Merge pull request #18 from galaxyproject/rename_match_to_if

Rename match clause to if for better readability

docs/topics/vortex_by_example.rst

@@ -181,30 +181,30 @@ Rules provide a means by which to conditionally change entity requirements.
         mem: cores * 3
         rules:
           - id: my_overridable_rule
-            match: input_size < 5
+            if: input_size < 5
             fail: We don't run piddling datasets of {input_size}GB
       bwa:
         scheduling:
           require:
             - pulsar
         rules:
           - id: my_overridable_rule
-            match: input_size < 1
+            if: input_size < 1
             fail: We don't run piddling datasets
-          - match: input_size <= 10
+          - if: input_size <= 10
             cores: 4
             mem: cores * 4
             execute: |
                from galaxy.jobs.mapper import JobNotReadyException
                raise JobNotReadyException()
-          - match: input_size > 10 and input_size < 20
+          - if: input_size > 10 and input_size < 20
             scheduling:
               require:
                 - highmem
-          - match: input_size >= 20
+          - if: input_size >= 20
             fail: Input size: {input_size} is too large shouldn't run
 
-The match clause can contain arbitrary python code, including multi-line python code. The only requirement is that the
+The if clause can contain arbitrary python code, including multi-line python code. The only requirement is that the
 last statement in the code block must evaluate to a boolean value. In this example, the `input_size` variable is an
 automatically available contextual variable which is computed by totalling the sizes of all inputs to the job.
 Additional available variables include app, job, tool, and user.

tests/fixtures/mapping-inheritance-invalid.yml

@@ -18,22 +18,22 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     gpus: 2
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         cores: 4
         mem: cores * 4
-      - match: input_size > 10 and input_size < 20
+      - if: input_size > 10 and input_size < 20
         scheduling:
           require:
             - highmem
-      - match: input_size >= 20
+      - if: input_size >= 20
         fail: Too much data, shouldn't run
   trinity:
     inherits: bwa

tests/fixtures/mapping-inheritance-no-default.yml

@@ -15,18 +15,18 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     gpus: 2
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         cores: 4
         mem: cores * 4
-      - match: input_size >= 20
+      - if: input_size >= 20
         fail: Too much data, shouldn't run
   trinity:
     inherits: bwa

tests/fixtures/mapping-inheritance.yml

@@ -18,18 +18,18 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     gpus: 2
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         cores: 4
         mem: cores * 4
-      - match: input_size >= 20
+      - if: input_size >= 20
         fail: Too much data, shouldn't run
   trinity:
     inherits: bwa

tests/fixtures/mapping-merge-multiple-local.yml

@@ -16,22 +16,22 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         mem: cores * 4
       - id: highmem_rule
-        match: input_size > 40
+        if: input_size > 40
         fail: ""
         scheduling:
           require:
             - highmem
-      - match: input_size >= 20 and input_size <= 30
+      - if: input_size >= 20 and input_size <= 30
         fail: Too much data, shouldn't run
 users:
   [email protected]:

tests/fixtures/mapping-merge-multiple-remote.yml

@@ -7,12 +7,12 @@ tools:
     mem: 8
     env: {}
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     rules:
       - id: highmem_rule
-        match: input_size > 40
+        if: input_size > 40
         fail: a different kind of error
     scheduling:
       require:

tests/fixtures/mapping-rule-argument-based.yml

@@ -14,7 +14,7 @@ tools:
         - general
   limbo:
     rules:
-      - match: |
+      - if: |
           helpers.job_args_match(job, app, {'input_opts': {'db_selector': 'db'}})
         scheduling:
           prefer:

tests/fixtures/mapping-rule-execute.yml

@@ -17,24 +17,24 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         cores: 4
         mem: cores * 4
         execute: |
           from galaxy.jobs.mapper import JobNotReadyException
           raise JobNotReadyException()
-      - match: input_size > 10 and input_size < 20
+      - if: input_size > 10 and input_size < 20
         scheduling:
           require:
             - highmem
-      - match: input_size >= 20
+      - if: input_size >= 20
         fail: Too much data, shouldn't run
 
 destinations:

tests/fixtures/mapping-rule-tool-limits.yml

@@ -14,14 +14,14 @@ tools:
         - general
   toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/.*:
     rules:
-      - match: |
+      - if: |
           helpers.concurrent_job_count_for_tool(app, tool, user) >= 2  # concurrent jobs per user
         execute: |
           from galaxy.jobs.mapper import JobNotReadyException
           raise JobNotReadyException()          
   toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*:
     rules:
-      - match: |
+      - if: |
           helpers.concurrent_job_count_for_tool(app, tool) >= 3  # total concurrent jobs
         execute: |
           from galaxy.jobs.mapper import JobNotReadyException

