Add Pawsey Setonix and NCI shared repository if89

Thanks to @marcodelapierre and @dsr900
AustralianBioCommons · Aug 10, 2022 · 31f6c55 · 31f6c55
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commit 31f6c55
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Showing 8 changed files with 1,597 additions and 1,530 deletions.
diff --git a/docs/2_1_workflows.html b/docs/2_1_workflows.html
diff --git a/docs/2_tools.html b/docs/2_tools.html
diff --git a/docs/5_attributions.html b/docs/5_attributions.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/main.py b/main.py
@@ -7,8 +7,10 @@
     mytooldb.add_provider(ToolMatrixDataProvider("external/tool_matrix_2021_11_15.xlsx"))
     mytooldb.add_provider(ZeusDataProvider("external/zeus.txt"))
     mytooldb.add_provider(MagnusDataProvider("external/magnus.txt"))
+    mytooldb.add_provider(SetonixDataProvider("external/setonix.txt"))
     mytooldb.add_provider(QriscloudDataProvider("external/qriscloud.txt"))
     mytooldb.add_provider(GadiDataProvider("./external/gadi.key.hdr"))
+    mytooldb.add_provider(if89DataProvider("./external/bioapps_token.txt"))
     gdp = GalaxyDataProvider(mytooldb, "./external/galaxy_tools_curation - DATA.csv")
     mytooldb.add_provider(gdp)
     mytooldb.add_provider(BiotoolsDataProvider("external/tool_matrix_2021_11_15.xlsx", mytooldb))

diff --git a/rmarkdowns/2_1_workflows.Rmd b/rmarkdowns/2_1_workflows.Rmd
@@ -12,7 +12,9 @@ title: "WorkflowFinder"
 
 [![](./images/Australian-Biocommons-Logo-Horizontal-144dpi-Transparent.png){width=15%}](https://www.biocommons.org.au/services)
 
-The interactive table below allows you to search for workflows registered by Australian BioCommons partners on [workflowhub](https://workflowhub.eu/programmes/8).
+The interactive table below allows you to search for workflows [registered by Australian BioCommons partners on WorkflowHub](https://workflowhub.eu/programmes/8).
+
+If you would like to add your bioinformatics workflows to [WorkflowHub](https://workflowhub.eu/), please see this [getting started guide](https://about.workflowhub.eu/docs/getting-started/).
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = FALSE, message = FALSE)

diff --git a/rmarkdowns/2_tools.Rmd b/rmarkdowns/2_tools.Rmd
@@ -12,7 +12,12 @@ title: "ToolFinder"
 
 [![](./images/Australian-Biocommons-Logo-Horizontal-144dpi-Transparent.png){width=15%}](https://www.biocommons.org.au/services)
 
-This page lists bioinformatics tools installed across several of the [**BioCommons infrastructure partner systems**](http://support.biocommons.org.au/support/solutions/articles/6000251977-compute-systems-at-the-biocommons-partner-infrastructures) and tool installation request mechanisms on these systems. Tool status on other partner infrastructures will be added over time.
+This page lists bioinformatics tools and software that are installed across several of the [**BioCommons infrastructure partner systems**](http://support.biocommons.org.au/support/solutions/articles/6000251977-compute-systems-at-the-biocommons-partner-infrastructures) as well as the tool installation request mechanisms on these systems. Tool status on other partner infrastructures will be added over time.
+
+**Please note:**
+
+- `Magnus` and `Zeus` (Pawsey) will be decommissioned once user migration to [`Setonix`](https://pawsey.org.au/setonix-fires-up-for-researchers/) is complete, during the second half of 2022. At this point Magnus and Zeus will be removed from ToolFinder.
+- `NCI (if89)` below refers to the [`Australian BioCommons Tools and Workflows repository`](https://australianbiocommons.github.io/ables/if89/), located in project allocation if89 at the National Computational Infrastructure (NCI).
 
 -----
 
@@ -55,12 +60,12 @@ container1 = htmltools::withTags(table(
     tr(
       #see https://stackoverflow.com/q/42153218
       th(class = 'dt-center', style="font-size:11pt", colspan = 9, 'Tool metadata'),
-      th(class = 'dt-center', style="font-size:11pt", colspan = 5, 'Availability on Australian compute infrastructures')
+      th(class = 'dt-center', style="font-size:11pt", colspan = 7, 'Availability on Australian compute infrastructures')
     ),
     tr(
       lapply(c("Tool / workflow name", "bio.tools documentation", "Tool identifier (module name / bio.tools ID / placeholder)",
                "Description", "EDAM topics", "Publications", "Containers available? (BioContainers)", "License",
-               "BioCommons Documentation", "Galaxy Australia", "NCI (Gadi)", "Pawsey (Zeus)", "Pawsey (Magnus)", 
+               "BioCommons Documentation", "Galaxy Australia", "NCI (Gadi)", "NCI (if89)", "Pawsey (Zeus)", "Pawsey (Magnus)", "Pawsey (Setonix)",
                "QRIScloud / UQ-RCC (Flashlite, Tinaroo)"), th)
     )
   )
@@ -91,7 +96,7 @@ options = list(
             buttons = c('copy', 'csv', I('colvis')),
             #see https://stackoverflow.com/a/32428537
             columnDefs = list(list(visible=FALSE, targets = c(2,7)),
-                              list(className = 'dt-center', targets = c(0:2, 5:13)))
+                              list(className = 'dt-center', targets = c(0:2, 5:15)))
             ), 
           class = 'cell-border stripe', escape = FALSE)
 

