diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 176a458..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -* text=auto diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 32858aa..0000000 --- a/.gitignore +++ /dev/null @@ -1,12 +0,0 @@ -*.class - -# Mobile Tools for Java (J2ME) -.mtj.tmp/ - -# Package Files # -*.jar -*.war -*.ear - -# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml -hs_err_pid* diff --git a/LICENSE.txt b/LICENSE.txt deleted file mode 100644 index 8f71f43..0000000 --- a/LICENSE.txt +++ /dev/null @@ -1,202 +0,0 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright {yyyy} {name of copyright owner} - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. - diff --git a/README.md b/README.md index 554d36b..3f5a543 100644 --- a/README.md +++ b/README.md @@ -1,79 +1 @@ -# SignalData - -## Basic Setup ## - -1. Create a LabKey Assay Project/Folder - 1. Hover over the Project or Folder menu, and click **Create Project** or **Create Subfolder**. - 1. Provide a Name and select type **Assay**. - 1. Click **Next**. - 1. Set permissions (optional) and click **Next**. - 1. Click **Finish**. -1. Create a Signal Data Assay Design - 1. In the **Assay List** web part, click **New Assay Design**. - 1. On the New Assay Design page, select **Signal Data** as the assay type. - 1. Click **Next**. - 1. Name is the only required field. (Design default values should work fine.) - 1. Click the **Save & Close** button. - -## Manual Import of Signal Data Results ## - -Importing data is a two step process: - -1. Upload the metadata file. (An example metadata file is available at: https://github.com/LabKey/signalData/blob/develop/test/sampledata/signaldata/RunsMetadata/datafiles.tsv) -1. Drag and drop the data files (Example data files are available at: https://github.com/LabKey/signalData/tree/develop/test/sampledata/signaldata/SignalDataAssayData/TestRun001) - -### Metadata Upload - -1. Go to the folder where you wish to upload results. -1. Add the **Signal Data Upload** webpart. -1. Confirm that **File** is selected, and click **Upload TXT, TSV, XLS, XLSX**. - -![Drag-and-drop to upload a run](https://github.com/LabKey/docs/blob/master/images/signal1.png?raw=true) - -1. Specify a Run Identifier (required). - -![Drag-and-drop to upload a run](https://github.com/LabKey/docs/blob/master/images/signal2.png?raw=true) - -### Data Upload - -1. Drag-and-drop any result files you want to import onto the dropzone. - -![Drag-and-drop to upload a run](https://github.com/LabKey/docs/blob/master/images/signal3.png?raw=true) - -1. Click the **Save Run** button. - -![Name and save a run](https://github.com/LabKey/docs/blob/master/images/signal4.png?raw=true) - -## View Results ## - -To view chromatograms for the results, follow these instructions: - -1. Go to the folder where your results reside. -1. On the **Assay List** webpart, click the name of the Signal Data assay you created. -1. Select the run(s) you want to look at, using the checkboxes. -1. Click **View Selected Runs**. - -![View runs](https://github.com/LabKey/docs/blob/master/images/hplc3.png?raw=true) - -1. Select the data run(s) you wish to view from the left. -1. Click the `Overlay Selected` button. - -![View runs](https://github.com/LabKey/docs/blob/master/images/hplc4.png?raw=true) - -1. The left selection pane will close, and the overlayed results will be displayed in the center pane. - -![View runs](https://github.com/LabKey/docs/blob/master/images/hplc5.png?raw=true) - -1. You can zoom into the graph by entering values in the **Time** and **mV Range** text boxes, or by drawing a new area inside the graph using the mouse. - -![View runs](https://github.com/LabKey/docs/blob/master/images/hplc6.png?raw=true) - -Enter values in the right pane to calculate areas under the