Merge branch 'develop'

README.md

@@ -1,9 +1,8 @@
 # LipidLynxX ![LipidLynx_Logo](doc/images/LipidLynxX_Logo_128.jpg)
 
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+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f2180cda82034653ba57eed4473ed135)](https://app.codacy.com/gh/SysMedOs/LipidLynxX?utm_source=github.com&utm_medium=referral&utm_content=SysMedOs/LipidLynxX&utm_campaign=Badge_Grade_Dashboard)
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 ![GitHub last commit](https://img.shields.io/github/last-commit/SysMedOs/LipidLynxX.svg)
 
 The LipidLynxX project is aimed to provide a unified identifier for major lipids, especially oxidized lipids
@@ -14,8 +13,8 @@ in the epilipidome.
 The current LipidLynxX source code was tested using our collection of lipid abbreviations
 for major lipid classes from following databases and programs:
 
-- Databases (3):
-  - `HMDB`, `LIPID MAPS`, `Swisslipid`
+- Databases (4):
+  - `HMDB`, `LIPID MAPS`, `LipidHome`, `SwissLipids`
 
 - Programs (17):
 

doc/sample_data/input/LipidLynxX_conveter_test.txt

@@ -0,0 +1,12 @@
+palmitic acid
+DHA
+HETE
+DPPE
+Plasmanyl-PC O-16:0_18:2
+GPEtn(18:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z))
+Cer(t18:0/26:0)
+SM(d18:1/26:0)
+MG(16:0)
+DG(16:0/18:2(9Z,12Z)/0:0)[iso2]
+TG(16:0/18:0/18:2(9Z,12Z))[iso6]
+TG(16:0/18:2/HETE)

lynx/__init__.py

@@ -31,7 +31,7 @@
 from lynx.utils.file_readers import get_table, create_output, create_equalizer_output
 from lynx.utils.toolbox import keep_string_only
 
-lynx_version = 0.4
+lynx_version = "0.4.12"
 
 app = Flask(__name__)
 app.config.from_object(DevConfig)

lynx/configurations/rules/input/LIPIDMAPS_LMSD.json

@@ -8,7 +8,7 @@
     "LIPIDMAPS",
     "LMSD",
     "Lipostar",
-    "Swisslipids"
+    "SwissLipids"
   ],
   "SEPARATORS": {
     "RESIDUE_SEPARATOR": "_|/",