diff --git a/toolfinder/__init__.py b/toolfinder/__init__.py
@@ -27,9 +27,11 @@ class FIELD_NAMES(Enum):
         PUBLICATIONS = "FIELD_NAMES.PUBLICATIONS"
         GALAXY_AUSTRALIA_LAUNCH_LINK = "FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK"
         NCI_GADI_VERSION = "FIELD_NAMES.NCI_GADI_VERSION"
+        NCI_IF89_VERSION = "FIELD_NAMES.NCI_IF89_VERSION"
         PAWSEY_ZEUS_VERSION = "FIELD_NAMES.PAWSEY_ZEUS_VERSION"
         PAWSEY_MAGNUS_VERSION = "FIELD_NAMES.PAWSEY_MAGNUS_VERSION"
         QRISCLOUD_VERSION = "FIELD_NAMES.QRISCLOUD_VERSION"
+        PAWSEY_SETONIX_VERSION = "FIELD_NAMES.PAWSEY_SETONIX_VERSION"
 
     def __init__(self):
         self.identifier = ""
@@ -173,6 +175,30 @@ def _render(self, data):
         return {Dataprovider.FIELD_NAMES.PAWSEY_MAGNUS_VERSION: data}
 
 
+class SetonixDataProvider(Dataprovider):
+    def __init__(self, filename):
+        super().__init__()
+        self.filename = filename
+        self.identifier = "SETONIX"
+
+    def _query_remote(self):
+        import re
+        self.available_data = {}
+        data = pd.read_csv(self.filename, delimiter="/", header=None)
+        data.columns = ["toolID", "version"]
+
+        for idx, row in data.iterrows():
+            toolID = row.toolID
+            toolID = re.sub(r"gatk4", "gatk", toolID)
+            toolID = re.sub(r"beast1", "beast", toolID)
+            if toolID not in self.available_data:
+                self.available_data[toolID] = []
+            self.available_data[toolID].append(row.version)
+
+    def _render(self, data):
+        return {Dataprovider.FIELD_NAMES.PAWSEY_SETONIX_VERSION: data}
+
+
 class QriscloudDataProvider(Dataprovider):
     def __init__(self, filename):
         super().__init__()
@@ -344,6 +370,32 @@ def _render(self, data):
         return {Dataprovider.FIELD_NAMES.NCI_GADI_VERSION: data}
 
 
+class if89DataProvider(Dataprovider):
+
+    def __init__(self, if89_key_file):
+        super().__init__()
+        self.key = open(if89_key_file, "r").readline()
+        self.identifier = "IF89"
+
+    def _query_remote(self):
+        self.available_data = {}
+        #https://stackoverflow.com/a/8685813
+        req = requests.get("http://130.56.246.237:5000/dump", headers={"Authorization": self.key})
+        if req.status_code != 200:
+            raise FileNotFoundError(req.url)
+        for line in req.text.split("\n")[:-1]:
+            line = line.split(",")
+            tool_id = line[0].strip()
+            tool_id = tool_id.lower()
+            version = line[1]
+            if tool_id not in self.available_data:
+                self.available_data[tool_id] = []
+            self.available_data[tool_id].append(version)
+
+    def _render(self, data):
+        return {Dataprovider.FIELD_NAMES.NCI_IF89_VERSION: data}
+
+
 class Tool:
     """
     Class representing a tool.
@@ -470,6 +522,10 @@ def get_formatted_table(self):
                 tool_line.append("<br \>".join(row[Dataprovider.FIELD_NAMES.NCI_GADI_VERSION]))
             else:
                 tool_line.append("")
+            if isinstance(row[Dataprovider.FIELD_NAMES.NCI_IF89_VERSION], list):
+                tool_line.append("<br \>".join(row[Dataprovider.FIELD_NAMES.NCI_IF89_VERSION]))
+            else:
+                tool_line.append("")
             if isinstance(row[Dataprovider.FIELD_NAMES.PAWSEY_ZEUS_VERSION], list):
                 tool_line.append("<br \>".join(row[Dataprovider.FIELD_NAMES.PAWSEY_ZEUS_VERSION]))
             else:
@@ -478,10 +534,14 @@ def get_formatted_table(self):
                 tool_line.append("<br \>".join(row[Dataprovider.FIELD_NAMES.PAWSEY_MAGNUS_VERSION]))
             else:
                 tool_line.append("")
+            if isinstance(row[Dataprovider.FIELD_NAMES.PAWSEY_SETONIX_VERSION], list):
+                tool_line.append("<br \>".join(row[Dataprovider.FIELD_NAMES.PAWSEY_SETONIX_VERSION]))
+            else:
+                tool_line.append("")
             if isinstance(row[Dataprovider.FIELD_NAMES.QRISCLOUD_VERSION], list):
                 tool_line.append("<br \>".join(row[Dataprovider.FIELD_NAMES.QRISCLOUD_VERSION]))
             else:
                 tool_line.append("")
             formatted_list.append(tool_line)
-        return pd.DataFrame(formatted_list, columns=["Tool / workflow name","bio.tools link","Tool identifier (module name / bio.tools ID / placeholder)","Description","Topic (EDAM, if available)","Publications","BioContainers link","License","BioCommons Documentation","Galaxy Australia","NCI (Gadi)","Pawsey (Zeus)","Pawsey (Magnus)","QRIScloud / UQ-RCC (Flashlite, Awoonga, Tinaroo)"])
+        return pd.DataFrame(formatted_list, columns=["Tool / workflow name","bio.tools link","Tool identifier (module name / bio.tools ID / placeholder)","Description","Topic (EDAM, if available)","Publications","BioContainers link","License","BioCommons Documentation","Galaxy Australia","NCI (Gadi)","NCI (if89)","Pawsey (Zeus)","Pawsey (Magnus)","Pawsey (Setonix)","QRIScloud / UQ-RCC (Flashlite, Awoonga, Tinaroo)"])