diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c269d5124c3a83a4115ad4c199fa1b96a3f9d5cc..8191ed18484ef7ff18ecc9a133d8f7926b6ca12c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -25,7 +25,8 @@ spell check:
allow_failure: true
script:
#- npm i markdown-spellcheck -g
- - mdspell '**/*.md' '!docs.it4i/module*.md' '!docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md' '!docs.it4i/downtimes_history.md' -rns --en-us
+ - mdspell '**/*.md' '!docs.it4i/module*.md' '!docs.it4i/anselm-/add
+cluster-documentation/software/omics-master/overview.md' '!docs.it4i/downtimes_history.md' -rns --en-us
ext_links:
stage: test
@@ -46,10 +47,10 @@ mkdocs:
script:
#- apt-get update
#- apt-get -y install git
- - bash add_version.sh
- - bash get_modules.sh
+ - bash scripts/add_version.sh
+ - bash scripts/get_modules.sh
- mkdocs build
- - bash clean_json.sh site/mkdocs/search_index.json
+ - bash scripts/clean_json.sh site/mkdocs/search_index.json
- sed -i 's,href="" title=",href="/" title=",g' site/404.html
artifacts:
paths:
diff --git a/add_version.sh b/scripts/add_version.sh
similarity index 100%
rename from add_version.sh
rename to scripts/add_version.sh
diff --git a/clean_json.sh b/scripts/clean_json.sh
similarity index 100%
rename from clean_json.sh
rename to scripts/clean_json.sh
diff --git a/cluster_modules.py b/scripts/cluster_modules.py
similarity index 100%
rename from cluster_modules.py
rename to scripts/cluster_modules.py
diff --git a/colors.sh b/scripts/colors.sh
similarity index 100%
rename from colors.sh
rename to scripts/colors.sh
diff --git a/get_cvs.sh b/scripts/get_cvs.sh
similarity index 100%
rename from get_cvs.sh
rename to scripts/get_cvs.sh
diff --git a/get_modules.sh b/scripts/get_modules.sh
similarity index 100%
rename from get_modules.sh
rename to scripts/get_modules.sh
diff --git a/scripts/modules.py b/scripts/modules.py
deleted file mode 100755
index a58c9747c3976e4ec40417495226c075800f5277..0000000000000000000000000000000000000000
--- a/scripts/modules.py
+++ /dev/null
@@ -1,95 +0,0 @@
-##!/usr/bin/env python
-#
-# Copyright (C) 2016 IT4Innovations
-#
-##
-
-import json
-import os
-import re
-import xmlrpclib
-
-
-def software_list(class_path):
- """List software from given module class"""
- os.chdir(class_path)
- software_list = next(os.walk('.'))[1]
- # In case that there is 'all' module
- if 'all' in software_list:
- software_list.remove('all')
- return software_list
-
-
-def get_software_versions(software_path):
- """List available versions of software"""
- os.chdir(software_path)
- return next(os.walk('.'))[2]
-
-
-def get_module_description(module_path):
- """Return software homepage URL and description"""
- url = ""
- description = " "
- with open(module_path) as f:
- content = f.read()
- data = re.search(r"module-whatis\s{(Description: )?(.+)\s-\sHomepage:\s(\S+)}",
- content, re.DOTALL)
- try:
- description = data.group(2)
- url = data.group(3)
- except AttributeError:
- pass
- return url, description
-
-def push_to_portal(page):
- """Push HTML page to the user portal"""
- remote = 'https://admin_write_modules_table:IcifomHantyi@docs.it4i.cz/'
- server = xmlrpclib.ServerProxy(remote)
- xmlout = server.xmlrpc_salomon_list_of_modules(page)
-
-
-if __name__ == "__main__":
- BASE_MODULES_DIR = '/apps/modules/'
- SKIP_DIRS = ['all']
- HTML_SOURCE_DATA = {}
- os.chdir(BASE_MODULES_DIR)
- subdirs = next(os.walk('.'))[1]
- # Delete unwanted directories
- for dir in SKIP_DIRS:
- subdirs.remove(dir)
-
- #print sorted(subdirs)
- #subdirs = ['base']
- # Create module class structure
- print "# List of Available Modules"
- for dir in sorted(subdirs):
- class_path = os.path.join(BASE_MODULES_DIR, dir)
- available_software = software_list(class_path)
- #print available_software
- print "\n###%s\n" % dir.title()
- print "|Module|Description|Available versions|"
- print "|--|--|--|"
- HTML_SOURCE_DATA[dir] = {}
- for soft in sorted(available_software, key=str.lower):
- software_path = os.path.join(class_path, soft)
- software_versions = get_software_versions(software_path)
- # In case that there's not any available software version
- if not software_versions:
- continue
- first_module_path = os.path.join(software_path, software_versions[0])
- software_url, software_description = get_module_description(first_module_path)
- #print software_description
- HTML_SOURCE_DATA[dir][soft] = {'versions': [],
- 'url': software_url,
