From 8c3ba12dd11ce8ceccca12599db815c5bc69eb73 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 31 May 2021 21:00:42 +0200
Subject: [PATCH] Update to wf_v7: sync in wf
---
gga_init.py | 1 +
utilities.py | 18 +-
...load_tripal_synchronize_jbrowse_2org_v7.ga | 490 +++++++++---------
3 files changed, 264 insertions(+), 245 deletions(-)
diff --git a/gga_init.py b/gga_init.py
index af8e2c1..f8c705e 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -89,6 +89,7 @@ class DeploySpeciesStack(species_data.SpeciesData):
picture_dest_name = "species%s" % picture_path_extension
picture_dest_path = os.path.join(self.species_dir, picture_dest_name)
shutil.copy(self.picture_path, picture_dest_path)
+ logging.info("Add picture %s" % self.picture_path)
else:
logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
else:
diff --git a/utilities.py b/utilities.py
index 1d88ad8..547a169 100755
--- a/utilities.py
+++ b/utilities.py
@@ -142,13 +142,21 @@ def get_sp_picture(sp_dict_list):
sp_picture_dict = {}
for sp in sp_dict_list:
- gspecies = get_gspecies_string_from_sp_dict(sp)
- if gspecies not in sp_picture_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
- sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ):
- sp_picture_dict[gspecies] = ""
+
+ genus_species = get_gspecies_string_from_sp_dict(sp)
+
+ if genus_species not in sp_picture_dict.keys() \
+ or (genus_species not in sp_picture_dict.keys()
+ and sp_picture_dict[genus_species] != "") \
+ or (constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys()
+ and sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ) :
+
if constants.ORG_PARAM_DESC_PICTURE_PATH in sp[constants.ORG_PARAM_DESC].keys() and \
sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH] != "":
- sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]
+ sp_picture_dict[genus_species] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]
+ else:
+ sp_picture_dict[genus_species] = ""
+
return sp_picture_dict
def get_sp_jbrowse_links(org_list):
diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga
index 0b79aad..4b08cba 100644
--- a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga
@@ -13,32 +13,32 @@
"inputs": [
{
"description": "",
- "name": "genome org1"
+ "name": "proteins org1"
}
],
- "label": "genome org1",
+ "label": "proteins org1",
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 132.3000030517578,
+ "bottom": 35.80000305175781,
"height": 61.80000305175781,
- "left": -366,
- "right": -166,
- "top": 70.5,
+ "left": 322.5,
+ "right": 522.5,
+ "top": -26,
"width": 200,
- "x": -366,
- "y": 70.5
+ "x": 322.5,
+ "y": -26
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
- "uuid": "79c0cd65-9be8-4cd1-be37-1f53c02b0af0",
+ "uuid": "d7151ff6-bc10-4ec3-831c-fd2152daf2c9",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
- "uuid": "8aea9f95-7c91-4cb6-9de9-416cbb488e32"
+ "uuid": "c5f726f2-1a44-494a-964a-9e6dfead2e48"
}
]
},
@@ -51,32 +51,32 @@
"inputs": [
{
"description": "",
- "name": "annotations org1"
+ "name": "genome org2"
}
],
- "label": "annotations org1",
+ "label": "genome org2",
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 222.3000030517578,
+ "bottom": 125.80000305175781,
"height": 61.80000305175781,
- "left": -367,
- "right": -167,
- "top": 160.5,
+ "left": 321.5,
+ "right": 521.5,
+ "top": 64,
"width": 200,
- "x": -367,
- "y": 160.5
+ "x": 321.5,
+ "y": 64
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
- "uuid": "6771d57a-2353-4f79-811b-9e873ef86caa",
+ "uuid": "9d1c5c88-0ec3-4d2c-93d8-11c6076bfe01",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
- "uuid": "429659d1-87f2-4594-bdfb-5491aa255473"
+ "uuid": "5e69bc68-86da-463d-b36b-e9c476db91e7"
}
]
},
@@ -89,32 +89,32 @@
"inputs": [
{
"description": "",
- "name": "proteins org1"
+ "name": "annotations org1"
}
],
- "label": "proteins org1",
+ "label": "annotations org1",
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 317.3000030517578,
+ "bottom": -59.19999694824219,
"height": 61.80000305175781,
- "left": -366,
- "right": -166,
- "top": 255.5,
+ "left": 321.5,
+ "right": 521.5,
+ "top": -121,
"width": 200,
- "x": -366,
- "y": 255.5
+ "x": 321.5,
+ "y": -121