curves. Select in the name column to highlight different graph lines. - -![View runs](https://github.com/LabKey/docs/blob/master/images/hplc7.png?raw=true) - -## Installing the Signal Data Module ## - -[Contact us](https://www.labkey.com/company/contact-us) for details on installing the Signal Data module. - - +Module moved to [LabKey/commonAssays](https://github.com/LabKey/commonAssays) in 25.3 diff --git a/build.gradle b/build.gradle deleted file mode 100644 index 405ae24..0000000 --- a/build.gradle +++ /dev/null @@ -1,3 +0,0 @@ -plugins { - id 'org.labkey.build.module' -} diff --git a/module.properties b/module.properties deleted file mode 100644 index acc4793..0000000 --- a/module.properties +++ /dev/null @@ -1,7 +0,0 @@ -ModuleClass: org.labkey.signaldata.SignalDataModule -Label: signaldata -Description: A module defining general X/Y plottable assays and tools for working with those assays. -URL: https://github.com/LabKey/signalData -License: Apache 2.0 -LicenseURL: http://www.apache.org/licenses/LICENSE-2.0 -ManageVersion: true diff --git a/pull_request_template.md b/pull_request_template.md deleted file mode 100644 index 2a1c8ac..0000000 --- a/pull_request_template.md +++ /dev/null @@ -1,8 +0,0 @@ -#### Rationale - - -#### Related Pull Requests -* - -#### Changes -* diff --git a/resources/assay/signalData/config.xml b/resources/assay/signalData/config.xml deleted file mode 100644 index fd5ee4a..0000000 --- a/resources/assay/signalData/config.xml +++ /dev/null @@ -1,7 +0,0 @@ - - Signal Data - X/Y plottable Signal Data - - SignalData - - diff --git a/resources/assay/signalData/domains/batch.xml b/resources/assay/signalData/domains/batch.xml deleted file mode 100644 index 1915a5e..0000000 --- a/resources/assay/signalData/domains/batch.xml +++ /dev/null @@ -1,19 +0,0 @@ - - Signal Data Assay Batch fields - - XAxis - true - http://www.w3.org/2001/XMLSchema#string - X-Axis Label - FixedValue - Time (m) - - - YAxis - true - http://www.w3.org/2001/XMLSchema#string - Y-Axis Label - FixedValue - mV - - \ No newline at end of file diff --git a/resources/assay/signalData/domains/result.xml b/resources/assay/signalData/domains/result.xml deleted file mode 100644 index 3c85971..0000000 --- a/resources/assay/signalData/domains/result.xml +++ /dev/null @@ -1,14 +0,0 @@ - - Signal Data Assay Results - - Name - true - http://www.w3.org/2001/XMLSchema#string - - - DataFile - true - http://cpas.fhcrc.org/exp/xml#fileLink - Data File - - diff --git a/resources/assay/signalData/domains/run.xml b/resources/assay/signalData/domains/run.xml deleted file mode 100644 index cebcdfc..0000000 --- a/resources/assay/signalData/domains/run.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - RunIdentifier - true - http://www.w3.org/2001/XMLSchema#string - Run Identifier - - diff --git a/resources/assay/signalData/queries/Data.query.xml b/resources/assay/signalData/queries/Data.query.xml deleted file mode 100644 index 332e318..0000000 --- a/resources/assay/signalData/queries/Data.query.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - - - - - /signaldata/update.view?protocolId=${Run/Protocol/RowId}&batchId=${Run/Batch/RowId}&runId=${Run/RowId}&rowId=${RowId}&runName=${Run/Name} - - /signaldata/QCView/SignalData.js - - LABKEY.SignalData.signalDataSelection(dataRegion, dataRegionName, 'signaldata') - - - - - - - SearchSignalDataData - RowId - - - -