- 'description': software_description}
- for version in software_versions:
- HTML_SOURCE_DATA[dir][soft]['versions'].append(version)
- #for version in software_versions:
- # HTML_SOURCE_DATA[dir][soft]['versions'].append(version)
- if software_url=="":
- print "|**%s**|%s|<nobr>%s</nobr>|" % (soft," ".join(software_description.split()),'</br>'.join(software_versions))
- else:
- print "|**[%s](%s)**|%s|<nobr>%s</nobr>|" % (soft,software_url," ".join(software_description.split()),'</br>'.join(software_versions))
- #json_obj = json.dumps(HTML_SOURCE_DATA, sort_keys=True, indent=4)
- #push_to_portal(json_obj)
- #print json_obj
diff --git a/scripts/modules_compare.py b/scripts/modules_compare.py
deleted file mode 100755
index e45c06570f3f593c7df1eddbc928606f59ef381d..0000000000000000000000000000000000000000
--- a/scripts/modules_compare.py
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env python
-#
-# Copyright (C) 2016 IT4Innovations
-#
-
-import os
-
-def software_list(class_path):
- """List software from given module class"""
- os.chdir(class_path)
- software_list = next(os.walk('.'))[1]
- # In case that there is 'all' module
- if 'all' in software_list:
- software_list.remove('all')
- return software_list
-
-
-def get_software_versions(software_path):
- """List available versions of software"""
- os.chdir(software_path)
- return next(os.walk('.'))[2]
-
-if __name__ == "__main__":
- BASE_MODULES_DIR = '/apps/modules/'
- SKIP_DIRS = ['all']
- HTML_SOURCE_DATA = {}
- os.chdir(BASE_MODULES_DIR)
- subdirs = next(os.walk('.'))[1]
- # Delete unwanted directories
- for dir in SKIP_DIRS:
- subdirs.remove(dir)
-
- # Create module class structure
- for dir in sorted(subdirs):
- class_path = os.path.join(BASE_MODULES_DIR, dir)
- available_software = software_list(class_path)
- HTML_SOURCE_DATA[dir] = {}
- for soft in sorted(available_software, key=str.lower):
- software_path = os.path.join(class_path, soft)
- software_versions = get_software_versions(software_path)
- # In case that there's not any available software version
- if not software_versions:
- continue
- first_module_path = os.path.join(software_path, software_versions[0])
- HTML_SOURCE_DATA[dir][soft] = {'versions': []}
- for version in software_versions:
- HTML_SOURCE_DATA[dir][soft]['versions'].append(version)
- print "%s|%s" % (soft.lower(),';'.join(software_versions))
diff --git a/scripts/motd.sh b/scripts/motd.sh
deleted file mode 100755
index 3d94de74b8f1278878b063ae094e869694c6fc0d..0000000000000000000000000000000000000000
--- a/scripts/motd.sh
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/bash
-
-### MOTD and Downtime history
-# autor: kru0052
-# 2016 IT4Innovations
-# version 1.0
-###
-
-printf "update"
-wget -q http://www.it4i.cz/support/?lang=en
-printf " ... OK\n"
-
-i="index.html?lang=en"
-
-HEAD=$(grep -n -m1 'class="matrix light-grey' "$i" |cut -f1 -d: | tr --delete '\n')
-END=$(grep -n -m1 '<h3>Other</h3>' "$i" |cut -f1 -d: | tr --delete '\n')
-LAST=$(wc -l "$i" | cut -f1 -d' ')
-DOWN=$((LAST-END+2))
-
-sed '1,'"$((HEAD-1))"'d' "$i" | sed -n -e :a -e '1,'"$DOWN"'!{P;N;D;};N;ba' | sed '/<div/d' > "TMP.html"
-rm "/srv/downtime/$i"
-
-title="Message of the day"
-head=$(cat TMP.html | grep "rss-item-title" | cut -d ">" -f 2 | cut -d "<" -f 1)
-date=$(cat TMP.html | grep "<i>" | cut -d ">" -f 2 | cut -d "<" -f 1 | cut -d " " -f 1)
-info=$(cat TMP.html | grep "<p>" | cut -d ">" -f 2 | cut -d "<" -f 1)
-rm /srv/downtime/TMP.html
-
-echo ""
-echo "$title"
-echo "$date - $head"
-echo "$info"
-echo ""
-
-# poovolene stavy - Salomon Maintenance, Anselm Maintenance, Back in Production, Infrastructure Maintenance, PBS Maintenance, SCRATCH Maintenance, HOME Maintenance, Salomon and Anselm Maintenance
-if [ "$head" = "Salomon Maintenance" ] || [ "$head" = "Anselm Maintenance" ] || [ "$head" = "Back in Production" ] || [ "$head" = "Infrastructure Maintenance" ] || [ "$head" = "PBS Maintenance" ] || [ "$head" = "SCRATCH Maintenance" ] || [ "$head" = "HOME Maintenance" ] || [ "$head" = "Salomon and Anselm Maintenance" ]; then
- dateDown=$(cat /srv/downtime/docs/index.md | sed -n '/---/{n;p;}' | cut -d "|" -f 2 | cut -d " " -f 1)
- headDown=$(cat /srv/downtime/docs/index.md | sed -n '/---/{n;p;}' | cut -d "|" -f 3 | cut -d "*" -f 3)
-
- echo "$date - $dateDown"
-
-
- if [ "$date" = "$dateDown" ] && [ "$head" = "$headDown" ]; then
- echo "Everything up-to-date..."