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
- "uuid": "d7151ff6-bc10-4ec3-831c-fd2152daf2c9",
+ "uuid": "6771d57a-2353-4f79-811b-9e873ef86caa",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
- "uuid": "be413801-2af8-4efd-9108-eb01cf625ccf"
+ "uuid": "2739db1f-9e6c-44b9-9c33-b2e04a3c30ee"
}
]
},
@@ -127,32 +127,32 @@
"inputs": [
{
"description": "",
- "name": "genome org2"
+ "name": "annotations org2"
}
],
- "label": "genome org2",
+ "label": "annotations org2",
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 407.3000030517578,
+ "bottom": 219.8000030517578,
"height": 61.80000305175781,
- "left": -367,
- "right": -167,
- "top": 345.5,
+ "left": 323.5,
+ "right": 523.5,
+ "top": 158,
"width": 200,
- "x": -367,
- "y": 345.5
+ "x": 323.5,
+ "y": 158
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
- "uuid": "9d1c5c88-0ec3-4d2c-93d8-11c6076bfe01",
+ "uuid": "46ffeb62-26f6-4d7d-b2fb-b37f0c30104c",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
- "uuid": "24b44e50-b4fe-4e6f-8993-da5ac2321de6"
+ "uuid": "7f4d06ce-6298-45db-ab0d-d02037613839"
}
]
},
@@ -165,32 +165,32 @@
"inputs": [
{
"description": "",
- "name": "annotations org2"
+ "name": "genome org1"
}
],
- "label": "annotations org2",
+ "label": "genome org1",
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 501.3000030517578,
+ "bottom": -149.1999969482422,
"height": 61.80000305175781,
- "left": -365,
- "right": -165,
- "top": 439.5,
+ "left": 322.5,
+ "right": 522.5,
+ "top": -211,
"width": 200,
- "x": -365,
- "y": 439.5
+ "x": 322.5,
+ "y": -211
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
- "uuid": "46ffeb62-26f6-4d7d-b2fb-b37f0c30104c",
+ "uuid": "79c0cd65-9be8-4cd1-be37-1f53c02b0af0",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
- "uuid": "241ba0f4-cf2e-4d93-ac8a-a7d3f92ff512"
+ "uuid": "2cf63ae7-fb2e-4196-8a9d-c6bd47781e4b"
}
]
},
@@ -210,14 +210,14 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 591.3000030517578,
+ "bottom": 309.8000030517578,
"height": 61.80000305175781,
- "left": -364,
- "right": -164,
- "top": 529.5,
+ "left": 324.5,
+ "right": 524.5,
+ "top": 248,
"width": 200,
- "x": -364,
- "y": 529.5
+ "x": 324.5,
+ "y": 248
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -228,124 +228,129 @@
{
"label": null,
"output_name": "output",
- "uuid": "c04327b1-6dc5-45fa-a9ed-08cec7bc3a53"
+ "uuid": "6d1ae9c0-b09f-4430-bc5e-86da8549caad"
}
]
},
"6": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
- "fasta": {
- "id": 0,
+ "reference_genome|genome": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "track_groups_0|data_tracks_0|data_format|annotation": {
+ "id": 3,
"output_name": "output"
}
},
"inputs": [
{
- "description": "runtime parameter for tool Chado load fasta",
- "name": "analysis_id"
- },
- {
- "description": "runtime parameter for tool Chado load fasta",
- "name": "organism"
- },
- {
- "description": "runtime parameter for tool Chado load fasta",
- "name": "wait_for"
+ "description": "runtime parameter for tool JBrowse",
+ "name": "reference_genome"
}
],
- "label": "Chado load fasta org1",
- "name": "Chado load fasta",
+ "label": "JBrowse org2",
+ "name": "JBrowse",
"outputs": [
{
- "name": "results",
- "type": "json"
+ "name": "output",
+ "type": "html"
}
],
"position": {
- "bottom": 234.89999389648438,
- "height": 164.39999389648438,
- "left": -81,
- "right": 119,
- "top": 70.5,
+ "bottom": 732.1999969482422,
+ "height": 205.1999969482422,
+ "left": 625.5,
+ "right": 825.5,
+ "top": 527,
"width": 200,
- "x": -81,
- "y": 70.5
+ "x": 625.5,
+ "y": 527
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
"tool_shed_repository": {
- "changeset_revision": "ba4d07fbaf47",
- "name": "chado_feature_load_fasta",
- "owner": "gga",
+ "changeset_revision": "4542035c1075",
+ "name": "jbrowse",
+ "owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.3.4+galaxy0",
+ "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"true\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"ec32_ortholog_description,note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": \"__MENU_URL_ORG2__\", \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "1.16.11+galaxy0",