- - - diff --git a/resources/assay/signalData/queries/SearchSignalDataData.sql b/resources/assay/signalData/queries/SearchSignalDataData.sql deleted file mode 100644 index f705afa..0000000 --- a/resources/assay/signalData/queries/SearchSignalDataData.sql +++ /dev/null @@ -1,23 +0,0 @@ -/* - * Copyright (c) 2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ --- noinspection SqlDialectInspectionForFile --- noinspection SqlNoDataSourceInspectionForFile --- This query is used to define the search criteria as used for the SignalData initial view -SELECT -Data.RowId, ---TODO: Identify search fields -COALESCE(Data.Name, '') || COALESCE(Data.Run.RunIdentifier, '')AS Search -FROM Data \ No newline at end of file diff --git a/resources/assay/signalData/views/begin.html b/resources/assay/signalData/views/begin.html deleted file mode 100644 index 280ee52..0000000 --- a/resources/assay/signalData/views/begin.html +++ /dev/null @@ -1,45 +0,0 @@ -
- - -
-
- \ No newline at end of file diff --git a/resources/assay/signalData/views/begin.view.xml b/resources/assay/signalData/views/begin.view.xml deleted file mode 100644 index 5fbe3ce..0000000 --- a/resources/assay/signalData/views/begin.view.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/resources/assay/signalData/views/upload.html b/resources/assay/signalData/views/upload.html deleted file mode 100644 index 3c251b0..0000000 --- a/resources/assay/signalData/views/upload.html +++ /dev/null @@ -1,9 +0,0 @@ -
- \ No newline at end of file diff --git a/resources/views/mockSignalDataWatch.html b/resources/views/mockSignalDataWatch.html deleted file mode 100644 index 7eeded3..0000000 --- a/resources/views/mockSignalDataWatch.html +++ /dev/null @@ -1,232 +0,0 @@ - -
-
- diff --git a/resources/views/mockSignalDataWatch.view.xml b/resources/views/mockSignalDataWatch.view.xml deleted file mode 100644 index 1e4bca5..0000000 --- a/resources/views/mockSignalDataWatch.view.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/resources/views/qc.html b/resources/views/qc.html deleted file mode 100644 index d35cdc4..0000000 --- a/resources/views/qc.html +++ /dev/null @@ -1,10 +0,0 @@ -
- diff --git a/resources/views/qc.view.xml b/resources/views/qc.view.xml deleted file mode 100644 index 1f2474c..0000000 --- a/resources/views/qc.view.xml +++ /dev/null @@ -1,14 +0,0 @@ - - - - - - - - - - - - - - diff --git a/resources/views/signalDataUpload.html b/resources/views/signalDataUpload.html deleted file mode 100644 index 91c86d7..0000000 --- a/resources/views/signalDataUpload.html +++ /dev/null @@ -1,59 +0,0 @@ -

Signal Data Files

-
    -
  1. - Import (or paste) the results file. Data must include a column that has the signal data filename (case-sensitive). -
    Download Spreadsheet Template
    -
    2. -
  2. - Enter Run-level data and import the relevant signal data files. -
    3. -
-
- - - - - - - - - -
Upload Type: - Cut/Paste
- File -
Data: -
-
-
-
-
-
- - - \ No newline at end of file diff --git a/resources/views/signalDataUpload.view.xml b/resources/views/signalDataUpload.view.xml deleted file mode 100644 index f529f15..0000000 --- a/resources/views/signalDataUpload.view.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - \ No newline at end of file diff --git a/resources/views/signalDataUpload.webpart.xml b/resources/views/signalDataUpload.webpart.xml deleted file mode 100644 index 6635cc2..0000000 --- a/resources/views/signalDataUpload.webpart.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - \ No newline at end of file diff --git a/resources/views/update.html b/resources/views/update.html deleted file mode 100644 index d7b2006..0000000 --- a/resources/views/update.html +++ /dev/null @@ -1,5 +0,0 @@ -

- Update Signal Data result -

-
-
\ No newline at end of file diff --git a/resources/views/update.view.xml b/resources/views/update.view.xml deleted file mode 100644 index b30f54a..0000000 --- a/resources/views/update.view.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff --git a/resources/web/signaldata-upload.lib.xml b/resources/web/signaldata-upload.lib.xml deleted file mode 100644 index c17acc4..0000000 --- a/resources/web/signaldata-upload.lib.xml +++ /dev/null @@ -1,13 +0,0 @@ - - -