_NAME):
+            self.cfg[PIPELINE_NAME] = self.cfg[CONFIG_KEY].get(PIPELINE_NAME)
+        elif self.cfg[SCHEMA_KEY] and self.cfg[SCHEMA_KEY].pipeline_name:
+            self.cfg[PIPELINE_NAME] = self.cfg[SCHEMA_KEY].pipeline_name
+        else:
+            self.cfg[PIPELINE_NAME] = DEFAULT_PIPELINE_NAME
 
         self.cfg[PROJECT_NAME] = self.cfg[CONFIG_KEY].priority_get(
             "project_name", env_var=ENV_VARS["project_name"], override=project_name

pipestat/reports.py

@@ -366,10 +366,7 @@ def create_object_htmls(self, navbar, footer):
             links = []
             html_page_path = os.path.join(self.pipeline_reports, f"{file_result}.html".lower())
 
-            if self.prj.cfg["multi_result_files"] is True:
-                pipeline_types = ["sample", "project"]
-            else:
-                pipeline_types = [self.prj.backend.pipeline_type]
+            pipeline_types = ["sample", "project"]
 
             for pipeline_type in pipeline_types:
                 self.prj.backend.pipeline_type = pipeline_type
@@ -425,10 +422,7 @@ def create_object_htmls(self, navbar, footer):
             html_page_path = os.path.join(self.pipeline_reports, f"{image_result}.html".lower())
             figures = []
 
-            if self.prj.cfg["multi_result_files"] is True:
-                pipeline_types = ["sample", "project"]
-            else:
-                pipeline_types = [self.prj.backend.pipeline_type]
+            pipeline_types = ["sample", "project"]
 
             for pipeline_type in pipeline_types:
                 self.prj.backend.pipeline_type = pipeline_type

tests/data/output_schema.yaml

@@ -4,9 +4,11 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-        result_name:
-          type: string
-          description: "ResultName"
+    type: array
+    items:
+      type: object
+      properties:
+          result_name:
+            type: string
+            description: "ResultName"
 

tests/data/output_schema_as_JSON_schema.yaml

@@ -4,54 +4,56 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-        number_of_things:
-          type: integer
-          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit."
-        output_image:
-          $ref: "#/$defs/image"
-          description: "This an output image"
-        output_file:
-          $ref: "#/$defs/file"
-          description: "This a path to the output image"
-        collection_of_images:
-          type: array
-          description: A collection of images.
-          items:
+    type: array
+    items:
+      type: object
+      properties:
+          number_of_things:
+            type: integer
+            description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit."
+          output_image:
+            $ref: "#/$defs/image"
+            description: "This an output image"
+          output_file:
+            $ref: "#/$defs/file"
+            description: "This a path to the output image"
+          collection_of_images:
+            type: array
+            description: A collection of images.
+            items:
+              type: object
+              properties:
+                prop1:
+                  $ref: "#/$defs/file"
+                  description: An example file.
+          nested_object:
             type: object
+            description: An object containing output file and image.
             properties:
-              prop1:
+              example_property_1:
                 $ref: "#/$defs/file"
                 description: An example file.
-        nested_object:
-          type: object
-          description: An object containing output file and image.
-          properties:
-            example_property_1:
-              $ref: "#/$defs/file"
-              description: An example file.
-            example_property_2:
-              $ref: "#/$defs/image"
-              description: An example image.
-        output_file_nested_object:
-          type: object
-          description: First Level
-          properties:
-            example_property_1:
-              type: object
-              description: Second Level
-              properties:
-                third_level_property_1:
-                  $ref: "#/$defs/file"
-                  description: Third Level
-            example_property_2:
-              type: object
-              description: Second Level
-              properties:
-                third_level_property_1:
-                  $ref: "#/$defs/file"
-                  description: Third Level
+              example_property_2:
+                $ref: "#/$defs/image"
+                description: An example image.
+          output_file_nested_object:
+            type: object
+            description: First Level
+            properties:
+              example_property_1:
+                type: object
+                description: Second Level
+                properties:
+                  third_level_property_1:
+                    $ref: "#/$defs/file"
+                    description: Third Level
+              example_property_2:
+                type: object
+                description: Second Level
+                properties:
+                  third_level_property_1:
+                    $ref: "#/$defs/file"
+                    description: Third Level
 $defs:
   image:
     type: object

tests/data/output_schema_html_report.yaml

@@ -19,26 +19,28 @@ properties:
         type: boolean
         description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus ipsum erat, porta in condimentum viverra, pellentesque in nisl. Nulla rhoncus nibh est, quis malesuada diam suscipit at. In ut diam."
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
-      output_file:
-        $ref: "#/$defs/file"
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
-      output_image:
-        $ref: "#/$defs/image"
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus ipsum erat, porta in condimentum viverra, pellentesque in nisl. Nulla rhoncus nibh est, quis malesuada diam suscipit at. In ut diam."
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
+        output_file:
+          $ref: "#/$defs/file"
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
+        output_image:
+          $ref: "#/$defs/image"
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
 $defs:
   image:
     type: object

tests/data/sample_output_schema.yaml

@@ -4,30 +4,32 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      number_of_things:
-        type: integer
-        description: "Number of things"
-      percentage_of_things:
-        type: number
-        description: "Percentage of things"
-      name_of_something:
-        type: string
-        description: "Name of something"
-      switch_value:
-        type: boolean
-        description: "Is the switch on or off"
-      output_file:
-        $ref: "#/$defs/file"
-        description: "This a path to the output file"
-      output_image:
-        $ref: "#/$defs/image"
-        description: "This a path to the output image"
-      md5sum:
-        type: string
-        description: "MD5SUM of an object"
-        highlight: true
+    type: array
+    items:
+      type: object
+      properties:
+        number_of_things:
+          type: integer
+          description: "Number of things"
+        percentage_of_things:
+          type: number
+          description: "Percentage of things"
+        name_of_something:
+          type: string
+          description: "Name of something"
+        switch_value:
+          type: boolean
+          description: "Is the switch on or off"
+        output_file:
+          $ref: "#/$defs/file"
+          description: "This a path to the output file"
+        output_image:
+          $ref: "#/$defs/image"
+          description: "This a path to the output image"
+        md5sum:
+          type: string
+          description: "MD5SUM of an object"
+          highlight: true
 $defs:
   image:
     type: object

tests/data/sample_output_schema__with_project_with_samples_with_status.yaml

@@ -19,20 +19,22 @@ properties:
         type: boolean
         description: "Is the switch on or off"
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "A smooth bigwig file"
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "A sorted, aligned BAM file"
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Peaks in BED format"
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "A smooth bigwig file"
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "A sorted, aligned BAM file"
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Peaks in BED format"
   status:
     type: object
     properties:

tests/data/sample_output_schema__with_project_with_samples_without_status.yaml

@@ -19,17 +19,19 @@ properties:
         type: boolean
         description: "Is the switch on or off"
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "A smooth bigwig file"
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "A sorted, aligned BAM file"
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Peaks in BED format"
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "A smooth bigwig file"
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "A sorted, aligned BAM file"
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Peaks in BED format"