lynx/configurations/rules/input/LipidHome.json

@@ -0,0 +1,238 @@
+{
+  "_DATE": 20200303,
+  "_AUTHORS": [
+    "zhixu.ni@uni-leipzig.de"
+  ],
+  "SOURCES": [
+    "LipidHome"
+  ],
+  "SEPARATORS": {
+    "RESIDUE_SEPARATOR": "_|/",
+    "MOD_SEPARATOR": "-",
+    "SPACE": "\\s",
+    "COLON": ":",
+    "SEMICOLON": ";",
+    "BRACKET_LEFT": "\\[",
+    "BRACKET_RIGHT": "\\]",
+    "SEPARATOR_LEVELS": {
+      "B": "",
+      "D": "_",
+      "S": "/"
+    }
+  },
+  "MODS": {
+    "MOD": {
+      "ORDER": [
+        "MOD_SITE",
+        "MOD_SITE_INFO",
+        "MOD_SEPARATOR",
+        "MOD_TYPE"
+      ],
+      "OPTIONAL": [
+        "MOD_SITE_INFO",
+        "MOD_SEPARATOR",
+        "MOD_TYPE"
+      ],
+      "MOD_SITE": "(\\s?,)?([0-9]{1,2})",
+      "MOD_SITE_INFO": "([EZRS])?",
+      "MOD_SEPARATOR": "$.SEPARATORS.MOD_SEPARATOR.0",
+      "MOD_TYPE": "([a-zA-Z]*[-0-9a-zA-Z]*)",
+      "EXAMPLES": [
+        "9",
+        "9Z",
+        "9OH",
+        "9S-OH"
+      ]
+    },
+    "SUM_MODS": {
+      "ORDER": [
+        "BRACKET_LEFT",
+        "MOD",
+        "BRACKET_RIGHT"
+      ],
+      "REPEAT": {
+        "MOD": [
+          1,
+          10
+        ]
+      },
+      "BRACKET_LEFT": "$.SEPARATORS.BRACKET_LEFT.0",
+      "MOD": "$.MODS.MOD.0",
+      "BRACKET_RIGHT": "$.SEPARATORS.BRACKET_RIGHT.0",
+      "EXAMPLES": [
+        "[9]",
+        "[9,12]"
+      ]
+    }
+  },
+  "RESIDUES": {
+    "RESIDUE": {
+      "ORDER": [
+        "RESIDUE_SEPARATOR",
+        "LINK",
+        "NUM_C",
+        "DB_SEPARATOR",
+        "DB",
+        "O_SEPARATOR",
+        "NUM_O",
+        "SUM_MODS"
+      ],
+      "OPTIONAL": [
+        "RESIDUE_SEPARATOR",
+        "LINK",
+        "DB",
+        "O_SEPARATOR",
+        "NUM_O",
+        "SUM_MODS"
+      ],
+      "REPEAT": {
+        "SUM_MODS": [
+          0,
+          10
+        ]
+      },
+      "RESIDUE_SEPARATOR": "$.SEPARATORS.RESIDUE_SEPARATOR.0",
+      "LINK": "[OP]-|C|[mdt]|h",
+      "NUM_C": "[0-9]{1,2}",
+      "DB_SEPARATOR": "$.SEPARATORS.COLON.0",
+      "DB": "[1,2]?[0-9]",
+      "O_SEPARATOR": "$.SEPARATORS.SEMICOLON.0",
+      "NUM_O": "[1-3]?O?",
+      "SUM_MODS": "$.MODS.SUM_MODS.0",
+      "EXAMPLES": [
+        "18:2",
+        "9:0",
+        "18:2[9Z,12Z]",
+        "/18:2[9Z,12Z]"
+      ]
+    },
+    "RESIDUE_ALIAS": {
+      "ORDER": [
+        "RESIDUE_SEPARATOR",
+        "ALIAS"
+      ],
+      "OPTIONAL": [
+        "RESIDUE_SEPARATOR"
+      ],
+      "RESIDUE_SEPARATOR": "$.SEPARATORS.RESIDUE_SEPARATOR.0",
+      "ALIAS": "[-,0-9a-zA-Z\\s]{3,}",
+      "EXAMPLES": [
+        "HETE",
+        "/HDoTE"
+      ]
+    },
+    "SUM_RESIDUES": {
+      "ORDER": [
+        "RESIDUE"
+      ],
+      "REPEAT": {
+        "RESIDUE": [
+          1,
+          4
+        ]
+      },
+      "RESIDUE": "($.RESIDUES.RESIDUE.0)|($.SEPARATORS.RESIDUE_ALIAS.0)",
+      "EXAMPLES": [
+        "18:2;3O",
+        "18:2;O",
+        "18:2",
+        "9:0",
+        "26:0;(2OH)",
+        "18:2;3O/18:2",
+        "18:2;O_18:2",
+        "18:0/20:4",
+        "18:0_20:4",
+        "18:0_9:0",
+        "18:0_26:0;(2OH)"
+      ]
+    }
+  },
+  "LIPID_CLASSES": {
+    "GL": {
+      "LMSD_CLASSES": [
+        "GL01",
+        "GL02",
+        "GL03"
+      ],
+      "ORDER": [
+        "CLASS",
+        "LIPID_CLASS_SEPARATOR",
+        "SUM_RESIDUES"
+      ],
+      "OPTIONAL": [],
+      "MAX_RESIDUES": 3,
+      "CLASS": "TG|DG|MG",
+      "LIPID_CLASS_SEPARATOR": "$.SEPARATORS.SPACE.0",
+      "SUM_RESIDUES": "$.RESIDUES.SUM_RESIDUES.0",
+      "EXAMPLES": [
+        "MG 16:0",
+        "DG 34:2",
+        "DG 16:0_18:2_0:0",
+        "TG 52:2",
+        "TG 16:0/16:0/18:2[9,12]",
+        "TG P-16:0/16:0/18:2[9,12]"
+      ]
+    },
+    "PL": {
+      "LMSD_CLASSES": [
+        "GP01",
+        "GP02",
+        "GP03",
+        "GP04",
+        "GP05",
+        "GP06",
+        "GP07",
+        "GP08",
+        "GP09",
+        "GP10",
+        "GP20"
+      ],
+      "ORDER": [
+        "PREFIX",
+        "CLASS",
+        "SUFFIX",
+        "LIPID_CLASS_SEPARATOR",
+        "SUM_RESIDUES"
+      ],
+      "OPTIONAL": [
+        "PREFIX",
+        "SUFFIX"
+      ],
+      "MAX_RESIDUES": 2,
+      "PREFIX": "L",
+      "CLASS": "P[ACEDGSI]|PIP|PIP[2-6]",
+      "SUFFIX": "\\w*",
+      "LIPID_CLASS_SEPARATOR": "$.SEPARATORS.SPACE.0",
+      "SUM_RESIDUES": "$.RESIDUES.SUM_RESIDUES.0",
+      "EXAMPLES": [
+        "PC 16:0/18:2[9,12]"
+      ]
+    },
+    "CL": {
+      "LMSD_CLASSES": [
+        "GP12"
+      ],
+      "ORDER": [
+        "PREFIX",
+        "CLASS",
+        "LIPID_CLASS_SEPARATOR",
+        "SUM_RESIDUES"
+      ],
+      "OPTIONAL": [
+        "PREFIX"
+      ],
+      "MAX_RESIDUES": 4,
+      "PREFIX": "ML|DL",
+      "CLASS": "CL",
+      "LIPID_CLASS_SEPARATOR": "$.SEPARATORS.SPACE.0",
+      "SUM_RESIDUES": "$.RESIDUES.SUM_RESIDUES.0",
+      "EXAMPLES": [
+        "CL 72:7",
+        "CL 18:1/18:2/18:2/18:2",
+        "CL 36:3_36:4",
+        "MLCL 18:1_18:2_18:2",
+        "DLCL 18:1_18:2"
+      ]
+    }
+  }
+}