- else
- echo "Updating Downtime History..."
- test=" |$date 00:00:00|**$head** $info|"
- sed '/---/a '"$test"'' /srv/downtime/docs/index.md > /srv/downtime/TMP.md
- cat /srv/downtime/TMP.md > /srv/downtime/docs/index.md
- # rm /srv/downtime/TMP.md
- fi
-
-# echo "### $title" > docs/index.md
-# echo "**$head**" >> docs/index.md
-# echo "$date - $info" >> docs/index.md
-else
- echo "Downtime History not updated..."
-fi
-
- echo "# $title" > docs/motd.md
- echo "**$head**" >> docs/motd.md
- echo "$date - $info" >> docs/motd.md
-
-time=$(date)
-
-sed '$d' /srv/downtime/docs/index.md > /srv/downtime/TMP.md
-cat /srv/downtime/TMP.md > /srv/downtime/docs/index.md
-rm /srv/downtime/TMP.md
-echo "updating $time" >> /srv/downtime/docs/index.md
diff --git a/scripts/html_md.sh b/scripts/preklopeni_dokumentace/html_md.sh
similarity index 100%
rename from scripts/html_md.sh
rename to scripts/preklopeni_dokumentace/html_md.sh
diff --git a/scripts/source/formatting b/scripts/preklopeni_dokumentace/source/formatting
similarity index 100%
rename from scripts/source/formatting
rename to scripts/preklopeni_dokumentace/source/formatting
diff --git a/scripts/source/lastFilter b/scripts/preklopeni_dokumentace/source/lastFilter
similarity index 100%
rename from scripts/source/lastFilter
rename to scripts/preklopeni_dokumentace/source/lastFilter
diff --git a/scripts/source/list_folder b/scripts/preklopeni_dokumentace/source/list_folder
similarity index 100%
rename from scripts/source/list_folder
rename to scripts/preklopeni_dokumentace/source/list_folder
diff --git a/scripts/source/list_image_mv b/scripts/preklopeni_dokumentace/source/list_image_mv
similarity index 100%
rename from scripts/source/list_image_mv
rename to scripts/preklopeni_dokumentace/source/list_image_mv
diff --git a/scripts/source/list_md_mv b/scripts/preklopeni_dokumentace/source/list_md_mv
similarity index 100%
rename from scripts/source/list_md_mv
rename to scripts/preklopeni_dokumentace/source/list_md_mv
diff --git a/scripts/source/list_rm b/scripts/preklopeni_dokumentace/source/list_rm
similarity index 100%
rename from scripts/source/list_rm
rename to scripts/preklopeni_dokumentace/source/list_rm
diff --git a/scripts/source/repairIMG b/scripts/preklopeni_dokumentace/source/repairIMG
similarity index 100%
rename from scripts/source/repairIMG
rename to scripts/preklopeni_dokumentace/source/repairIMG
diff --git a/scripts/source/replace b/scripts/preklopeni_dokumentace/source/replace
similarity index 100%
rename from scripts/source/replace
rename to scripts/preklopeni_dokumentace/source/replace
diff --git a/scripts/source/tab b/scripts/preklopeni_dokumentace/source/tab
similarity index 100%
rename from scripts/source/tab
rename to scripts/preklopeni_dokumentace/source/tab
diff --git a/scripts/source/tabREPLACE b/scripts/preklopeni_dokumentace/source/tabREPLACE
similarity index 100%
rename from scripts/source/tabREPLACE
rename to scripts/preklopeni_dokumentace/source/tabREPLACE