[UPDATE] Adding sandbox_path property to the json schemas

bioexcel · Jul 4, 2024 · ba34268 · ba34268
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diff --git a/biobb_analysis/docs/source/command_line.md b/biobb_analysis/docs/source/command_line.md
@@ -47,6 +47,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -183,6 +184,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -319,6 +321,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -458,6 +461,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -540,6 +544,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -672,6 +677,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -817,6 +823,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -900,6 +907,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -986,6 +994,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1136,6 +1145,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1272,6 +1282,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1399,6 +1410,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1536,6 +1548,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1666,6 +1679,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1800,6 +1814,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -1918,6 +1933,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -2052,6 +2068,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -2196,6 +2213,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (afandiadib/ambertools:serial) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -2335,6 +2353,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..
@@ -2449,6 +2468,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Container path definition..
 * **container_image** (*string*): (gromacs/gromacs:2022.2) Container image definition..
 * **container_volume_path** (*string*): (/tmp) Container volume path definition..

diff --git a/biobb_analysis/json_schemas/cpptraj_average.json b/biobb_analysis/json_schemas/cpptraj_average.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_bfactor.json b/biobb_analysis/json_schemas/cpptraj_bfactor.json
@@ -382,6 +382,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_convert.json b/biobb_analysis/json_schemas/cpptraj_convert.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_dry.json b/biobb_analysis/json_schemas/cpptraj_dry.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_image.json b/biobb_analysis/json_schemas/cpptraj_image.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_mask.json b/biobb_analysis/json_schemas/cpptraj_mask.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_rgyr.json b/biobb_analysis/json_schemas/cpptraj_rgyr.json
@@ -341,6 +341,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_rms.json b/biobb_analysis/json_schemas/cpptraj_rms.json
@@ -542,6 +542,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_rmsf.json b/biobb_analysis/json_schemas/cpptraj_rmsf.json
@@ -382,6 +382,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_slice.json b/biobb_analysis/json_schemas/cpptraj_slice.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_snapshot.json b/biobb_analysis/json_schemas/cpptraj_snapshot.json
@@ -492,6 +492,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/cpptraj_strip.json b/biobb_analysis/json_schemas/cpptraj_strip.json
@@ -510,6 +510,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/gmx_cluster.json b/biobb_analysis/json_schemas/gmx_cluster.json
@@ -523,6 +523,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/gmx_energy.json b/biobb_analysis/json_schemas/gmx_energy.json
@@ -364,6 +364,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/gmx_image.json b/biobb_analysis/json_schemas/gmx_image.json
@@ -865,6 +865,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_analysis/json_schemas/gmx_rgyr.json b/biobb_analysis/json_schemas/gmx_rgyr.json
@@ -333,6 +333,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,