lynx/controllers/encoder.py

@@ -337,7 +337,9 @@ def export_levels(
         # "PE O-18:1p/18:1",
         # "PE-C16:0-C18:2",
         # "HETE",
-        "TG(16:0/18:2/18:2[2xDB,1xOH])",
+        # "TG(16:0/18:2/18:2[2xDB,1xOH])",
+        "PC 16:0/18:2[9,12]",
+        "DG 16:2[9,12]_O-18:2_0:0"
     ]
     lynx_gen = Encoder()
     for t_in in t_in_lst:

lynx/templates/about.html

@@ -12,6 +12,9 @@ <h5>&nbsp;</h5>
         <li><h5>LipidLynxX version: {{ lynx_version }}</h5></li>
         <li><h5>API version: {{ api_version }}</h5></li>
     </ul>
+    <a href="https://github.com/SysMedOs/LipidLynxX" class="text-dark" target="_blank">
+        Check latest version of LipidLynxX on GitHub &#128279;
+    </a>
     <h4>&nbsp;</h4>
     <h4>Developed by Team SysMedOs</h4>
     <p>

lynx/templates/base.html

@@ -74,6 +74,12 @@
             <div class="col">
                 <h5><strong>LipidLynxX</strong></h5>
                 <p class="text-dark">Link lipid identifiers into an unified nomenclature</p>
+                <p class="text-dark"></p>
+                <p class="text-dark">
+                    <a href="https://github.com/SysMedOs/LipidLynxX" class="text-dark" target="_blank">
+                        Check latest version of LipidLynxX on GitHub &#128279;
+                    </a>
+                </p>
             </div>
             <div class="col">
                 <h5><strong>About Us</strong></h5>

lynx/templates/user_guide.html

@@ -44,5 +44,64 @@ <h5>This user guide is designed for:</h5>
         <li><h6>API version: {{ api_version }}</h6></li>
     </ul>
     <h5>Instructions:</h5>
-    <h5>......</h5>
+
+    <ul>
+        <li>Test input file: "LipidLynxX\doc\sample_data\input"</li>
+        <li>Test output file: "LipidLynxX\doc\sample_data\output"</li>
+    </ul>
+
+    <h5>Converter</h5>
+    <p>For Conversion, type/paste your lipid annotations or choose your .xlsx or .csv files. Press “convert
+        abbreviations” or “convert table”, wait for results. You will see the output on the right-hand side
+        or just download the table with converted IDs.</p>
+    <ul>
+        <li><p>Convert by text input</p>
+            <ul>
+                <li>Paste list of abbreviations in the text input field and press “convert abbreviations”.
+                    <br>
+                    <img src="..\static\images\user_guide_converter_01.png" alt="user_guide_converter_01" width="600">
+                </li>
+
+                <li>You will see the output on the right-hand side
+                    or just download the table with converted IDs.<br>
+                    <img src="..\static\images\user_guide_converter_02.png" alt="user_guide_converter_02" width="600">
+                </li>
+
+            </ul>
+        </li>
+        <li><p>Convert by table input</p>
+            <ul>
+                <li>Press "Choose file"<br>
+                    <img src="..\static\images\user_guide_converter_03.png" alt="user_guide_converter_03" width="600">
+                </li>
+                <li>Select the input file in .xlsx or .csv format and press “Convert table”<br>
+                    <img src="..\static\images\user_guide_converter_04.png" alt="user_guide_converter_04" width="600">
+                </li>
+                <li>You will see the output on the right-hand side or just download the table with converted IDs.<br>
+                    <img src="..\static\images\user_guide_converter_05.png" alt="user_guide_converter_05" width="600">
+                </li>
+            </ul>
+        </li>
+    </ul>
+    <h5>Equalizer</h5>
+    <p>To Equalize, select LipidLynxX Equalizer tab from Home page. Select the level of annotations to which you would
+        like to cross-match your lipid annotations (you can select more than one). For details on annotation levels see
+        the tables on the right hand-side. Choose you datafile and press “Equalize”. Download your results as .xlsx
+        file. </p>
+    <ul>
+        <li><p>Convert by table input</p>
+            <ul>
+                <li>Press "Choose file" and select the input file in .xlsx or .csv format. Then select the level of
+                    annotations to which you would like to cross-match your lipid annotations
+                    (you can select more than one), in this case levels B0, D0 and D1 are chosen. Then you can press
+                    “Equalize” to start processing.<br>
+                    <img src="..\static\images\user_guide_equalizer_01.png" alt="user_guide_equalizer_01" width="600">
+                </li>
+                <li>You will see the output when the processing is finished and you can download the file in .xlsx
+                    format.<br>
+                    <img src="..\static\images\user_guide_equalizer_02.png" alt="user_guide_equalizer_02" width="600">
+                </li>
+            </ul>
+        </li>
+    </ul>
 {% endblock %}