tests/fixtures/mapping-rules-changed-extra.yml

@@ -5,6 +5,6 @@ tools:
         - pulsar
     rules:
       - id: firstrule
-        match: input_size <= 10
+        if: input_size <= 10
         cores: 5
         mem: cores * 4

tests/fixtures/mapping-rules-changed.yml

@@ -17,21 +17,21 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         cores: 4
         mem: cores * 4
-      - match: input_size > 10 and input_size < 20
+      - if: input_size > 10 and input_size < 20
         scheduling:
           require:
             - highmem
-      - match: input_size >= 20
+      - if: input_size >= 20
         fail: Too much data, shouldn't run
 users:
   [email protected]:
@@ -47,10 +47,10 @@ users:
       require:
         - earth
     rules:
-      - match: True
+      - if: True
         cores: 6
         mem: cores * 6
-      - match: input_size >= 5
+      - if: input_size >= 5
         fail: Just because
   [email protected]:
     scheduling:

tests/fixtures/mapping-rules-extra.yml

@@ -5,6 +5,6 @@ tools:
         - pulsar
     rules:
       - id: firstrule
-        match: input_size <= 10
+        if: input_size <= 10
         cores: 3
         mem: cores * 4

tests/fixtures/mapping-rules.yml

@@ -17,21 +17,21 @@ tools:
       reject:
         - pulsar
     rules:
-      - match: input_size < 5
+      - if: input_size < 5
         fail: We don't run piddling datasets
   bwa:
     scheduling:
       require:
         - pulsar
     rules:
-      - match: input_size <= 10
+      - if: input_size <= 10
         cores: 4
         mem: cores * 4
-      - match: input_size > 10 and input_size < 20
+      - if: input_size > 10 and input_size < 20
         scheduling:
           require:
             - highmem
-      - match: input_size >= 20
+      - if: input_size >= 20
         fail: Too much data, shouldn't run
 users:
   [email protected]:
@@ -47,10 +47,10 @@ users:
       require:
         - earth
     rules:
-      - match: True
+      - if: True
         cores: 6
         mem: cores * 6
-      - match: input_size >= 5
+      - if: input_size >= 5
         fail: Just because
   [email protected]:
     scheduling:

tests/fixtures/scenario-admin-group-user.yml

@@ -46,7 +46,7 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 0.1
+      - if: input_size >= 0.1
         scheduling:
           require:
             - highmem

tests/fixtures/scenario-jenkins-bot-user.yml

@@ -46,7 +46,7 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 0.1
+      - if: input_size >= 0.1
         scheduling:
           require:
             - highmem

tests/fixtures/scenario-job-too-small-for-highmem.yml

@@ -46,9 +46,9 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 10
+      - if: input_size >= 10
         cores: 16
-      - match: input_size >= 20
+      - if: input_size >= 20
         scheduling:
           require:
             - highmem

tests/fixtures/scenario-node-offline-high-cpu.yml

@@ -46,9 +46,9 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 10
+      - if: input_size >= 10
         cores: 16
-      - match: input_size >= 20
+      - if: input_size >= 20
         scheduling:
           require:
             - highmem

tests/fixtures/scenario-too-many-highmem-jobs.yml

@@ -47,15 +47,15 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 0.1
+      - if: input_size >= 0.1
         scheduling:
           require:
             - highmem
 
 users:
   default:
     rules:
-      - match: |
+      - if: |
           from galaxy.jobs.rule_helper import RuleHelper
           from vortex.core.entities import TagType
 

tests/fixtures/scenario-trinity-job-too-much-data.yml

@@ -46,11 +46,11 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 0.1
+      - if: input_size >= 0.1
         scheduling:
           require:
             - highmem
-      - match: input_size >= 200
+      - if: input_size >= 200
         fail: "Input file size of {input_size}GB is > maximum allowed 200GB limit"
 destinations:
   slurm:

tests/fixtures/scenario-trinity-job-with-rules.yml

@@ -46,7 +46,7 @@ tools:
       reject:
         - offline
     rules:
-      - match: input_size >= 0.1
+      - if: input_size >= 0.1
         scheduling:
           require:
             - highmem

tests/fixtures/scenario-usegalaxy-dev.yml

@@ -35,14 +35,13 @@ tools:
       prefer:
         - pulsar
     rules:
-      - match: input_size >= 0.2
+      - if: input_size >= 0.2
         cores: 16
 
 users:
   default:
     rules:
-      - match: |
-          False
+      - if: False
         fail: "You cannot have more than 4 high-mem jobs running concurrently"
 destinations:
   slurm: