Merge pull request #15581 from mvdbeek/dev

Merge 23.0 into dev
galaxyproject · Feb 15, 2023 · 6da0832 · 6da0832
2 parents 9de2630 + 8b7c237
commit 6da0832
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Showing 17 changed files with 24 additions and 26 deletions.
diff --git a/client/src/components/admin/DataManager/DataManagerTable.vue b/client/src/components/admin/DataManager/DataManagerTable.vue
@@ -98,9 +98,7 @@ export default {
     },
     methods: {
         fields(columns) {
-            // Columns and data are given as arrays. Use each column index as field
-            // key for the table and the column values as labels
-            return columns.reduce((acc, c, i) => Object.assign(acc, { [i]: { label: c } }), {});
+            return columns.map((elem, index) => ({ key: index.toString(), label: elem }));
         },
         reload() {
             axios

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" version="1.0.0" hidden="true" profile="16.04">
+<tool id="CONVERTER_Bam_Bai_0" name="Convert Bam to Bai" version="1.0.0" hidden="true" profile="16.04">
     <requirements>
         <requirement type="package" version="1.10">samtools</requirement>
     </requirements>

diff --git a/lib/galaxy/datatypes/converters/bcf_bcf_uncompressed_converter.xml b/lib/galaxy/datatypes/converters/bcf_bcf_uncompressed_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_bcf_uncompressed_to_bcf" name="Converter for BCF and uncompressed BCF" version="0.0.1" hidden="false" profile="21.09">
+<tool id="CONVERTER_bcf_uncompressed_to_bcf" name="Convert compressed and uncompressed BCF files" version="0.0.1" hidden="false" profile="21.09">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
         <requirement type="package" version="1.12">bcftools</requirement>

diff --git a/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml b/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
@@ -1,4 +1,4 @@
-<tool id="bigwigtowig" name="bigWigToWig" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
+<tool id="bigwigtowig" name="Convert BigWig to Wiggle" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
     <description>Convert bigWig to wig</description>
     <macros>
         <token name="@TOOL_VERSION@">377</token>

diff --git a/lib/galaxy/datatypes/converters/cml_to_smi_converter.xml b/lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="2.4.1">
+<tool id="CONVERTER_cml_to_smiles" name="Convert CML to SMILES" version="2.4.1">
     <description></description>
     <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
     <requirements>

diff --git a/lib/galaxy/datatypes/converters/gro_to_pdb.xml b/lib/galaxy/datatypes/converters/gro_to_pdb.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_Gro_to_Pdb_0" name="GRO to PDB" version="1.0.0" hidden="true" profile="20.09">
+<tool id="CONVERTER_Gro_to_Pdb_0" name="Convert GRO to PDB" version="1.0.0" hidden="true" profile="20.09">
     <requirements>
         <requirement type="package" version="2020.4">gromacs</requirement>
     </requirements>

diff --git a/lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml b/lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_inchi_to_mol" name="InChI to MOL" version="2.4.1">
+<tool id="CONVERTER_inchi_to_mol" name="Convert InChI to MOL" version="2.4.1">
     <description></description>
     <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
     <requirements>

diff --git a/lib/galaxy/datatypes/converters/mdconvert.xml b/lib/galaxy/datatypes/converters/mdconvert.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_mdconvert" name="Converter for XTC, DCD, and TRR" version="1.0.0" hidden="true" profile="21.09">
+<tool id="CONVERTER_mdconvert" name="Convert XTC, DCD, and TRR" version="1.0.0" hidden="true" profile="21.09">
     <requirements>
         <requirement type="package" version="1.9.4">mdtraj</requirement>
     </requirements>

diff --git a/lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml b/lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_mol2_to_mol" name="MOL2 to MOL" version="2.4.1">
+<tool id="CONVERTER_mol2_to_mol" name="Convert MOL2 to MOL" version="2.4.1">
     <description></description>
     <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
     <requirements>

diff --git a/lib/galaxy/datatypes/converters/pdb_to_gro.xml b/lib/galaxy/datatypes/converters/pdb_to_gro.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_Pdb_to_Gro_0" name="PDB to GRO" version="1.0.0" hidden="true" profile="20.09">
+<tool id="CONVERTER_Pdb_to_Gro_0" name="Convert PDB to GRO" version="1.0.0" hidden="true" profile="20.09">
     <requirements>
         <requirement type="package" version="2020.4">gromacs</requirement>
     </requirements>

diff --git a/lib/galaxy/datatypes/converters/smi_to_mol_converter.xml b/lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_SMILES_to_MOL" name="SMILES to MOL" version="2.4.1">
+<tool id="CONVERTER_SMILES_to_MOL" name="Convert SMILES to MOL" version="2.4.1">
     <description></description>
     <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
     <requirements>

diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval" version="1.0.1" profile="16.04">
+<tool id="CONVERTER_wiggle_to_interval_0" name="Convert Wiggle to Interval" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <requirements>

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -69,7 +69,7 @@ funcsigs==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
-gravity @ git+https://github.com/galaxyproject/gravity.git@release_1.x ; python_version >= "3.7" and python_version < "3.12"
+gravity==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12"
 gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12"
 gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.12"

diff --git a/lib/galaxy/model/migrations/dbscript.py b/lib/galaxy/model/migrations/dbscript.py
@@ -34,8 +34,8 @@
     "22.01": "base",
     "release_22.05": "186d4835587b",
     "22.05": "186d4835587b",
-    "release_23.0": "186d4835587b",
-    "23.0": "186d4835587b",
+    "release_23.0": "c39f1de47a04",
+    "23.0": "c39f1de47a04",
 }
 
 

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -425,13 +425,13 @@ def load_builtin_converters(self):
         id = "builtin_converters"
         section = ToolSection({"name": "Built-in Converters", "id": id})
         self._tool_panel[id] = section
-        converters = self.app.datatypes_registry.datatype_converters
-        for source, targets in converters.items():
-            for target, tool in targets.items():
-                tool.name = f"{source}-to-{target}"
-                tool.description = "converter"
-                tool.hidden = False
-                section.elems.append_tool(tool)
+
+        converters = {
+            tool for target in self.app.datatypes_registry.datatype_converters.values() for tool in target.values()
+        }
+        for tool in converters:
+            tool.hidden = False
+            section.elems.append_tool(tool)
 
     def persist_cache(self, register_postfork=False):
         """

diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -122,7 +122,7 @@ def __authorize_job_access(self, trans, encoded_job_id, **kwargs):
 
         job_id = trans.security.decode_id(encoded_job_id)
         job_key = trans.security.encode_id(job_id, kind="jobs_files")
-        if not util.safe_str_cmp(kwargs["job_key"], job_key):
+        if not util.safe_str_cmp(str(kwargs["job_key"]), job_key):
             raise exceptions.ItemAccessibilityException("Invalid job_key supplied.")
 
         # Verify job is active. Don't update the contents of complete jobs.

diff --git a/pyproject.toml b/pyproject.toml
@@ -55,7 +55,7 @@ fastapi-utils = "*"
 fs = "*"
 future = "*"
 galaxy_sequence_utils = "*"
-gravity = {git = "https://github.com/galaxyproject/gravity.git", branch = "release_1.x"}  # https://github.com/galaxyproject/gravity/issues/92
+gravity = ">=1.0"
 gunicorn = "*"
 gxformat2 = "*"
 h5py = "*"