"type": "tool",
- "uuid": "03b2e556-7d24-4e40-b1d3-0049e147e450",
+ "uuid": "71b04d1f-8f19-4010-bc9c-9877586995a4",
"workflow_outputs": [
{
"label": null,
- "output_name": "results",
- "uuid": "74a4d9b1-735f-45af-8fba-b567cdcdbeeb"
+ "output_name": "output",
+ "uuid": "9850c240-de34-4e21-9ba7-aaf55ec2e2d2"
}
]
},
"7": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
"errors": null,
"id": 7,
"input_connections": {
- "reference_genome|genome": {
- "id": 0,
- "output_name": "output"
- },
- "track_groups_0|data_tracks_0|data_format|annotation": {
- "id": 1,
+ "fasta": {
+ "id": 4,
"output_name": "output"
}
},
- "inputs": [],
- "label": "JBrowse org1",
- "name": "JBrowse",
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "analysis_id"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "organism"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "wait_for"
+ }
+ ],
+ "label": "Chado load fasta org1",
+ "name": "Chado load fasta",
"outputs": [
{
- "name": "output",
- "type": "html"
+ "name": "results",
+ "type": "json"
}
],
"position": {
- "bottom": 795.6999969482422,
- "height": 205.1999969482422,
- "left": -50,
- "right": 150,
- "top": 590.5,
+ "bottom": -46.600006103515625,
+ "height": 164.39999389648438,
+ "left": 607.5,
+ "right": 807.5,
+ "top": -211,
"width": 200,
- "x": -50,
- "y": 590.5
+ "x": 607.5,
+ "y": -211
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
"tool_shed_repository": {
- "changeset_revision": "4542035c1075",
- "name": "jbrowse",
- "owner": "iuc",
+ "changeset_revision": "ba4d07fbaf47",
+ "name": "chado_feature_load_fasta",
+ "owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"true\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"ec32_ortholog_description,note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": \"https://abims-ggadev.sb-roscoff.fr/sp/ectocarpus_species5/feature/Ectocarpus/species5-Ec13f_Ec_sil_Jap16_a_8_f-female/mRNA/{id}\", \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "1.16.11+galaxy0",
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.4+galaxy0",
"type": "tool",
- "uuid": "941cff4b-3d04-40a2-9f91-3390be0cdc2f",
+ "uuid": "03b2e556-7d24-4e40-b1d3-0049e147e450",
"workflow_outputs": [
{
"label": null,
- "output_name": "output",
- "uuid": "b56405f2-2c53-4795-8038-968c5a5b915f"
+ "output_name": "results",
+ "uuid": "d3be47d8-988f-4a04-a9e8-e3048f39925b"
}
]
},
@@ -356,16 +361,21 @@
"id": 8,
"input_connections": {
"reference_genome|genome": {
- "id": 3,
+ "id": 4,
"output_name": "output"
},
"track_groups_0|data_tracks_0|data_format|annotation": {
- "id": 4,
+ "id": 2,
"output_name": "output"
}
},
- "inputs": [],
- "label": "JBrowse org2",
+ "inputs": [
+ {
+ "description": "runtime parameter for tool JBrowse",
+ "name": "reference_genome"
+ }
+ ],
+ "label": "JBrowse org1",
"name": "JBrowse",
"outputs": [
{
@@ -374,14 +384,14 @@
}
],
"position": {
- "bottom": 1013.6999969482422,
+ "bottom": 514.1999969482422,
"height": 205.1999969482422,
- "left": -63,
- "right": 137,
- "top": 808.5,
+ "left": 638.5,
+ "right": 838.5,
+ "top": 309,
"width": 200,
- "x": -63,
- "y": 808.5
+ "x": 638.5,
+ "y": 309
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
@@ -391,15 +401,15 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
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@@ -441,14 +451,14 @@
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@@ -477,11 +487,11 @@
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@@ -550,14 +560,14 @@
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@@ -613,14 +623,14 @@
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@@ -925,7 +935,7 @@
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@@ -955,14 +965,14 @@
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@@ -1010,14 +1020,14 @@
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@@ -1065,14 +1075,14 @@
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@@ -1115,14 +1125,14 @@
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@@ -1165,14 +1175,14 @@
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@@ -1190,12 +1200,12 @@
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\ No newline at end of file
--
GitLab